PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

obo:SO_0000541 a rdfs:Class ;
  rdfs:label "VDJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

<http://purl.obolibrary.org/obo/so#has_part> a rdf:Property ;
  rdfs:label "has_part" ;
  rdfs:comment "Inverse of part_of." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000432 a rdfs:Class ;
  rdfs:label "U5_three_prime_LTR_region" ;
  rdfs:comment "The U5 segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000849 .

<http://purl.obolibrary.org/obo/so#part_of> a rdf:Property ;
  rdfs:label "part_of" ;
  rdfs:comment "X part_of Y if X is a subregion of Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000957 a rdfs:Class ;
  rdfs:label "linear_double_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." ;
  rdfs:subClassOf obo:SO_0000955 .

<http://purl.obolibrary.org/obo/so#has_quality> a rdf:Property ;
  rdfs:label "has_quality" ;
  rdfs:comment "The relationship between a feature and an attribute." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0001322 a rdfs:Class ;
  rdfs:label "seven_aminomethyl_seven_deazaguanosine" ;
  rdfs:comment "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0000880 a rdfs:Class ;
  rdfs:label "polycistronic" ;
  rdfs:comment "An attribute describing a sequence that contains the code for more than one gene product." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0000801 a rdfs:Class ;
  rdfs:label "assortment_derived_deficiency_plus_duplication" ;
  rdfs:comment "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." ;
  rdfs:subClassOf obo:SO_0001504 .

obo:SO_0001803 a rdfs:Class ;
  rdfs:label "decreased_polyadenylation_variant" ;
  rdfs:comment "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." ;
  rdfs:subClassOf obo:SO_0001545 .

obo:SO_0001536 a rdfs:Class ;
  rdfs:label "functional_effect_variant" ;
  rdfs:comment "A variant whereby the effect is evaluated with respect to a reference." ;
  rdfs:subClassOf obo:SO_0001060 .

obo:SO_0001377 a rdfs:Class ;
  rdfs:label "three_methylpseudouridine" ;
  rdfs:comment "3_methylpseudouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001405 a rdfs:Class ;
  rdfs:label "modified_L_tyrosine" ;
  rdfs:comment "A post translationally modified tyrosine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000336 a rdfs:Class ;
  rdfs:label "pseudogene" ;
  rdfs:comment "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." ;
  rdfs:subClassOf obo:SO_0001411 .

<http://purl.obolibrary.org/obo/so#non_functional_homolog_of> a rdf:Property ;
  rdfs:label "non_functional_homolog_of" ;
  rdfs:comment "A relationship between a pseudogenic feature and its functional ancestor." ;
  rdfs:range <https://w3id.org/linkml/Any> ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#homologous_to> .

obo:SO_0001638 a rdfs:Class ;
  rdfs:label "piRNA_gene" ;
  rdfs:comment "A gene that encodes for an piwi associated RNA." ;
  rdfs:subClassOf obo:SO_0002342 .

<http://purl.obolibrary.org/obo/so#member_of> a rdf:Property ;
  rdfs:label "member_of" ;
  rdfs:comment "A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444." ;
  rdfs:range <https://w3id.org/linkml/Any> ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#part_of> .

obo:SO_0000776 a rdfs:Class ;
  rdfs:label "symbiosis_island" ;
  rdfs:comment "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_0000920 a rdfs:Class ;
  rdfs:label "insert_C" ;
  rdfs:comment "An edit to insert a cytidine." .

obo:SO_0001463 a rdfs:Class ;
  rdfs:label "lincRNA" ;
  rdfs:comment "Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand." ;
  rdfs:subClassOf obo:SO_0001877 .

<http://purl.obolibrary.org/obo/so#derives_from> a rdf:Property ;
  rdfs:label "derives_from" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#overlaps> a rdf:Property ;
  rdfs:label "overlaps" ;
  rdfs:comment "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000443 a rdfs:Class ;
  rdfs:label "polymer_attribute" ;
  rdfs:comment "An attribute to describe the kind of biological sequence." ;
  rdfs:subClassOf obo:SO_0000400 .

obo:SO_0001442 a rdfs:Class ;
  rdfs:label "methionine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codon ATG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001907 a rdfs:Class ;
  rdfs:label "feature_elongation" ;
  rdfs:comment "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0000862 a rdfs:Class ;
  rdfs:label "capped_mRNA" ;
  rdfs:comment "An mRNA that is capped." ;
  rdfs:subClassOf obo:SO_0000234 .

<http://purl.obolibrary.org/obo/so#adjacent_to> a rdf:Property ;
  rdfs:label "adjacent_to" ;
  rdfs:comment "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0002083 a rdfs:Class ;
  rdfs:label "2KB_downstream_variant" ;
  rdfs:comment "A sequence variant located within 2KB 3' of a gene." ;
  rdfs:subClassOf obo:SO_0001632 .

obo:SO_0000718 a rdfs:Class ;
  rdfs:label "blocked_reading_frame" ;
  rdfs:comment "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." ;
  rdfs:subClassOf obo:SO_0000717 .

obo:SO_0000247 a rdfs:Class ;
  rdfs:label "mRNA_not_polyadenylated" .

obo:SO_0001762 a rdfs:Class ;
  rdfs:label "variant_origin" ;
  rdfs:comment "A quality inhering in a variant by virtue of its origin." ;
  rdfs:subClassOf obo:SO_0001761 .

obo:SO_0000642 a rdfs:Class ;
  rdfs:label "SRP_RNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a signal recognition particle RNA (SRP RNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0001218 a rdfs:Class ;
  rdfs:label "transgenic_insertion" ;
  rdfs:comment "An insertion that derives from another organism, via the use of recombinant DNA technology." ;
  rdfs:subClassOf obo:SO_0000667 .

obo:SO_0000173 a rdfs:Class ;
  rdfs:label "GC_rich_promoter_region" ;
  rdfs:comment "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001152 a rdfs:Class ;
  rdfs:label "beta_turn_type_six_a_one" ;
  rdfs:comment "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees." ;
  rdfs:subClassOf obo:SO_0001151 .

obo:SO_0100003 a rdfs:Class ;
  rdfs:label "intrinsically_unstructured_polypeptide_region" ;
  rdfs:comment "A region of polypeptide chain with high conformational flexibility." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0001526 a rdfs:Class ;
  rdfs:label "base_call_error_correction" ;
  rdfs:comment "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." ;
  rdfs:subClassOf obo:SO_0000413 .

obo:SO_0000494 a rdfs:Class ;
  rdfs:label "three_prime_D_nonamer" ;
  rdfs:comment "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000562 .

obo:SO_0001297 a rdfs:Class ;
  rdfs:label "N6_methyladenosine" ;
  rdfs:comment "N6_methyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0002362 a rdfs:Class ;
  rdfs:label "cytosolic_SSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for cytosolic SSU rRNA." ;
  rdfs:subClassOf obo:SO_0002360 .

obo:SO_0002208 a rdfs:Class ;
  rdfs:label "long_terminal_repeat_transcript" ;
  rdfs:comment "An RNA that is transcribed from a long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000968 a rdfs:Class ;
  rdfs:label "sequence_replication_mode" ;
  rdfs:comment "This has been obsoleted as it represents a process. replaced_by: GO:0034961." .

obo:SO_0001142 a rdfs:Class ;
  rdfs:label "st_turn_left_handed_type_one" ;
  rdfs:comment "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0001141 .

obo:SO_0000386 a rdfs:Class ;
  rdfs:label "RNase_P_RNA" ;
  rdfs:comment "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." ;
  rdfs:subClassOf obo:SO_0000372 .

obo:SO_0000192 a rdfs:Class ;
  rdfs:label "three_prime_intron" ;
  rdfs:comment "An intron that is the most 3-prime in a given transcript." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0001188 a rdfs:Class ;
  rdfs:label "LNA" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0000133 a rdfs:Class ;
  rdfs:label "epigenetically_modified" ;
  rdfs:comment "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0002040 a rdfs:Class ;
  rdfs:label "vaultRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a vaultRNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000467 a rdfs:Class ;
  rdfs:label "post_translationally_regulated_by_protein_stability" ;
  rdfs:comment "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." ;
  rdfs:subClassOf obo:SO_0000130 .

obo:SO_0000794 a rdfs:Class ;
  rdfs:label "engineered_rescue_region" ;
  rdfs:comment "A rescue region that is engineered." ;
  rdfs:subClassOf obo:SO_0000411 , obo:SO_0000804 .

obo:SO_0001897 a rdfs:Class ;
  rdfs:label "transposable_element_pseudogene" ;
  rdfs:comment "A pseudogene contained within a transposable element." ;
  rdfs:subClassOf obo:SO_0000336 .

obo:SO_0000620 a rdfs:Class ;
  rdfs:label "B_box" ;
  rdfs:comment "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0001098 a rdfs:Class ;
  rdfs:label "polypeptide_magnesium_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0000483 a rdfs:Class ;
  rdfs:label "nc_primary_transcript" ;
  rdfs:comment "A primary transcript that is never translated into a protein." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000512 a rdfs:Class ;
  rdfs:label "inversion_derived_deficiency_plus_aneuploid" ;
  rdfs:comment "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." ;
  rdfs:subClassOf obo:SO_1000029 .

obo:SO_0001982 a rdfs:Class ;
  rdfs:label "I-box" ;
  rdfs:comment "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." ;
  rdfs:subClassOf obo:SO_0001678 .

obo:SO_0001057 a rdfs:Class ;
  rdfs:label "enhanceosome" .

obo:SO_0002264 a rdfs:Class ;
  rdfs:label "Copia_LTR_retrotransposon" ;
  rdfs:comment "LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001817 a rdfs:Class ;
  rdfs:label "inframe" ;
  rdfs:comment "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." ;
  rdfs:subClassOf obo:SO_0000863 .

obo:SO_0001756 a rdfs:Class ;
  rdfs:label "SL11_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0001797 a rdfs:Class ;
  rdfs:label "centromeric_repeat" ;
  rdfs:comment "A repeat region found within the modular centromere." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0001335 a rdfs:Class ;
  rdfs:label "undermodified_hydroxywybutosine" ;
  rdfs:comment "Undermodified_hydroxywybutosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001964 a rdfs:Class ;
  rdfs:label "modified_guanine" ;
  rdfs:comment "A modified guanine DNA base feature." ;
  rdfs:subClassOf obo:SO_0000305 .

obo:SO_0001849 a rdfs:Class ;
  rdfs:label "homol_E_box" ;
  rdfs:comment "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000783 a rdfs:Class ;
  rdfs:label "engineered" ;
  rdfs:comment "An attribute to describe a region that was modified in vitro." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_1000177 a rdfs:Class .

obo:SO_0001806 a rdfs:Class ;
  rdfs:label "ER_retention_signal" ;
  rdfs:comment "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0002097 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_pseudogene" ;
  rdfs:comment "A pseudogene derived from a vertebrate immune system gene." ;
  rdfs:subClassOf obo:SO_0000336 .

obo:SO_0100016 a rdfs:Class ;
  rdfs:label "central_hydrophobic_region_of_signal_peptide" ;
  rdfs:comment "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0000207 a rdfs:Class ;
  rdfs:label "simple_sequence_length_variation" ;
  rdfs:comment "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." ;
  rdfs:subClassOf obo:SO_0000248 .

obo:SO_0000013 a rdfs:Class ;
  rdfs:label "scRNA" ;
  rdfs:comment "A small non coding RNA sequence, present in the cytoplasm." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001592 a rdfs:Class ;
  rdfs:label "minus_1_frameshift_variant" ;
  rdfs:comment "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." ;
  rdfs:subClassOf obo:SO_0001589 .

obo:SO_0000393 a rdfs:Class ;
  rdfs:label "U4_snRNA" ;
  rdfs:comment "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0002122 a rdfs:Class ;
  rdfs:label "immunoglobulin_gene" ;
  rdfs:comment "A germline immunoglobulin gene." ;
  rdfs:subClassOf obo:SO_0002121 .

obo:BS_00227 a rdfs:Class .

obo:SO_0001542 a rdfs:Class ;
  rdfs:label "increased_transcript_level_variant" ;
  rdfs:comment "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001540 .

obo:SO_0000220 a rdfs:Class ;
  rdfs:label "isoleucine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding isoleucyl tRNA (SO:0000263)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000422 a rdfs:Class ;
  rdfs:label "U5_LTR_region" ;
  rdfs:comment "The U5 segment of the long terminal repeats." ;
  rdfs:subClassOf obo:SO_0000848 .

obo:SO_0001474 a rdfs:Class ;
  rdfs:label "trans_splice_junction" ;
  rdfs:comment "The boundary between the spliced leader and the first exon of the mRNA." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001315 a rdfs:Class ;
  rdfs:label "N6_acetyladenosine" ;
  rdfs:comment "N6_acetyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000202 a rdfs:Class ;
  rdfs:label "three_prime_coding_exon" ;
  rdfs:comment "The coding exon that is most 3-prime on a given transcript." ;
  rdfs:subClassOf obo:SO_0000195 .

obo:SO_0001834 a rdfs:Class ;
  rdfs:label "C_region" ;
  rdfs:comment "The constant region of an immunoglobulin polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0001832 .

obo:SO_0000230 a rdfs:Class ;
  rdfs:label "valine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding valyl tRNA (SO:000273)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0001243 a rdfs:Class ;
  rdfs:label "miRNA_primary_transcript_region" ;
  rdfs:comment "A part of an miRNA primary_transcript." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0001691 a rdfs:Class ;
  rdfs:label "blunt_end_restriction_enzyme_cleavage_site" ;
  rdfs:comment "A restriction enzyme recognition site that, when cleaved, results in no overhangs." ;
  rdfs:subClassOf obo:SO_0001687 .

obo:SO_0001169 a rdfs:Class ;
  rdfs:label "ds_RNA_viral_sequence" ;
  rdfs:comment "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." ;
  rdfs:subClassOf obo:SO_0001041 .

obo:SO_0001017 a rdfs:Class ;
  rdfs:label "silent_mutation" ;
  rdfs:comment "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0000873 a rdfs:Class ;
  rdfs:label "edited_transcript" ;
  rdfs:comment "A transcript that is edited." ;
  rdfs:subClassOf obo:SO_0000673 .

<http://purl.obolibrary.org/obo/so#guided_by> a rdf:Property ;
  rdfs:label "guided_by" ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000353 a rdfs:Class ;
  rdfs:label "sequence_assembly" ;
  rdfs:comment "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." ;
  rdfs:subClassOf obo:SO_0001248 .

obo:SO_0002015 a rdfs:Class ;
  rdfs:label "3_prime_UTR_truncation" ;
  rdfs:comment "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001624 .

obo:SO_0001286 a rdfs:Class ;
  rdfs:label "five_formylcytidine" ;
  rdfs:comment "5-formylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0000704 a rdfs:Class ;
  rdfs:label "gene" ;
  rdfs:comment "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000746 a rdfs:Class ;
  rdfs:label "cyanelle_sequence" ;
  rdfs:comment "DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_0002289 a rdfs:Class ;
  rdfs:label "Viper_YR_retrotransposon" ;
  rdfs:comment "VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes." ;
  rdfs:subClassOf obo:SO_0002286 .

obo:SO_0000020 a rdfs:Class ;
  rdfs:label "RNA_internal_loop" ;
  rdfs:comment "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." ;
  rdfs:subClassOf obo:SO_0000715 .

obo:SO_0001129 a rdfs:Class ;
  rdfs:label "asx_turn_left_handed_type_one" ;
  rdfs:comment "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0000912 .

obo:SO_0001600 a rdfs:Class ;
  rdfs:label "complex_3D_structural_variant" ;
  rdfs:comment "A sequence variant that changes the resulting polypeptide structure." ;
  rdfs:subClassOf obo:SO_0001599 .

obo:SO_0002096 a rdfs:Class ;
  rdfs:label "short_tandem_repeat_variation" ;
  rdfs:comment "A variation that expands or contracts a tandem repeat with regard to a reference." ;
  rdfs:subClassOf obo:SO_0000248 .

obo:SO_0001203 a rdfs:Class ;
  rdfs:label "RNA_polymerase_promoter" ;
  rdfs:comment "A region (DNA) to which RNA polymerase binds, to begin transcription." .

obo:SO_0001025 a rdfs:Class ;
  rdfs:label "polymorphic_sequence_variant" ;
  rdfs:comment "A sequence variant that is segregating in one or more natural populations of a species." ;
  rdfs:subClassOf obo:SO_0001023 .

<http://purl.obolibrary.org/obo/so#variant_of> a rdf:Property ;
  rdfs:label "variant_of" ;
  rdfs:comment "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000523 a rdfs:Class ;
  rdfs:label "V_VJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_1000109 a rdfs:Class ;
  rdfs:label "mutation_causing_out_of_frame_polypeptide_C_terminal_elongation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0002029 a rdfs:Class ;
  rdfs:label "tnaORF" ;
  rdfs:comment "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." ;
  rdfs:subClassOf obo:SO_0000236 .

obo:SO_0001453 a rdfs:Class ;
  rdfs:label "aspartic_acid" ;
  rdfs:comment "A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001561 a rdfs:Class ;
  rdfs:label "polypeptide_partial_loss_of_function" ;
  rdfs:comment "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001559 .

obo:SO_0001384 a rdfs:Class ;
  rdfs:label "CDS_fragment" ;
  rdfs:comment "A portion of a CDS that is not the complete CDS." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:SO_0002316 a rdfs:Class ;
  rdfs:label "decreased_gene_product_level" ;
  rdfs:comment "A sequence variant that decreases the level or amount of gene product produced." ;
  rdfs:subClassOf obo:SO_0002314 .

obo:SO_0001035 a rdfs:Class ;
  rdfs:label "piRNA" ;
  rdfs:comment "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0001496 a rdfs:Class ;
  rdfs:label "telomeric_repeat" ;
  rdfs:comment "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0000856 a rdfs:Class ;
  rdfs:label "conserved" ;
  rdfs:comment "A region that is similar or identical across more than one species." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0100011 a rdfs:Class ;
  rdfs:label "cleaved_peptide_region" ;
  rdfs:comment "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001350 a rdfs:Class ;
  rdfs:label "four_thiouridine" ;
  rdfs:comment "4_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002075 a rdfs:Class ;
  rdfs:label "incomplete_transcript_variant" ;
  rdfs:comment "A sequence variant that intersects an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_1001264 a rdfs:Class ;
  rdfs:label "mRNA_recoded_by_translational_bypass" ;
  rdfs:comment "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_1001261 .

obo:BS_00233 a rdfs:Class .

obo:SO_0000144 a rdfs:Class ;
  rdfs:label "primary_transcript_attribute" .

obo:SO_1000010 a rdfs:Class ;
  rdfs:label "pyrimidine_transition" ;
  rdfs:comment "A substitution of a pyrimidine, C or T, for another pyrimidine." ;
  rdfs:subClassOf obo:SO_1000009 .

obo:SO_0000035 a rdfs:Class ;
  rdfs:label "riboswitch" ;
  rdfs:comment "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001087 a rdfs:Class ;
  rdfs:label "cross_link" ;
  rdfs:comment "Posttranslationally formed amino acid bonds." .

obo:SO_0001178 a rdfs:Class ;
  rdfs:label "pyrrolysine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000080 a rdfs:Class ;
  rdfs:label "operon_member" ;
  rdfs:comment "A gene that is a member of an operon, which is a set of genes transcribed together as a unit." ;
  rdfs:subClassOf obo:SO_0000081 .

obo:SO_0000462 a rdfs:Class ;
  rdfs:label "pseudogenic_region" ;
  rdfs:comment "A non-functional descendant of a functional entity." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002033 a rdfs:Class ;
  rdfs:label "loR" ;
  rdfs:comment "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0001324 a rdfs:Class ;
  rdfs:label "one_methylguanosine" ;
  rdfs:comment "1_methylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000183 a rdfs:Class ;
  rdfs:label "non_transcribed_region" ;
  rdfs:comment "A region of the gene which is not transcribed." ;
  rdfs:subClassOf obo:SO_0000842 .

obo:SO_0002195 a rdfs:Class ;
  rdfs:label "unitary_pseudogenic_rRNA" ;
  rdfs:comment "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain." ;
  rdfs:subClassOf obo:SO_0000777 .

obo:SO_0002227 a rdfs:Class ;
  rdfs:label "CDS_extension" ;
  rdfs:comment "A sequence variant extending the CDS, that causes elongation of the resulting polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:SO_0001390 a rdfs:Class ;
  rdfs:label "modified_L_cysteine" ;
  rdfs:comment "A post translationally modified cysteine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001814 a rdfs:Class ;
  rdfs:label "coding_variant_quality" ;
  rdfs:comment "An attribute of a coding genomic variant." ;
  rdfs:subClassOf obo:SO_0001761 .

obo:SO_0002152 a rdfs:Class ;
  rdfs:label "genic_downstream_transcript_variant" ;
  rdfs:comment "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." ;
  rdfs:subClassOf obo:SO_0001564 .

obo:SO_0000371 a rdfs:Class ;
  rdfs:label "conjugative_transposon" ;
  rdfs:comment "A transposon that encodes function required for conjugation." ;
  rdfs:subClassOf obo:SO_0000182 .

obo:SO_0001344 a rdfs:Class ;
  rdfs:label "five_methyluridine" ;
  rdfs:comment "5_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001416 a rdfs:Class ;
  rdfs:label "five_prime_flanking_region" ;
  rdfs:comment "A flanking region located five prime of a specific region." ;
  rdfs:subClassOf obo:SO_0000239 .

obo:SO_0001554 a rdfs:Class ;
  rdfs:label "polypeptide_function_variant" ;
  rdfs:comment "A sequence variant which changes polypeptide functioning with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001539 .

obo:SO_0000935 a rdfs:Class ;
  rdfs:label "edited_CDS" ;
  rdfs:comment "A CDS that is edited." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:SO_0002187 a rdfs:Class ;
  rdfs:label "HERV_insertion" ;
  rdfs:comment "An insertion of sequence from the HERV family of mobile elements with respect to a reference." ;
  rdfs:subClassOf obo:SO_0001837 .

<http://purl.obolibrary.org/obo/so#contains> a rdf:Property ;
  rdfs:label "contains" ;
  rdfs:comment "The inverse of contained_by." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0005855 a rdfs:Class ;
  rdfs:label "gene_group" ;
  rdfs:comment "A collection of related genes." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001975 a rdfs:Class ;
  rdfs:label "five_prime_sticky_end_restriction_enzyme_cleavage_site" ;
  rdfs:comment "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." ;
  rdfs:subClassOf obo:SO_0001692 .

obo:SO_0001778 a rdfs:Class ;
  rdfs:label "germline_variant" ;
  rdfs:comment "A variant present in the embryo that is carried by every cell in the body." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0000046 a rdfs:Class ;
  rdfs:label "insert" ;
  rdfs:comment "To insert a subsection of sequence." .

obo:SO_0002256 a rdfs:Class ;
  rdfs:label "non_complimentary_stem" ;
  rdfs:comment "A region of a stem in a stem loop structure where the sequences are non-complimentary." ;
  rdfs:subClassOf obo:SO_0002255 .

obo:SO_0000538 a rdfs:Class ;
  rdfs:label "V_gene_recombination_feature" ;
  rdfs:comment "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000939 .

obo:SO_0000400 a rdfs:Class ;
  rdfs:label "sequence_attribute" ;
  rdfs:comment "An attribute describes a quality of sequence." .

obo:SO_0002322 a rdfs:Class ;
  rdfs:label "stop_gained_NMD_escaping" ;
  rdfs:comment "A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001587 , obo:SO_0002320 .

obo:SO_0001528 a rdfs:Class ;
  rdfs:label "nuclear_localization_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the nucleus." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0000459 a rdfs:Class ;
  rdfs:label "gene_with_trans_spliced_transcript" ;
  rdfs:comment "A gene with a transcript that is trans-spliced." ;
  rdfs:subClassOf obo:SO_0000704 .

<http://purl.obolibrary.org/obo/so#transcribed_to> a rdf:Property ;
  rdfs:label "transcribed_to" ;
  rdfs:comment "Inverse of transcribed_from." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0000225 a rdfs:Class ;
  rdfs:label "proline_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding prolyl tRNA (SO:0000268)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0001167 a rdfs:Class ;
  rdfs:label "NDM2_motif" ;
  rdfs:comment "A non directional promoter motif with consensus CGMYGYCR." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002061 a rdfs:Class ;
  rdfs:label "intrachromosomal_translocation" ;
  rdfs:comment "A translocation where the regions involved are from the same chromosome." ;
  rdfs:subClassOf obo:SO_1000044 .

obo:SO_1001263 a rdfs:Class ;
  rdfs:label "plus_1_translationally_frameshifted" ;
  rdfs:comment "An attribute describing a translational frameshift of +1." ;
  rdfs:subClassOf obo:SO_0000887 .

obo:SO_0001355 a rdfs:Class ;
  rdfs:label "five_methoxyuridine" ;
  rdfs:comment "5_methoxyuridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001559 a rdfs:Class ;
  rdfs:label "polypeptide_loss_of_function_variant" ;
  rdfs:comment "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0002022 a rdfs:Class ;
  rdfs:label "priRNA" ;
  rdfs:comment "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:BS_00143 a rdfs:Class .

obo:SO_1000149 a rdfs:Class ;
  rdfs:label "bipartite_duplication" ;
  rdfs:comment "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." ;
  rdfs:subClassOf obo:SO_1000031 , obo:SO_1000038 .

obo:SO_0000245 a rdfs:Class ;
  rdfs:label "mRNA_by_polyadenylation_status" .

obo:SO_0000360 a rdfs:Class ;
  rdfs:label "codon" ;
  rdfs:comment "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0000595 a rdfs:Class ;
  rdfs:label "C_D_box_snoRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a small nucleolar RNA of the box C/D family." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0001259 a rdfs:Class ;
  rdfs:label "apicoplast_chromosome" ;
  rdfs:comment "A chromosome originating in an apicoplast." ;
  rdfs:subClassOf obo:SO_0000340 .

<http://purl.obolibrary.org/obo/so#has_origin> a rdf:Property ;
  rdfs:label "has_origin" ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0001784 a rdfs:Class ;
  rdfs:label "complex_structural_alteration" ;
  rdfs:comment "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." ;
  rdfs:subClassOf obo:SO_0001785 , obo:SO_1000183 .

obo:SO_0001504 a rdfs:Class ;
  rdfs:label "assortment_derived_variation" ;
  rdfs:comment "A chromosome variation derived from an event during meiosis." ;
  rdfs:subClassOf obo:SO_0000240 .

obo:SO_0002176 a rdfs:Class ;
  rdfs:label "substitution_artifact" ;
  rdfs:comment "A substitution that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002172 .

obo:BS_00071 a rdfs:Class .

obo:SO_0001305 a rdfs:Class ;
  rdfs:label "N6_threonylcarbamoyladenosine" ;
  rdfs:comment "N6_threonylcarbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001825 a rdfs:Class ;
  rdfs:label "conservative_inframe_deletion" ;
  rdfs:comment "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." ;
  rdfs:subClassOf obo:SO_0001822 .

obo:SO_0001279 a rdfs:Class ;
  rdfs:label "one_two_prime_O_dimethylinosine" ;
  rdfs:comment "1,2'-O-dimethylinosine is a modified inosine." ;
  rdfs:subClassOf obo:SO_0001274 .

obo:SO_0001644 a rdfs:Class ;
  rdfs:label "targeting_vector" ;
  rdfs:comment "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." ;
  rdfs:subClassOf obo:SO_0000440 , obo:SO_0000804 .

obo:SO_0000772 a rdfs:Class ;
  rdfs:label "genomic_island" ;
  rdfs:comment "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_1000161 a rdfs:Class ;
  rdfs:label "unoriented_interchromosomal_transposition" ;
  rdfs:comment "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." ;
  rdfs:subClassOf obo:SO_1000155 .

obo:SO_0001183 a rdfs:Class ;
  rdfs:label "morpholino_backbone" ;
  rdfs:comment "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0001517 a rdfs:Class ;
  rdfs:label "inversion_attribute" ;
  rdfs:comment "When a region of a chromosome is changed to the reverse order without duplication or deletion." ;
  rdfs:subClassOf obo:SO_0001508 .

obo:SO_0001730 a rdfs:Class ;
  rdfs:label "H4K5_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001972 .

obo:BS_00042 a rdfs:Class .

obo:SO_0002309 a rdfs:Class ;
  rdfs:label "core_promoter_element" ;
  rdfs:comment "An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001333 a rdfs:Class ;
  rdfs:label "peroxywybutosine" ;
  rdfs:comment "Peroxywybutosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001819 a rdfs:Class ;
  rdfs:label "synonymous_variant" ;
  rdfs:comment "A sequence variant where there is no resulting change to the encoded amino acid." ;
  rdfs:subClassOf obo:SO_0001580 .

obo:SO_0000331 a rdfs:Class ;
  rdfs:label "STS" ;
  rdfs:comment "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." ;
  rdfs:subClassOf obo:SO_0000324 .

obo:SO_0002253 a rdfs:Class ;
  rdfs:label "stem_loop_region" ;
  rdfs:comment "A portion of a stem loop secondary structure in RNA." ;
  rdfs:subClassOf obo:SO_0000122 .

obo:SO_0001875 a rdfs:Class ;
  rdfs:label "unassigned_supercontig" ;
  rdfs:comment "A supercontig that is not been assigned to any ultracontig during a genome assembly project." ;
  rdfs:subClassOf obo:SO_0000148 .

obo:SO_0000848 a rdfs:Class ;
  rdfs:label "LTR_component" ;
  rdfs:comment "The long terminal repeat found at the ends of the sequence to be inserted into the host genome." ;
  rdfs:subClassOf obo:SO_0000840 .

obo:SO_0000504 a rdfs:Class ;
  rdfs:label "D_DJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0002007 a rdfs:Class ;
  rdfs:label "MNV" ;
  rdfs:comment "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." ;
  rdfs:subClassOf obo:SO_1000002 .

obo:BS_00216 a rdfs:Class .

obo:SO_0001929 a rdfs:Class ;
  rdfs:label "mitochondrial_DNA_read" ;
  rdfs:comment "A sequencer read of a mitochondrial DNA sample." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0000472 a rdfs:Class ;
  rdfs:label "tiling_path" ;
  rdfs:comment "A set of regions which overlap with minimal polymorphism to form a linear sequence." ;
  rdfs:subClassOf obo:SO_0000353 .

obo:SO_0000942 a rdfs:Class ;
  rdfs:label "attP_site" ;
  rdfs:comment "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0001773 a rdfs:Class ;
  rdfs:label "lethal_variant" ;
  rdfs:comment "A sequence variant where the mutated gene product does not allow for one or more basic functions necessary for survival." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0000285 a rdfs:Class ;
  rdfs:label "foreign_gene" ;
  rdfs:comment "A gene that is foreign." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000837 a rdfs:Class ;
  rdfs:label "UTR_region" ;
  rdfs:comment "A region of UTR." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0002198 a rdfs:Class ;
  rdfs:label "unprocessed_pseudogenic_tRNA" ;
  rdfs:comment "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions." ;
  rdfs:subClassOf obo:SO_0000778 .

obo:SO_0001918 a rdfs:Class ;
  rdfs:label "5_methylcytosine" ;
  rdfs:comment "A cytosine methylated at the 5 carbon." ;
  rdfs:subClassOf obo:SO_0000114 .

obo:SO_0001968 a rdfs:Class ;
  rdfs:label "coding_transcript_variant" ;
  rdfs:comment "A transcript variant of a protein coding gene." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0002275 a rdfs:Class ;
  rdfs:label "7SL_SINE_retrotransposon" ;
  rdfs:comment "Short interspersed elements that originated from 7SL RNAs." ;
  rdfs:subClassOf obo:SO_0000206 .

obo:SO_1001286 a rdfs:Class ;
  rdfs:label "three_prime_repeat_recoding_signal" ;
  rdfs:comment "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." ;
  rdfs:subClassOf obo:SO_1001277 .

obo:SO_0001597 a rdfs:Class ;
  rdfs:label "compensatory_transcript_secondary_structure_variant" ;
  rdfs:comment "A secondary structure variant that compensate for the change made by a previous variant." ;
  rdfs:subClassOf obo:SO_0001596 .

obo:SO_0001046 a rdfs:Class ;
  rdfs:label "IRLinv_site" ;
  rdfs:comment "Component of the inversion site located at the left of a region susceptible to site-specific inversion." ;
  rdfs:subClassOf obo:SO_0001048 .

obo:SO_0001413 a rdfs:Class ;
  rdfs:label "translocation_breakpoint" ;
  rdfs:comment "The point within a chromosome where a translocation begins or ends." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0001254 a rdfs:Class ;
  rdfs:label "polyploid" ;
  rdfs:comment "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." ;
  rdfs:subClassOf obo:SO_1000182 .

obo:SO_0001515 a rdfs:Class ;
  rdfs:label "inverted" ;
  rdfs:comment "A quality of an insertion where the insert is in a cytologically inverted orientation." ;
  rdfs:subClassOf obo:SO_0001512 .

obo:SO_0000320 a rdfs:Class ;
  rdfs:label "intronic_splice_enhancer" ;
  rdfs:comment "Sequences within the intron that modulate splice site selection for some introns." ;
  rdfs:subClassOf obo:SO_0000344 .

obo:SO_0000213 a rdfs:Class ;
  rdfs:label "asparagine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding asparaginyl tRNA (SO:0000256)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0001586 a rdfs:Class ;
  rdfs:label "non_conservative_missense_variant" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." ;
  rdfs:subClassOf obo:SO_0001583 .

obo:SO_0002150 a rdfs:Class ;
  rdfs:label "AUG_initiated_uORF" ;
  rdfs:comment "A uORF beginning with the canonical start codon AUG." ;
  rdfs:subClassOf obo:SO_0002027 .

obo:SO_0001881 a rdfs:Class ;
  rdfs:label "feature_translocation" ;
  rdfs:comment "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_0001326 a rdfs:Class ;
  rdfs:label "seven_methylguanosine" ;
  rdfs:comment "7_methylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0002123 a rdfs:Class ;
  rdfs:label "IG_C_gene" ;
  rdfs:comment "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002122 .

obo:SO_0001922 a rdfs:Class ;
  rdfs:label "mitochondrial_supercontig" ;
  rdfs:comment "A scaffold composed of mitochondrial contigs." ;
  rdfs:subClassOf obo:SO_0000148 .

obo:SO_0000924 a rdfs:Class ;
  rdfs:label "insert_GC" ;
  rdfs:comment "An edit to insert a GC dinucleotide." .

obo:SO_0100001 a rdfs:Class ;
  rdfs:label "biochemical_region_of_peptide" ;
  rdfs:comment "A region of a peptide that is involved in a biochemical function." ;
  rdfs:subClassOf obo:SO_0001067 .

obo:SO_0000585 a rdfs:Class ;
  rdfs:label "C_D_box_snoRNA_encoding" ;
  rdfs:comment "snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end." ;
  rdfs:subClassOf obo:SO_0000578 .

obo:SO_0000196 a rdfs:Class ;
  rdfs:label "five_prime_coding_exon_coding_region" ;
  rdfs:comment "The sequence of the five_prime_coding_exon that codes for protein." ;
  rdfs:subClassOf obo:SO_0001215 .

obo:SO_0002379 a rdfs:Class ;
  rdfs:label "methylation_guide_snoRNA_gene" ;
  rdfs:comment "A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." ;
  rdfs:subClassOf obo:SO_0002375 .

obo:SO_0000845 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter_type_1_region" ;
  rdfs:comment "A region of sequence which is a promoter for RNA polymerase III type 1." .

obo:SO_0001431 a rdfs:Class ;
  rdfs:label "cryptic_gene" ;
  rdfs:comment "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001734 a rdfs:Class ;
  rdfs:label "H3K4_methylation_site" ;
  rdfs:comment "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0001311 a rdfs:Class ;
  rdfs:label "N6_N6_dimethyladenosine" ;
  rdfs:comment "N6_N6_dimethyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001214 a rdfs:Class ;
  rdfs:label "noncoding_region_of_exon" ;
  rdfs:comment "The maximal intersection of exon and UTR." ;
  rdfs:subClassOf obo:SO_0000852 .

obo:SO_0001539 a rdfs:Class ;
  rdfs:label "translational_product_function_variant" ;
  rdfs:comment "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0002204 a rdfs:Class ;
  rdfs:label "nucleotide_cleavage_site" ;
  rdfs:comment "A point in nucleic acid where a cleavage event occurs." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0000790 a rdfs:Class ;
  rdfs:label "invalidated" ;
  rdfs:comment "An attribute describing a feature that is invalidated." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0001751 a rdfs:Class ;
  rdfs:label "SL6_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0000676 a rdfs:Class ;
  rdfs:label "canonical_three_prime_splice_site" ;
  rdfs:comment "The canonical 3' splice site has the sequence \"AG\"." ;
  rdfs:subClassOf obo:SO_0000164 .

obo:SO_1001275 a rdfs:Class ;
  rdfs:label "retron" ;
  rdfs:comment "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000972 a rdfs:Class ;
  rdfs:label "RNA_replication_mode" ;
  rdfs:comment "This has been obsoleted as it represents a process. replaced_by: GO:0034961." .

obo:SO_0002044 a rdfs:Class ;
  rdfs:label "TCS_element" ;
  rdfs:comment "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000653 a rdfs:Class ;
  rdfs:label "cytosolic_28S_rRNA" ;
  rdfs:comment "Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_1000043 a rdfs:Class ;
  rdfs:label "Robertsonian_fusion" ;
  rdfs:comment "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." ;
  rdfs:subClassOf obo:SO_1000044 .

obo:SO_0002064 a rdfs:Class ;
  rdfs:label "LINE1_insertion" ;
  rdfs:comment "An insertion from the Line1 family of mobile elements." ;
  rdfs:subClassOf obo:SO_0001837 .

obo:SO_0000122 a rdfs:Class ;
  rdfs:label "RNA_sequence_secondary_structure" ;
  rdfs:comment "A folded RNA sequence." ;
  rdfs:subClassOf obo:SO_0000002 .

obo:SO_0002053 a rdfs:Class ;
  rdfs:label "gain_of_function_variant" ;
  rdfs:comment "A sequence variant whereby new or enhanced function is conferred on the gene product." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0001845 a rdfs:Class ;
  rdfs:label "DRE" ;
  rdfs:comment "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000516 a rdfs:Class ;
  rdfs:label "pseudogenic_transcript" ;
  rdfs:comment "A non functional descendant of a transcript, part of a pseudogene." ;
  rdfs:subClassOf obo:SO_0000462 .

obo:SO_0001886 a rdfs:Class ;
  rdfs:label "transcript_fusion" ;
  rdfs:comment "A feature fusion where the deletion brings together transcript regions." ;
  rdfs:subClassOf obo:SO_0001882 .

obo:SO_0001746 a rdfs:Class ;
  rdfs:label "paternal_uniparental_disomy" ;
  rdfs:comment "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." ;
  rdfs:subClassOf obo:SO_0001744 .

obo:SO_0000660 a rdfs:Class ;
  rdfs:label "DNA_invertase_target_sequence" .

obo:SO_0002401 a rdfs:Class ;
  rdfs:label "upstream_intergenic_fusion" ;
  rdfs:comment "A sequence variant whereby two genomic features have become joined with one breakend proximally upstream of a gene." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0002238 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_5S_gene" ;
  rdfs:comment "A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0000002 a rdfs:Class ;
  rdfs:label "sequence_secondary_structure" ;
  rdfs:comment "A folded sequence." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001372 a rdfs:Class ;
  rdfs:label "three_methyluridine" ;
  rdfs:comment "3_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000426 a rdfs:Class ;
  rdfs:label "three_prime_LTR" ;
  rdfs:comment "The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome." ;
  rdfs:subClassOf obo:SO_0000286 .

obo:SO_0000274 a rdfs:Class ;
  rdfs:label "snRNA" ;
  rdfs:comment "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." ;
  rdfs:subClassOf obo:SO_0002247 .

obo:SO_0001572 a rdfs:Class ;
  rdfs:label "exon_loss_variant" ;
  rdfs:comment "A sequence variant whereby an exon is lost from the transcript." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0000057 a rdfs:Class ;
  rdfs:label "operator" ;
  rdfs:comment "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0000487 a rdfs:Class ;
  rdfs:label "VDJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:BS_00028 a rdfs:Class .

obo:SO_1000080 a rdfs:Class ;
  rdfs:label "sequence_variant_increasing_rate_of_transcription" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001366 a rdfs:Class ;
  rdfs:label "five_methylaminomethyl_two_selenouridine" ;
  rdfs:comment "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001060 a rdfs:Class ;
  rdfs:label "sequence_variant" ;
  rdfs:comment "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." .

obo:SO_0000234 a rdfs:Class ;
  rdfs:label "mRNA" ;
  rdfs:comment "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." ;
  rdfs:subClassOf obo:SO_0000233 .

obo:SO_0002173 a rdfs:Class ;
  rdfs:label "indel_artifact" ;
  rdfs:comment "An indel that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002172 .

obo:SO_0000606 a rdfs:Class ;
  rdfs:label "editing_domain" ;
  rdfs:comment "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." ;
  rdfs:subClassOf obo:SO_0000579 .

obo:SO_0001156 a rdfs:Class ;
  rdfs:label "DRE_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001957 a rdfs:Class ;
  rdfs:label "RNA_stability_element" ;
  rdfs:comment "RNA secondary structure that affects the stability of an RNA molecule." .

obo:SO_1000042 a rdfs:Class ;
  rdfs:label "compound_chromosome" ;
  rdfs:comment "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0001606 a rdfs:Class ;
  rdfs:label "amino_acid_substitution" ;
  rdfs:comment "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_0000834 a rdfs:Class ;
  rdfs:label "mature_transcript_region" ;
  rdfs:comment "A region of a mature transcript." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0001195 a rdfs:Class ;
  rdfs:label "R_GNA_oligo" ;
  rdfs:comment "An oligo composed of (R)-GNA residues." ;
  rdfs:subClassOf obo:SO_0001193 .

obo:SO_0001633 a rdfs:Class ;
  rdfs:label "5KB_downstream_variant" ;
  rdfs:comment "A sequence variant located within 5 KB of the end of a gene." ;
  rdfs:subClassOf obo:SO_0001632 .

obo:SO_0000570 a rdfs:Class ;
  rdfs:label "three_prime_D_recombination_signal_sequence" ;
  rdfs:comment "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." ;
  rdfs:subClassOf obo:SO_0000492 .

obo:SO_0000913 a rdfs:Class ;
  rdfs:label "cloned_cDNA_insert" ;
  rdfs:comment "A clone insert made from cDNA." ;
  rdfs:subClassOf obo:SO_0000753 .

obo:SO_0000700 a rdfs:Class ;
  rdfs:label "remark" ;
  rdfs:comment "A comment about the sequence." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0002058 a rdfs:Class ;
  rdfs:label "exonic_splicing_silencer" ;
  rdfs:comment "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." ;
  rdfs:subClassOf obo:SO_0000625 , obo:SO_0000852 .

obo:SO_0001093 a rdfs:Class ;
  rdfs:label "protein_protein_contact" ;
  rdfs:comment "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." ;
  rdfs:subClassOf obo:SO_0000410 , obo:SO_0100002 .

obo:SO_0000091 a rdfs:Class ;
  rdfs:label "apicoplast_gene" ;
  rdfs:comment "A gene from apicoplast sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0000162 a rdfs:Class ;
  rdfs:label "splice_site" ;
  rdfs:comment "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0001006 a rdfs:Class ;
  rdfs:label "prophage" ;
  rdfs:comment "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." ;
  rdfs:subClassOf obo:SO_0000113 .

obo:SO_0000067 a rdfs:Class ;
  rdfs:label "gene_to_gene_feature" ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0002011 a rdfs:Class ;
  rdfs:label "intragenic_variant" ;
  rdfs:comment "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:BS_00157 a rdfs:Class .

obo:SO_1000091 a rdfs:Class .

obo:SO_0001506 a rdfs:Class ;
  rdfs:label "variant_genome" ;
  rdfs:comment "A collection of sequences (often chromosomes) of an individual." ;
  rdfs:subClassOf obo:SO_0001026 .

obo:SO_0002090 a rdfs:Class ;
  rdfs:label "3_prime_UTR_intron_variant" ;
  rdfs:comment "A UTR variant of intronic sequence of the 3' UTR." ;
  rdfs:subClassOf obo:SO_0001624 , obo:SO_0001969 .

obo:SO_0000107 a rdfs:Class ;
  rdfs:label "sequencing_primer" ;
  rdfs:comment "A single stranded oligo used for polymerase chain reaction." ;
  rdfs:subClassOf obo:SO_0000112 .

obo:SO_0000761 a rdfs:Class ;
  rdfs:label "phagemid_clone" .

obo:SO_0000359 a rdfs:Class ;
  rdfs:label "floxed" ;
  rdfs:comment "An attribute describing sequence that is flanked by Lox-P sites." ;
  rdfs:subClassOf obo:SO_0000357 .

obo:SO_0000859 a rdfs:Class ;
  rdfs:label "paralogous" ;
  rdfs:comment "An attribute describing a kind of homology where divergence occurred after a duplication event." ;
  rdfs:subClassOf obo:SO_0000857 .

obo:SO_0000314 a rdfs:Class ;
  rdfs:label "direct_repeat" ;
  rdfs:comment "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0001767 a rdfs:Class ;
  rdfs:label "common_variant" ;
  rdfs:comment "When a variant from the genomic sequence is commonly found in the general population." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_0000269 a rdfs:Class ;
  rdfs:label "seryl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:BS_00205 a rdfs:Class .

obo:SO_0002216 a rdfs:Class ;
  rdfs:label "Pho7_binding_site" ;
  rdfs:comment "A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001158 a rdfs:Class ;
  rdfs:label "E_box_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001261 a rdfs:Class ;
  rdfs:label "overlapping_feature_set" ;
  rdfs:comment "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." ;
  rdfs:subClassOf obo:SO_0000703 .

obo:SO_0001118 a rdfs:Class ;
  rdfs:label "pi_helix" ;
  rdfs:comment "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." ;
  rdfs:subClassOf obo:SO_0001116 .

obo:SO_0001808 a rdfs:Class ;
  rdfs:label "mitochondrial_targeting_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the mitochondrion." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0001380 a rdfs:Class ;
  rdfs:label "five_isopentenylaminomethyl_uridine" ;
  rdfs:comment "5_isopentenylaminomethyl_uridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000985 a rdfs:Class ;
  rdfs:label "double" ;
  rdfs:comment "When a nucleotide polymer has two strands that are reverse-complement to one another and pair together." ;
  rdfs:subClassOf obo:SO_0000983 .

obo:SO_0002246 a rdfs:Class ;
  rdfs:label "three_prime_duplicated_transcript" ;
  rdfs:comment "A partially_duplicated_transcript where the 3' end of the transcript is duplicated." ;
  rdfs:subClassOf obo:SO_0002244 .

obo:SO_0001550 a rdfs:Class ;
  rdfs:label "rate_of_transcription_variant" ;
  rdfs:comment "A sequence variant that changes the rate of transcription with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001549 .

obo:SO_0001174 a rdfs:Class ;
  rdfs:label "anticodon" ;
  rdfs:comment "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." ;
  rdfs:subClassOf obo:SO_0001172 .

obo:SO_0000296 a rdfs:Class ;
  rdfs:label "origin_of_replication" ;
  rdfs:comment "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001838 a rdfs:Class ;
  rdfs:label "novel_sequence_insertion" ;
  rdfs:comment "An insertion the sequence of which cannot be mapped to the reference genome." ;
  rdfs:subClassOf obo:SO_0000667 .

obo:SO_0001565 a rdfs:Class ;
  rdfs:label "gene_fusion" ;
  rdfs:comment "A sequence variant whereby a two genes have become joined." ;
  rdfs:subClassOf obo:SO_0001564 , obo:SO_0001882 .

obo:SO_0001079 a rdfs:Class ;
  rdfs:label "polypeptide_structural_motif" ;
  rdfs:comment "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0000979 a rdfs:Class ;
  rdfs:label "gRNA_encoding" ;
  rdfs:comment "A non-protein_coding gene that encodes a guide_RNA." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0000909 a rdfs:Class ;
  rdfs:label "supported_by_EST_or_cDNA" ;
  rdfs:comment "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." ;
  rdfs:subClassOf obo:SO_0000907 .

obo:BS_00012 a rdfs:Class .

obo:SO_0001394 a rdfs:Class ;
  rdfs:label "modified_L_glutamine" ;
  rdfs:comment "A post translationally modified glutamine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001940 a rdfs:Class ;
  rdfs:label "H2BK120_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002143 .

obo:SO_0001275 a rdfs:Class ;
  rdfs:label "modified_cytidine" ;
  rdfs:comment "A modified cytidine is a cytidine base feature which has been altered." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_0002037 a rdfs:Class ;
  rdfs:label "miR_encoding_tRNA_primary_transcript" ;
  rdfs:comment "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000307 a rdfs:Class ;
  rdfs:label "CpG_island" ;
  rdfs:comment "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_1000111 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_3D_structure_of_polypeptide" ;
  rdfs:comment "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." .

obo:SO_0000931 a rdfs:Class ;
  rdfs:label "anchor_region" ;
  rdfs:comment "A region of a guide_RNA that base-pairs to a target mRNA." ;
  rdfs:subClassOf obo:SO_0000930 .

obo:SO_0001221 a rdfs:Class ;
  rdfs:label "silenced_by_histone_modification" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by histone modification." ;
  rdfs:subClassOf obo:SO_0000893 .

obo:SO_0001337 a rdfs:Class ;
  rdfs:label "methylwyosine" ;
  rdfs:comment "Methylwyosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000319 a rdfs:Class ;
  rdfs:label "stop_codon" ;
  rdfs:comment "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. In genomic sequence, a stop codon may be only one or two nucleotides where the additional nucleotides are provided in the RNA via polyadenylation." ;
  rdfs:subClassOf obo:SO_0000360 .

obo:SO_0001361 a rdfs:Class ;
  rdfs:label "five_methoxycarbonylmethyl_two_prime_O_methyluridine" ;
  rdfs:comment "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1000069 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_minus_2_frameshift" ;
  rdfs:comment "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." .

obo:SO_0002072 a rdfs:Class ;
  rdfs:label "sequence_comparison" ;
  rdfs:comment "A position or feature where two sequences have been compared." ;
  rdfs:subClassOf obo:SO_0000110 .

obo:SO_0001979 a rdfs:Class ;
  rdfs:label "RNA_stability_element" ;
  rdfs:comment "A motif that affects the stability of RNA." ;
  rdfs:subClassOf obo:SO_0000715 .

obo:SO_0001821 a rdfs:Class ;
  rdfs:label "inframe_insertion" ;
  rdfs:comment "An inframe non synonymous variant that inserts bases into in the coding sequence." ;
  rdfs:subClassOf obo:SO_0001820 , obo:SO_0001908 .

obo:SO_1000037 a rdfs:Class ;
  rdfs:label "chromosomal_duplication" ;
  rdfs:comment "An extra chromosome." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0001933 a rdfs:Class ;
  rdfs:label "restriction_enzyme_three_prime_single_strand_overhang" ;
  rdfs:comment "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." ;
  rdfs:subClassOf obo:SO_0001695 .

obo:SO_0000812 a rdfs:Class ;
  rdfs:label "polyA_primed_cDNA_clone" ;
  rdfs:comment "A cDNA clone invalidated by polyA priming." ;
  rdfs:subClassOf obo:SO_0000809 .

obo:SO_0001993 a rdfs:Class ;
  rdfs:label "extended_cis_splice_site" ;
  rdfs:comment "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." ;
  rdfs:subClassOf obo:SO_0001419 .

obo:SO_0001655 a rdfs:Class ;
  rdfs:label "nucleotide_binding_site" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:SO_0000534 a rdfs:Class ;
  rdfs:label "V_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0000256 a rdfs:Class ;
  rdfs:label "asparaginyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000348 a rdfs:Class ;
  rdfs:label "nucleic_acid" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." ;
  rdfs:subClassOf obo:SO_0000443 .

obo:SO_0000375 a rdfs:Class ;
  rdfs:label "cytosolic_5_8S_rRNA" ;
  rdfs:comment "Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_0002328 a rdfs:Class ;
  rdfs:label "splice_acceptor_variant_NMD_escaping" ;
  rdfs:comment "A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001574 , obo:SO_0002320 .

obo:SO_0001900 a rdfs:Class .

obo:SO_0001232 a rdfs:Class ;
  rdfs:label "ribothymidine" ;
  rdfs:comment "A modified RNA base in which thymine is bound to the ribose ring." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_0002141 a rdfs:Class ;
  rdfs:label "late_origin_of_replication" ;
  rdfs:comment "An origin of replication that initiates late in S phase." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001627 a rdfs:Class ;
  rdfs:label "intron_variant" ;
  rdfs:comment "A transcript variant occurring within an intron." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_1000151 a rdfs:Class ;
  rdfs:label "bipartite_inversion" ;
  rdfs:comment "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." ;
  rdfs:subClassOf obo:SO_1000030 .

obo:SO_0001780 a rdfs:Class ;
  rdfs:label "population_specific_variant" ;
  rdfs:comment "A variant found within only speficic populations." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0001039 a rdfs:Class ;
  rdfs:label "integrated_mobile_genetic_element" ;
  rdfs:comment "An MGE that is integrated into the host chromosome." ;
  rdfs:subClassOf obo:SO_0001037 .

obo:SO_0000906 a rdfs:Class ;
  rdfs:label "independently_known" ;
  rdfs:comment "Attribute to describe a feature that is independently known - not predicted." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0000151 a rdfs:Class ;
  rdfs:label "clone" ;
  rdfs:comment "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0001301 a rdfs:Class ;
  rdfs:label "two_methylthio_N6_isopentenyladenosine" ;
  rdfs:comment "2_methylthio_N6_isopentenyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0002305 a rdfs:Class ;
  rdfs:label "topologically_associated_domain_boundary" ;
  rdfs:comment "A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0000111 a rdfs:Class ;
  rdfs:label "transposable_element_gene" ;
  rdfs:comment "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000454 a rdfs:Class ;
  rdfs:label "rasiRNA" ;
  rdfs:comment "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." ;
  rdfs:subClassOf obo:SO_0001035 .

obo:SO_0001220 a rdfs:Class ;
  rdfs:label "silenced_by_RNA_interference" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." ;
  rdfs:subClassOf obo:SO_0000893 .

obo:SO_0000527 a rdfs:Class ;
  rdfs:label "V_D_DJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000218 a rdfs:Class ;
  rdfs:label "glycine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding glycyl tRNA (SO:0000263)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0001589 a rdfs:Class ;
  rdfs:label "frameshift_variant" ;
  rdfs:comment "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." ;
  rdfs:subClassOf obo:SO_0001818 .

obo:SO_0002109 a rdfs:Class ;
  rdfs:label "transcribed_processed_pseudogene" ;
  rdfs:comment "A processed_pseudogene overlapped by locus-specific evidence of transcription." ;
  rdfs:subClassOf obo:SO_0000043 .

obo:SO_0000258 a rdfs:Class ;
  rdfs:label "cysteinyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0002292 a rdfs:Class ;
  rdfs:label "circular_mRNA" ;
  rdfs:comment "An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_1000122 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_polypeptide_post_translational_processing_change" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001485 a rdfs:Class ;
  rdfs:label "Y_prime_element" ;
  rdfs:comment "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0000476 a rdfs:Class ;
  rdfs:label "contig_read" ;
  rdfs:comment "A DNA sequencer read which is part of a contig." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0001892 a rdfs:Class ;
  rdfs:label "TFBS_amplification" ;
  rdfs:comment "A feature amplification of a region containing a transcription factor binding site." ;
  rdfs:subClassOf obo:SO_0001891 .

obo:SO_0000869 a rdfs:Class ;
  rdfs:label "plus_2_framshift" ;
  rdfs:comment "A frameshift caused by inserting two bases." ;
  rdfs:subClassOf obo:SO_0000865 .

obo:SO_0000754 a rdfs:Class ;
  rdfs:label "lambda_vector" ;
  rdfs:comment "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0001163 a rdfs:Class ;
  rdfs:label "INR1_motif" ;
  rdfs:comment "A promoter motif with consensus sequence TCATTCG." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000996 a rdfs:Class ;
  rdfs:label "predicted_gene" ;
  rdfs:comment "A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001076 a rdfs:Class ;
  rdfs:label "membrane_peptide_loop" ;
  rdfs:comment "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." ;
  rdfs:subClassOf obo:SO_0001075 .

obo:SO_0001998 a rdfs:Class ;
  rdfs:label "sgRNA" ;
  rdfs:comment "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0000988 a rdfs:Class ;
  rdfs:label "circular" ;
  rdfs:comment "A quality of a nucleotide polymer that has no terminal nucleotide residues." ;
  rdfs:subClassOf obo:SO_0000986 .

obo:SO_0000308 a rdfs:Class ;
  rdfs:label "sequence_feature_locating_method" .

obo:SO_0001796 a rdfs:Class ;
  rdfs:label "regional_centromere_central_core" ;
  rdfs:comment "A conserved region within the central region of a modular centromere, where the kinetochore is formed." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0001738 a rdfs:Class ;
  rdfs:label "H4K_acylation_region" ;
  rdfs:comment "A region of the H4 histone whereby multiple lysines are acylated." ;
  rdfs:subClassOf obo:SO_0001737 .

obo:SO_0001290 a rdfs:Class ;
  rdfs:label "N4_methylcytidine" ;
  rdfs:comment "N4-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0000652 a rdfs:Class ;
  rdfs:label "cytosolic_5S_rRNA" ;
  rdfs:comment "Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_0002224 a rdfs:Class ;
  rdfs:label "2A_self_cleaving_peptide_region" ;
  rdfs:comment "A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0000927 a rdfs:Class ;
  rdfs:label "insert_AU" ;
  rdfs:comment "An edit to insert a AU dinucleotide." .

obo:SO_0001199 a rdfs:Class ;
  rdfs:label "ss_RNA_viral_sequence" ;
  rdfs:comment "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." ;
  rdfs:subClassOf obo:SO_0001041 .

obo:SO_0002000 a rdfs:Class .

obo:SO_0002327 a rdfs:Class ;
  rdfs:label "splice_acceptor_variant_NMD_triggering" ;
  rdfs:comment "A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001574 , obo:SO_0002319 .

obo:SO_0002021 a rdfs:Class ;
  rdfs:label "mating_type_region_replication_fork_barrier" ;
  rdfs:comment "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000237 a rdfs:Class ;
  rdfs:label "transcript_attribute" ;
  rdfs:comment "An attribute describing a transcript." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0002048 a rdfs:Class ;
  rdfs:label "disabled_reading_frame" ;
  rdfs:comment "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." ;
  rdfs:subClassOf obo:SO_0000717 .

obo:SO_0001237 a rdfs:Class ;
  rdfs:label "amino_acid" ;
  rdfs:comment "A sequence feature that corresponds to a single amino acid residue in a polypeptide." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000217 a rdfs:Class ;
  rdfs:label "glutamine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding glutamyl tRNA (SO:0000260)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000870 a rdfs:Class ;
  rdfs:label "trans_spliced" ;
  rdfs:comment "An attribute describing transcript sequence that is created by splicing exons from diferent genes." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0000737 a rdfs:Class ;
  rdfs:label "mitochondrial_sequence" ;
  rdfs:comment "DNA belonging to the genome of a mitochondria." ;
  rdfs:subClassOf obo:SO_0000736 .

obo:SO_0001250 a rdfs:Class ;
  rdfs:label "fingerprint_map" ;
  rdfs:comment "A fingerprint_map is a physical map composed of restriction fragments." ;
  rdfs:subClassOf obo:SO_0001249 .

obo:SO_0001582 a rdfs:Class ;
  rdfs:label "initiator_codon_variant" ;
  rdfs:comment "A codon variant that changes at least one base of the first codon of a transcript." ;
  rdfs:subClassOf obo:SO_0001580 .

obo:BS_00029 a rdfs:Class .

obo:SO_0001577 a rdfs:Class ;
  rdfs:label "complex_transcript_variant" ;
  rdfs:comment "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0001226 a rdfs:Class ;
  rdfs:label "gene_silenced_by_histone_methylation" ;
  rdfs:comment "A gene that is silenced by histone methylation." ;
  rdfs:subClassOf obo:SO_0001225 .

obo:SO_1000004 a rdfs:Class .

obo:SO_0000389 a rdfs:Class ;
  rdfs:label "spot_42_RNA" ;
  rdfs:comment "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0001593 a rdfs:Class ;
  rdfs:label "minus_2_frameshift_variant" ;
  rdfs:comment "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward." ;
  rdfs:subClassOf obo:SO_0001589 .

obo:SO_0001458 a rdfs:Class ;
  rdfs:label "unigene_cluster" ;
  rdfs:comment "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." ;
  rdfs:subClassOf obo:SO_0001457 .

obo:SO_0001961 a rdfs:Class ;
  rdfs:label "5_formylcytosine" ;
  rdfs:comment "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." ;
  rdfs:subClassOf obo:SO_0001963 .

obo:BS_00204 a rdfs:Class .

obo:SO_0000610 a rdfs:Class ;
  rdfs:label "polyA_sequence" ;
  rdfs:comment "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001302 a rdfs:Class ;
  rdfs:label "N6_cis_hydroxyisopentenyl_adenosine" ;
  rdfs:comment "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000749 a rdfs:Class ;
  rdfs:label "plasmid_location" ;
  rdfs:comment "The location of DNA that has come from a plasmid sequence." ;
  rdfs:subClassOf obo:SO_0000735 .

obo:SO_0001666 a rdfs:Class ;
  rdfs:label "DCE_SII" ;
  rdfs:comment "A sub element of the DCE core promoter element with consensus sequence CTGT." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000671 a rdfs:Class ;
  rdfs:label "internal_eliminated_sequence" ;
  rdfs:comment "A sequence eliminated from the genome of ciliates during nuclear differentiation." ;
  rdfs:subClassOf obo:SO_0000669 .

obo:SO_0002279 a rdfs:Class ;
  rdfs:label "hAT_TIR_transposon" ;
  rdfs:comment "The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0000657 a rdfs:Class ;
  rdfs:label "repeat_region" ;
  rdfs:comment "A region of sequence containing one or more repeat units." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002280 a rdfs:Class ;
  rdfs:label "Mutator_TIR_transposon" ;
  rdfs:comment "Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal G…C nucleotides, or with the G…C nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0002167 a rdfs:Class ;
  rdfs:label "isomiR" ;
  rdfs:comment "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA." ;
  rdfs:subClassOf obo:SO_0000276 .

obo:SO_0000841 a rdfs:Class ;
  rdfs:label "spliceosomal_intron_region" ;
  rdfs:comment "A region within an intron." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0002068 a rdfs:Class ;
  rdfs:label "SVA_deletion" ;
  rdfs:comment "A deletion of an SVA mobile element." ;
  rdfs:subClassOf obo:SO_0002066 .

obo:SO_0002074 a rdfs:Class ;
  rdfs:label "intergenic_1kb_variant" ;
  rdfs:comment "A variant that falls in an intergenic region that is 1 kb or less between 2 genes." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0000170 a rdfs:Class ;
  rdfs:label "RNApol_II_promoter" ;
  rdfs:comment "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0002221 .

obo:SO_0000507 a rdfs:Class ;
  rdfs:label "pseudogenic_exon" ;
  rdfs:comment "A non functional descendant of an exon, part of a pseudogene." ;
  rdfs:subClassOf obo:SO_0000462 .

obo:BS_00230 a rdfs:Class .

obo:SO_0001841 a rdfs:Class ;
  rdfs:label "polymorphic_pseudogene" ;
  rdfs:comment "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." ;
  rdfs:subClassOf obo:SO_0000336 .

obo:BS_00211 a rdfs:Class .

obo:SO_0001678 a rdfs:Class ;
  rdfs:label "regulatory_promoter_element" ;
  rdfs:comment "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002370 a rdfs:Class ;
  rdfs:label "H_ACA_box_scaRNA" ;
  rdfs:comment "A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002095 .

obo:SO_0000896 a rdfs:Class ;
  rdfs:label "translationally_regulated_gene" ;
  rdfs:comment "A gene that is translationally regulated." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000592 a rdfs:Class ;
  rdfs:label "H_pseudoknot" ;
  rdfs:comment "A pseudoknot which contains two stems and at least two loops." ;
  rdfs:subClassOf obo:SO_0000591 .

obo:SO_0002057 a rdfs:Class ;
  rdfs:label "intronic_splicing_enhancer" .

obo:SO_0001637 a rdfs:Class ;
  rdfs:label "rRNA_gene" ;
  rdfs:comment "A gene that encodes for ribosomal RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0001661 a rdfs:Class ;
  rdfs:label "RNA_polymerase_II_TATA_box" ;
  rdfs:comment "A TATA box core promoter of a gene transcribed by RNA polymerase II." ;
  rdfs:subClassOf obo:SO_0000174 .

obo:SO_0001082 a rdfs:Class ;
  rdfs:label "polypeptide_sequencing_information" ;
  rdfs:comment "Incompatibility in the sequence due to some experimental problem." ;
  rdfs:subClassOf obo:SO_0000700 .

obo:SO_0000101 a rdfs:Class ;
  rdfs:label "transposable_element" ;
  rdfs:comment "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_0001702 a rdfs:Class ;
  rdfs:label "histone_acetylation_site" ;
  rdfs:comment "A histone modification where the modification is the acylation of the residue." ;
  rdfs:subClassOf obo:SO_0001700 .

obo:SO_0001615 a rdfs:Class ;
  rdfs:label "elongated_out_of_frame_polypeptide_N_terminal" ;
  rdfs:comment "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." ;
  rdfs:subClassOf obo:SO_0001611 .

obo:SO_0000053 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_regulatory_region" ;
  rdfs:comment "A sequence_variant_effect which changes the regulatory region of a gene." .

obo:SO_0002191 a rdfs:Class ;
  rdfs:label "imprinting_control_region" ;
  rdfs:comment "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs." ;
  rdfs:subClassOf obo:SO_0001720 .

obo:SO_0002231 a rdfs:Class ;
  rdfs:label "self_cleaving_ribozyme" ;
  rdfs:comment "An RNA that catalyzes its own cleavage." ;
  rdfs:subClassOf obo:SO_0000374 .

obo:SO_0000278 a rdfs:Class ;
  rdfs:label "transcript_bound_by_nucleic_acid" ;
  rdfs:comment "A transcript that is bound by a nucleic acid." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0001033 a rdfs:Class ;
  rdfs:label "chloroplast_DNA" ;
  rdfs:comment "DNA belonging to the genome of a chloroplast, a photosynthetic plastid." ;
  rdfs:subClassOf obo:SO_0000745 .

obo:SO_0000830 a rdfs:Class ;
  rdfs:label "chromosome_part" ;
  rdfs:comment "A region of a chromosome." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000682 a rdfs:Class ;
  rdfs:label "splicing_feature" .

obo:SO_0002094 a rdfs:Class ;
  rdfs:label "non_allelic_homologous_recombination_region" ;
  rdfs:comment "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination." ;
  rdfs:subClassOf obo:SO_0000339 .

obo:SO_0000212 a rdfs:Class ;
  rdfs:label "arginine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding arginyl tRNA (SO:0000255)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000325 a rdfs:Class ;
  rdfs:label "rRNA_large_subunit_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a large ribosomal subunit RNA." ;
  rdfs:subClassOf obo:SO_0000209 .

obo:SO_0002063 a rdfs:Class ;
  rdfs:label "Alu_insertion" ;
  rdfs:comment "An insertion of sequence from the Alu family of mobile elements." ;
  rdfs:subClassOf obo:SO_0001837 .

obo:SO_0000549 a rdfs:Class ;
  rdfs:label "inversion_derived_duplication_plus_aneuploid" ;
  rdfs:comment "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." ;
  rdfs:subClassOf obo:SO_1000038 .

obo:SO_0001576 a rdfs:Class ;
  rdfs:label "transcript_variant" ;
  rdfs:comment "A sequence variant that changes the structure of the transcript." ;
  rdfs:subClassOf obo:SO_0001564 .

obo:SO_0000627 a rdfs:Class ;
  rdfs:label "insulator" ;
  rdfs:comment "A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region." ;
  rdfs:subClassOf obo:SO_0000727 .

obo:SO_0000437 a rdfs:Class ;
  rdfs:label "assortment_derived_duplication" .

obo:SO_0002395 a rdfs:Class ;
  rdfs:label "lost_polypeptide" ;
  rdfs:comment "A complete loss of polypeptide (i.e. protein) expression, as a consequence of a variant in the gene." ;
  rdfs:subClassOf obo:SO_0002317 .

obo:SO_0001953 a rdfs:Class ;
  rdfs:label "restriction_enzyme_assembly_scar" ;
  rdfs:comment "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." ;
  rdfs:subClassOf obo:SO_0001954 .

obo:SO_0001447 a rdfs:Class ;
  rdfs:label "cysteine" ;
  rdfs:comment "A polar amino acid encoded by the codons TGT and TGC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_1001197 a rdfs:Class ;
  rdfs:label "dicistronic_primary_transcript" ;
  rdfs:comment "A primary transcript that has the quality dicistronic." ;
  rdfs:subClassOf obo:SO_0000079 , obo:SO_0000185 , obo:SO_0000631 .

obo:SO_0001566 a rdfs:Class ;
  rdfs:label "regulatory_region_variant" ;
  rdfs:comment "A sequence variant located within a regulatory region." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0000877 a rdfs:Class ;
  rdfs:label "alternatively_spliced" ;
  rdfs:comment "An attribute describing a situation where a gene may encode for more than 1 transcript." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_1000015 a rdfs:Class ;
  rdfs:label "A_to_G_transition" ;
  rdfs:comment "A transition of an adenine to a guanine." ;
  rdfs:subClassOf obo:SO_1000014 .

obo:SO_0001650 a rdfs:Class ;
  rdfs:label "inframe_variant" ;
  rdfs:comment "A sequence variant which does not cause a disruption of the translational reading frame." ;
  rdfs:subClassOf obo:SO_0001818 .

obo:SO_0001707 a rdfs:Class ;
  rdfs:label "H3K9_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001736 .

obo:SO_0002311 a rdfs:Class ;
  rdfs:label "viral_promoter" ;
  rdfs:comment "A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0000693 a rdfs:Class ;
  rdfs:label "gene_with_recoded_mRNA" ;
  rdfs:comment "A gene that encodes an mRNA that is recoded." ;
  rdfs:subClassOf obo:SO_0001217 .

obo:SO_0001617 a rdfs:Class ;
  rdfs:label "polypeptide_truncation" ;
  rdfs:comment "A sequence variant of the CD that causes a truncation of the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_0002249 a rdfs:Class ;
  rdfs:label "mature_protein_region_of_CDS" ;
  rdfs:comment "A CDS region corresponding to a mature protein region of a polypeptide." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0001520 a rdfs:Class ;
  rdfs:label "translocaton_attribute" ;
  rdfs:comment "An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." ;
  rdfs:subClassOf obo:SO_0001508 .

obo:SO_0001852 a rdfs:Class ;
  rdfs:label "mating_type_M_box" ;
  rdfs:comment "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000088 a rdfs:Class ;
  rdfs:label "mt_gene" ;
  rdfs:comment "A gene located in mitochondrial sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001623 a rdfs:Class ;
  rdfs:label "5_prime_UTR_variant" ;
  rdfs:comment "A UTR variant of the 5' UTR." ;
  rdfs:subClassOf obo:SO_0001622 .

obo:SO_1000009 a rdfs:Class ;
  rdfs:label "transition" ;
  rdfs:comment "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." ;
  rdfs:subClassOf obo:SO_0001483 .

obo:SO_0002213 a rdfs:Class ;
  rdfs:label "transcription_termination_signal" ;
  rdfs:comment "Termination signal preferentially observed downstream of polyadenylation signal" ;
  rdfs:subClassOf obo:SO_0000951 .

obo:SO_0000865 a rdfs:Class ;
  rdfs:label "frameshift" ;
  rdfs:comment "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." ;
  rdfs:subClassOf obo:SO_0000863 .

obo:SO_0000916 a rdfs:Class ;
  rdfs:label "edit_operation" .

obo:BS_00209 a rdfs:Class .

obo:SO_1000066 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_plus_1_frameshift_mutation" ;
  rdfs:comment "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." .

obo:SO_0001038 a rdfs:Class ;
  rdfs:label "extrachromosomal_mobile_genetic_element" ;
  rdfs:comment "An MGE that is not integrated into the host chromosome." ;
  rdfs:subClassOf obo:SO_0001037 .

obo:SO_0000975 a rdfs:Class ;
  rdfs:label "minicircle_gene" ;
  rdfs:comment "A gene found within a minicircle." ;
  rdfs:subClassOf obo:SO_0000089 .

obo:SO_0000888 a rdfs:Class ;
  rdfs:label "maternally_imprinted_gene" ;
  rdfs:comment "A gene that is maternally_imprinted." ;
  rdfs:subClassOf obo:SO_0000704 , obo:SO_0000898 .

obo:SO_0000722 a rdfs:Class ;
  rdfs:label "gene_with_dicistronic_mRNA" ;
  rdfs:comment "A gene that encodes a polycistronic mRNA." ;
  rdfs:subClassOf obo:SO_0000692 .

obo:SO_0001398 a rdfs:Class ;
  rdfs:label "modified_L_histidine" ;
  rdfs:comment "A post translationally modified histidine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0002402 a rdfs:Class ;
  rdfs:label "downstream_intergenic_fusion" ;
  rdfs:comment "A sequence variant whereby two genomic features have become joined with one breakend proximally downstream of a gene." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0000451 a rdfs:Class ;
  rdfs:label "gene_with_polyadenylated_mRNA" ;
  rdfs:comment "A gene that encodes a polyadenylated mRNA." ;
  rdfs:subClassOf obo:SO_0001217 .

obo:SO_0001944 a rdfs:Class ;
  rdfs:label "H2AK9_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002142 .

obo:SO_0000905 a rdfs:Class ;
  rdfs:label "status" ;
  rdfs:comment "An attribute describing the status of a feature, based on the available evidence." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001424 a rdfs:Class ;
  rdfs:label "pyrosequenced_read" ;
  rdfs:comment "A read produced by pyrosequencing technology." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_1000155 a rdfs:Class ;
  rdfs:label "interchromosomal_transposition" ;
  rdfs:comment "A chromosome structure variation whereby a transposition occurred between chromosomes." ;
  rdfs:subClassOf obo:SO_0000453 , obo:SO_1000031 .

obo:SO_0001857 a rdfs:Class ;
  rdfs:label "Ace2_UAS" ;
  rdfs:comment "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000252 a rdfs:Class ;
  rdfs:label "rRNA" ;
  rdfs:comment "rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002112 a rdfs:Class ;
  rdfs:label "coding_transcript_with_retained_intron" ;
  rdfs:comment "A protein coding transcript containing a retained intron." ;
  rdfs:subClassOf obo:SO_0000120 .

obo:SO_0100006 a rdfs:Class ;
  rdfs:label "catmat_right_handed_three" ;
  rdfs:comment "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0000603 a rdfs:Class ;
  rdfs:label "group_II_intron" ;
  rdfs:comment "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." ;
  rdfs:subClassOf obo:SO_0000588 .

obo:SO_0001864 a rdfs:Class ;
  rdfs:label "Sap1_recognition_motif" ;
  rdfs:comment "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:BS_00186 a rdfs:Class .

obo:SO_0001211 a rdfs:Class ;
  rdfs:label "plus_1_translational_frameshift" ;
  rdfs:comment "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." ;
  rdfs:subClassOf obo:SO_0001210 .

obo:SO_0001673 a rdfs:Class ;
  rdfs:label "minus_12_signal" ;
  rdfs:comment "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001684 a rdfs:Class ;
  rdfs:label "experimental_feature_attribute" ;
  rdfs:comment "An attribute of an experimentally derived feature." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000665 a rdfs:Class ;
  rdfs:label "monocistronic_transcript" ;
  rdfs:comment "A transcript that is monocistronic." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0001265 a rdfs:Class ;
  rdfs:label "miRNA_gene" ;
  rdfs:comment "A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression." ;
  rdfs:subClassOf obo:SO_0002342 .

obo:SO_0001722 a rdfs:Class ;
  rdfs:label "H3K36_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001733 .

obo:SO_0001194 a rdfs:Class ;
  rdfs:label "R_GNA" ;
  rdfs:comment "An attribute describing a GNA sequence in the (R)-GNA enantiomer." ;
  rdfs:subClassOf obo:SO_0001192 .

obo:SO_0000578 a rdfs:Class ;
  rdfs:label "snoRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a small nucleolar RNA (snoRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0000367 a rdfs:Class ;
  rdfs:label "attI_site" ;
  rdfs:comment "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:BS_00067 a rdfs:Class .

obo:SO_0000581 a rdfs:Class ;
  rdfs:label "cap" ;
  rdfs:comment "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001160 a rdfs:Class ;
  rdfs:label "DMv3_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000850 a rdfs:Class ;
  rdfs:label "five_prime_LTR_component" ;
  rdfs:comment "A component of the five-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000848 .

obo:SO_0001481 a rdfs:Class ;
  rdfs:label "RAPD" ;
  rdfs:comment "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." ;
  rdfs:subClassOf obo:SO_0000006 .

obo:SO_0000635 a rdfs:Class ;
  rdfs:label "mini_exon_donor_RNA" ;
  rdfs:comment "A primary transcript that donates the spliced leader to other mRNA." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000563 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_gene_recombination_spacer" ;
  rdfs:comment "A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0000823 a rdfs:Class ;
  rdfs:label "leucoplast_chromosome" ;
  rdfs:comment "A chromosome with origin in a leucoplast." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0000318 a rdfs:Class ;
  rdfs:label "start_codon" ;
  rdfs:comment "First codon to be translated by a ribosome." ;
  rdfs:subClassOf obo:SO_0000360 .

obo:SO_1000140 a rdfs:Class ;
  rdfs:label "hetero_compound_chromosome" ;
  rdfs:comment "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." ;
  rdfs:subClassOf obo:SO_1000042 .

obo:SO_0002341 a rdfs:Class ;
  rdfs:label "RNA_7SK_gene" ;
  rdfs:comment "A gene encoding a 7SK RNA (SO:0002340)." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0002203 a rdfs:Class ;
  rdfs:label "replication_start_site" ;
  rdfs:comment "A nucleotide site from which replication initiates." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0002368 a rdfs:Class ;
  rdfs:label "plastid_SSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for plastid SSU rRNA." ;
  rdfs:subClassOf obo:SO_0002366 .

obo:SO_0002184 a rdfs:Class ;
  rdfs:label "sense_intronic_lncRNA_gene" ;
  rdfs:comment "A gene that encodes a sense intronic long non-coding RNA." ;
  rdfs:subClassOf obo:SO_0002127 .

obo:SO_0000450 a rdfs:Class ;
  rdfs:label "interband" ;
  rdfs:comment "A light region between two darkly staining bands in a polytene chromosome." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0002161 a rdfs:Class ;
  rdfs:label "short_tandem_repeat_change" ;
  rdfs:comment "A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded." ;
  rdfs:subClassOf obo:SO_0002160 .

obo:SO_0000815 a rdfs:Class ;
  rdfs:label "mini_gene" ;
  rdfs:comment "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." ;
  rdfs:subClassOf obo:SO_0000236 .

obo:SO_0000448 a rdfs:Class ;
  rdfs:label "three_prime_UTR_intron" ;
  rdfs:comment "An intron located in the 3' UTR." ;
  rdfs:subClassOf obo:SO_0000446 .

obo:SO_0002354 a rdfs:Class ;
  rdfs:label "sbRNA" ;
  rdfs:comment "A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000077 a rdfs:Class ;
  rdfs:label "antisense" ;
  rdfs:comment "A region sequence that is complementary to a sequence of messenger RNA." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_0002145 a rdfs:Class ;
  rdfs:label "H2AZK4_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002144 .

obo:SO_0000343 a rdfs:Class ;
  rdfs:label "match" ;
  rdfs:comment "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_1000100 a rdfs:Class ;
  rdfs:label "mutation_causing_polypeptide_N_terminal_elongation" ;
  rdfs:comment "." .

obo:SO_0000303 a rdfs:Class ;
  rdfs:label "clip" ;
  rdfs:comment "Part of the primary transcript that is clipped off during processing." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0000061 a rdfs:Class ;
  rdfs:label "restriction_enzyme_binding_site" ;
  rdfs:comment "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." ;
  rdfs:subClassOf obo:SO_0000059 .

obo:SO_0000598 a rdfs:Class ;
  rdfs:label "edited_by_C_insertion_and_dinucleotide_insertion" .

obo:SO_0001393 a rdfs:Class ;
  rdfs:label "modified_L_tryptophan" ;
  rdfs:comment "A post translationally modified tryptophan amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_1000181 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_gene_fusion" ;
  rdfs:comment "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." .

obo:BS_00222 a rdfs:Class .

obo:SO_0000758 a rdfs:Class ;
  rdfs:label "double_stranded_cDNA" ;
  rdfs:comment "DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded." ;
  rdfs:subClassOf obo:SO_0000756 .

obo:SO_0000711 a rdfs:Class ;
  rdfs:label "gene_with_mRNA_recoded_by_translational_bypass" ;
  rdfs:comment "A gene with mRNA recoded by translational bypass." ;
  rdfs:subClassOf obo:SO_0000693 , obo:SO_0001217 .

obo:SO_0001120 a rdfs:Class ;
  rdfs:label "polypeptide_nest_motif" ;
  rdfs:comment "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0000919 a rdfs:Class ;
  rdfs:label "substitute_A_to_I" ;
  rdfs:comment "An edit to substitute an I for an A." .

obo:SO_0002381 a rdfs:Class ;
  rdfs:label "bidirectional_promoter_lncRNA" ;
  rdfs:comment "A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction." ;
  rdfs:subClassOf obo:SO_0001877 .

obo:SO_0001089 a rdfs:Class ;
  rdfs:label "post_translationally_modified_region" ;
  rdfs:comment "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." ;
  rdfs:subClassOf obo:SO_0100001 .

obo:SO_0000114 a rdfs:Class ;
  rdfs:label "methylated_cytosine" ;
  rdfs:comment "A methylated deoxy-cytosine." ;
  rdfs:subClassOf obo:SO_0000306 , obo:SO_0001963 .

obo:SO_0002343 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA" ;
  rdfs:comment "Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes." ;
  rdfs:subClassOf obo:SO_0000252 .

obo:BS_00215 a rdfs:Class .

obo:SO_0002235 a rdfs:Class ;
  rdfs:label "SUMO_interaction_motif" ;
  rdfs:comment "A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3." ;
  rdfs:subClassOf obo:SO_0001093 .

obo:SO_0000938 a rdfs:Class ;
  rdfs:label "vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_1000059 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_missense_codon_change_in_transcript" ;
  rdfs:comment "The nucleotide change in the codon leads to a new codon coding for a new amino acid." .

obo:SO_0005845 a rdfs:Class ;
  rdfs:label "exon_of_single_exon_gene" ;
  rdfs:comment "An exon that is the only exon in a gene." ;
  rdfs:subClassOf obo:SO_0000147 .

obo:SO_1000027 a rdfs:Class ;
  rdfs:label "G_to_T_transversion" ;
  rdfs:comment "A transversion from guanine to thymine." ;
  rdfs:subClassOf obo:SO_1000023 .

obo:SO_0002018 a rdfs:Class ;
  rdfs:label "conserved_intron_variant" ;
  rdfs:comment "A transcript variant occurring within a conserved region of an intron." ;
  rdfs:subClassOf obo:SO_0001627 .

obo:SO_0000964 a rdfs:Class ;
  rdfs:label "linear_double_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." ;
  rdfs:subClassOf obo:SO_0000965 .

obo:SO_1000099 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_polypeptide_elongation" ;
  rdfs:comment "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." .

obo:SO_0001373 a rdfs:Class ;
  rdfs:label "one_methyl_three_three_amino_three_carboxypropyl_pseudouridine" ;
  rdfs:comment "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001470 a rdfs:Class ;
  rdfs:label "UST_match" ;
  rdfs:comment "A match against an UST sequence." ;
  rdfs:subClassOf obo:SO_0000102 .

obo:SO_0000646 a rdfs:Class ;
  rdfs:label "siRNA" ;
  rdfs:comment "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_1000127 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_compensatory_transcript_secondary_structure_mutation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001349 a rdfs:Class ;
  rdfs:label "two_thiouridine" ;
  rdfs:comment "2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002050 a rdfs:Class ;
  rdfs:label "constitutive_promoter" ;
  rdfs:comment "A promoter that allows for continual transcription of gene." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0000382 a rdfs:Class ;
  rdfs:label "group_IIB_intron" ;
  rdfs:comment "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon." ;
  rdfs:subClassOf obo:SO_0000603 .

obo:SO_0002004 a rdfs:Class ;
  rdfs:label "ARS_consensus_sequence" ;
  rdfs:comment "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0002332 a rdfs:Class ;
  rdfs:label "epigenomically_modified_region" ;
  rdfs:comment "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." ;
  rdfs:subClassOf obo:SO_0001720 .

obo:SO_0000263 a rdfs:Class ;
  rdfs:label "isoleucyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000769 a rdfs:Class ;
  rdfs:label "tmRNA_coding_piece" ;
  rdfs:comment "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." ;
  rdfs:subClassOf obo:SO_0000847 .

obo:SO_0001184 a rdfs:Class ;
  rdfs:label "PNA" ;
  rdfs:comment "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0000498 a rdfs:Class ;
  rdfs:label "five_prime_D_spacer" ;
  rdfs:comment "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000563 .

obo:SO_0005839 a rdfs:Class .

obo:SO_0000733 a rdfs:Class ;
  rdfs:label "feature_attribute" ;
  rdfs:comment "An attribute describing a located_sequence_feature." ;
  rdfs:subClassOf obo:SO_0000400 .

obo:SO_0000609 a rdfs:Class ;
  rdfs:label "oligo_U_tail" ;
  rdfs:comment "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000125 a rdfs:Class ;
  rdfs:label "transcriptionally_induced" ;
  rdfs:comment "An inducer molecule is required for transcription to occur." ;
  rdfs:subClassOf obo:SO_0000123 .

obo:SO_0001610 a rdfs:Class ;
  rdfs:label "elongated_polypeptide_C_terminal" ;
  rdfs:comment "An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS." ;
  rdfs:subClassOf obo:SO_0001609 .

obo:SO_0001171 a rdfs:Class ;
  rdfs:label "rRNA_21S" ;
  rdfs:comment "A component of the large ribosomal subunit in mitochondrial rRNA." .

obo:SO_0001065 a rdfs:Class .

obo:SO_0001789 a rdfs:Class ;
  rdfs:label "mating_type_region" ;
  rdfs:comment "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0000614 a rdfs:Class ;
  rdfs:label "bacterial_terminator" ;
  rdfs:comment "A terminator signal for bacterial transcription." ;
  rdfs:subClassOf obo:SO_0000141 .

obo:SO_0000993 a rdfs:Class ;
  rdfs:label "consensus" ;
  rdfs:comment "A sequence produced from an aligment algorithm that uses multiple sequences as input." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0000707 a rdfs:Class ;
  rdfs:label "trans_splice_donor_site" ;
  rdfs:comment "The 5' five prime splice site region of the donor RNA." ;
  rdfs:subClassOf obo:SO_0001420 .

obo:BS_00124 a rdfs:Class .

obo:SO_1000048 a rdfs:Class ;
  rdfs:label "reciprocal_chromosomal_translocation" ;
  rdfs:comment "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." ;
  rdfs:subClassOf obo:SO_1000044 .

obo:SO_0001609 a rdfs:Class ;
  rdfs:label "elongated_polypeptide" ;
  rdfs:comment "An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_0000826 a rdfs:Class .

obo:SO_0000096 a rdfs:Class ;
  rdfs:label "proplastid_gene" ;
  rdfs:comment "A gene from proplastid sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0001911 a rdfs:Class ;
  rdfs:label "copy_number_increase" ;
  rdfs:comment "A sequence variant where copies of a feature are increased relative to the reference." ;
  rdfs:subClassOf obo:SO_0001563 .

obo:SO_0000433 a rdfs:Class ;
  rdfs:label "non_LTR_retrotransposon_polymeric_tract" ;
  rdfs:comment "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." ;
  rdfs:subClassOf obo:SO_0000657 , obo:SO_0000840 .

obo:SO_0001003 a rdfs:Class ;
  rdfs:label "solo_LTR" ;
  rdfs:comment "A recombination product between the 2 LTR of the same element." ;
  rdfs:subClassOf obo:SO_0000286 .

obo:SO_0000491 a rdfs:Class ;
  rdfs:label "VJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001213 a rdfs:Class ;
  rdfs:label "group_III_intron" ;
  rdfs:comment "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." ;
  rdfs:subClassOf obo:SO_0000588 .

obo:SO_0001870 a rdfs:Class ;
  rdfs:label "enhancerRNA" ;
  rdfs:comment "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." ;
  rdfs:subClassOf obo:SO_0000655 .

<http://purl.obolibrary.org/obo/so#transcribed_from> a rdf:Property ;
  rdfs:label "transcribed_from" ;
  rdfs:comment "X is transcribed_from Y if X is synthesized from template Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

obo:SO_0002245 a rdfs:Class ;
  rdfs:label "five_prime_duplicated_transcript" ;
  rdfs:comment "A partially_duplicated_transcript where the 5' end of the transcript is duplicated." ;
  rdfs:subClassOf obo:SO_0002244 .

obo:SO_0002268 a rdfs:Class ;
  rdfs:label "Endogenous_Retrovirus_LTR_retrotransposon" ;
  rdfs:comment "Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0000378 a rdfs:Class ;
  rdfs:label "DsrA_RNA" ;
  rdfs:comment "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0000397 a rdfs:Class ;
  rdfs:label "U6atac_snRNA" ;
  rdfs:comment "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0000329 a rdfs:Class ;
  rdfs:label "mRNA_with_plus_2_frameshift" ;
  rdfs:comment "An mRNA with a plus 2 frameshift." ;
  rdfs:subClassOf obo:SO_0000108 .

obo:SO_0000085 a rdfs:Class ;
  rdfs:label "gene_by_genome_location" .

obo:SO_0001049 a rdfs:Class ;
  rdfs:label "defective_conjugative_transposon" ;
  rdfs:comment "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_0001830 a rdfs:Class ;
  rdfs:label "AFLP_fragment" ;
  rdfs:comment "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." ;
  rdfs:subClassOf obo:SO_0000006 .

obo:SO_0001014 a rdfs:Class ;
  rdfs:label "intron_domain" ;
  rdfs:comment "An intronic region that has an attribute." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0000574 a rdfs:Class ;
  rdfs:label "VDJ_gene_segment" ;
  rdfs:comment "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." ;
  rdfs:subClassOf obo:SO_0000936 .

obo:SO_0001695 a rdfs:Class ;
  rdfs:label "restriction_enzyme_single_strand_overhang" ;
  rdfs:comment "A terminal region of DNA sequence where the end of the region is not blunt ended." ;
  rdfs:subClassOf obo:SO_0001954 .

obo:SO_0000953 a rdfs:Class ;
  rdfs:label "oriC" ;
  rdfs:comment "An origin of bacterial chromosome replication." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001439 a rdfs:Class ;
  rdfs:label "proline" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000024 a rdfs:Class ;
  rdfs:label "sarcin_like_RNA_motif" ;
  rdfs:comment "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." ;
  rdfs:subClassOf obo:SO_0000021 .

obo:SO_0002030 a rdfs:Class ;
  rdfs:label "X_region" ;
  rdfs:comment "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." ;
  rdfs:subClassOf obo:SO_0001999 .

obo:SO_0000099 a rdfs:Class ;
  rdfs:label "proviral_gene" ;
  rdfs:comment "A gene from proviral sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001319 a rdfs:Class ;
  rdfs:label "galactosyl_queuosine" ;
  rdfs:comment "Galactosyl_queuosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0000206 a rdfs:Class ;
  rdfs:label "SINE_element" ;
  rdfs:comment "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." ;
  rdfs:subClassOf obo:SO_0000189 .

obo:SO_0000356 a rdfs:Class ;
  rdfs:label "RNA" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0001531 a rdfs:Class ;
  rdfs:label "nuclear_export_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to he cytoplasm." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0000556 a rdfs:Class ;
  rdfs:label "five_prime_D_recombination_signal_sequence" ;
  rdfs:comment "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." ;
  rdfs:subClassOf obo:SO_0000492 .

obo:SO_1000088 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_translational_product" ;
  rdfs:comment "A sequence variant causing a change in primary translation product of a transcript." .

obo:SO_0001972 a rdfs:Class ;
  rdfs:label "histone_4_acetylation_site" ;
  rdfs:comment "A histone 4 modification where the modification is the acetylation of the residue." ;
  rdfs:subClassOf obo:SO_0001702 .

obo:SO_0000623 a rdfs:Class ;
  rdfs:label "snRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a small nuclear RNA (snRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0002134 a rdfs:Class ;
  rdfs:label "TR_C_Gene" ;
  rdfs:comment "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain." ;
  rdfs:subClassOf obo:SO_0002133 .

obo:SO_0002166 a rdfs:Class ;
  rdfs:label "ref_miRNA" ;
  rdfs:comment "A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA." ;
  rdfs:subClassOf obo:SO_0000276 .

obo:SO_0001202 a rdfs:Class ;
  rdfs:label "ambisense_ssRNA_viral_sequence" ;
  rdfs:comment "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." ;
  rdfs:subClassOf obo:SO_0001199 .

obo:SO_0002352 a rdfs:Class ;
  rdfs:label "sisRNA" ;
  rdfs:comment "A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000180 a rdfs:Class ;
  rdfs:label "retrotransposon" ;
  rdfs:comment "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." ;
  rdfs:subClassOf obo:SO_0000101 .

obo:SO_0001414 a rdfs:Class ;
  rdfs:label "insertion_breakpoint" ;
  rdfs:comment "The point within a chromosome where a insertion begins or ends." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0000891 a rdfs:Class ;
  rdfs:label "negatively_autoregulated_gene" ;
  rdfs:comment "A gene that is negatively autoreguated." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000742 a rdfs:Class ;
  rdfs:label "maxicircle" ;
  rdfs:comment "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." ;
  rdfs:subClassOf obo:SO_0001235 .

obo:SO_0000630 a rdfs:Class ;
  rdfs:label "upstream_AUG_codon" ;
  rdfs:comment "A start codon upstream of the ORF." ;
  rdfs:subClassOf obo:SO_0000837 .

obo:SO_0100009 a rdfs:Class ;
  rdfs:label "lipoprotein_signal_peptide" ;
  rdfs:comment "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0002220 a rdfs:Class ;
  rdfs:label "function_uncertain_variant" ;
  rdfs:comment "A sequence variant in which the function of a gene product is unknown with respect to a reference." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:BS_00129 a rdfs:Class .

obo:SO_0002052 a rdfs:Class ;
  rdfs:label "dominant_negative_variant" ;
  rdfs:comment "A variant where the mutated gene product adversely affects the other (wild type) gene product." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0000455 a rdfs:Class ;
  rdfs:label "gene_with_mRNA_with_frameshift" ;
  rdfs:comment "A gene that encodes an mRNA with a frameshift." ;
  rdfs:subClassOf obo:SO_0001217 .

obo:SO_0001207 a rdfs:Class ;
  rdfs:label "T7_RNA_Polymerase_Promoter" ;
  rdfs:comment "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0001204 .

obo:SO_0000901 a rdfs:Class ;
  rdfs:label "unequally_crossed_over" ;
  rdfs:comment "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." .

obo:SO_0000031 a rdfs:Class ;
  rdfs:label "aptamer" ;
  rdfs:comment "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0001604 a rdfs:Class ;
  rdfs:label "amino_acid_deletion" ;
  rdfs:comment "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_1000072 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_splice_donor" ;
  rdfs:comment "A sequence_variant_effect that changes the splice donor sequence." .

obo:SO_0001131 a rdfs:Class ;
  rdfs:label "asx_turn_right_handed_type_two" ;
  rdfs:comment "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0000912 .

obo:SO_0002300 a rdfs:Class ;
  rdfs:label "unit_of_gene_expression" ;
  rdfs:comment "Transcription units or transcribed coding sequences." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000415 a rdfs:Class ;
  rdfs:label "invalidated_by_genomic_polyA_primed_cDNA" ;
  rdfs:comment "An attribute to describe a feature that is invalidated due to polyA priming." ;
  rdfs:subClassOf obo:SO_0000790 .

obo:SO_1000116 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_conformational_change" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000029 a rdfs:Class ;
  rdfs:label "WC_base_pair" ;
  rdfs:comment "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." ;
  rdfs:subClassOf obo:SO_0000028 .

obo:SO_0000119 a rdfs:Class ;
  rdfs:label "regulated" ;
  rdfs:comment "An attribute to describe a sequence that is regulated." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0000219 a rdfs:Class ;
  rdfs:label "histidine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding histidyl tRNA (SO:0000262)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000726 a rdfs:Class ;
  rdfs:label "repeat_unit" ;
  rdfs:comment "The simplest repeated component of a repeat region. A single repeat." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001055 a rdfs:Class ;
  rdfs:label "transcriptional_cis_regulatory_region" ;
  rdfs:comment "A regulatory_region that modulates the transcription of a gene or genes." ;
  rdfs:subClassOf obo:SO_0005836 .

obo:SO_0001403 a rdfs:Class ;
  rdfs:label "modified_L_valine" ;
  rdfs:comment "A post translationally modified valine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000201 a rdfs:Class ;
  rdfs:label "interior_exon" ;
  rdfs:comment "An exon that is bounded by 5' and 3' splice sites." ;
  rdfs:subClassOf obo:SO_0000147 .

obo:SO_0000140 a rdfs:Class ;
  rdfs:label "attenuator" ;
  rdfs:comment "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." ;
  rdfs:subClassOf obo:SO_0001680 .

obo:SO_0001107 a rdfs:Class ;
  rdfs:label "beta_bulge" ;
  rdfs:comment "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_1001269 a rdfs:Class ;
  rdfs:label "four_bp_start_codon" ;
  rdfs:comment "A non-canonical start codon with 4 base pairs." ;
  rdfs:subClassOf obo:SO_0000680 .

obo:SO_0001028 a rdfs:Class ;
  rdfs:label "diplotype" ;
  rdfs:comment "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." ;
  rdfs:subClassOf obo:SO_0001507 .

obo:SO_0001828 a rdfs:Class ;
  rdfs:label "genomic_DNA_read" ;
  rdfs:comment "A sequencer read of a genomic DNA substrate." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0001868 a rdfs:Class ;
  rdfs:label "positional_candidate_gene" ;
  rdfs:comment "A candidate gene whose association with a trait is based on the gene's location on a chromosome." ;
  rdfs:subClassOf obo:SO_0001867 .

obo:SO_0002133 a rdfs:Class ;
  rdfs:label "T_cell_receptor_gene" ;
  rdfs:comment "A T-cell receptor germline gene." ;
  rdfs:subClassOf obo:SO_0002121 .

obo:SO_0001071 a rdfs:Class ;
  rdfs:label "membrane_structure" ;
  rdfs:comment "Arrangement of the polypeptide with respect to the lipid bilayer." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0000552 a rdfs:Class ;
  rdfs:label "Shine_Dalgarno_sequence" ;
  rdfs:comment "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." ;
  rdfs:subClassOf obo:SO_0000139 .

obo:SO_1000184 a rdfs:Class ;
  rdfs:label "sequence_variant_causes_exon_loss" ;
  rdfs:comment "A sequence variant affecting splicing and causes an exon loss." .

obo:SO_1000032 a rdfs:Class ;
  rdfs:label "delins" ;
  rdfs:comment "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." ;
  rdfs:subClassOf obo:SO_0001059 .

obo:SO_0001547 a rdfs:Class ;
  rdfs:label "decreased_transcript_stability_variant" ;
  rdfs:comment "A sequence variant that decreases transcript stability with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001546 .

obo:SO_0001334 a rdfs:Class ;
  rdfs:label "hydroxywybutosine" ;
  rdfs:comment "Hydroxywybutosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_2000061 a rdfs:Class ;
  rdfs:label "databank_entry" ;
  rdfs:comment "The sequence referred to by an entry in a databank such as GenBank or SwissProt." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0000042 a rdfs:Class ;
  rdfs:label "pseudogene_attribute" ;
  rdfs:comment "An attribute of a pseudogene (SO:0000336)." .

obo:SO_0000421 a rdfs:Class ;
  rdfs:label "three_prime_terminal_inverted_repeat" ;
  rdfs:comment "An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon." ;
  rdfs:subClassOf obo:SO_0000481 .

obo:SO_0001987 a rdfs:Class ;
  rdfs:label "downstream_transcript_variant" ;
  rdfs:comment "A feature variant, where the alteration occurs downstream of the transcript termination site." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0002101 a rdfs:Class ;
  rdfs:label "IG_J_pseudogene" ;
  rdfs:comment "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002098 .

obo:SO_0000852 a rdfs:Class ;
  rdfs:label "exon_region" ;
  rdfs:comment "A region of an exon." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0001740 a rdfs:Class ;
  rdfs:label "gene_with_start_codon_CUG" ;
  rdfs:comment "A gene with a translational start codon of CUG." ;
  rdfs:subClassOf obo:SO_0001739 .

obo:SO_0002085 a rdfs:Class ;
  rdfs:label "unidirectional_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genes, on the same strand have become joined." ;
  rdfs:subClassOf obo:SO_0001565 .

obo:SO_0001810 a rdfs:Class ;
  rdfs:label "PIP_box" ;
  rdfs:comment "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." ;
  rdfs:subClassOf obo:SO_0001093 .

obo:SO_0002392 a rdfs:Class ;
  rdfs:label "increased_enzyme_activity_variant" ;
  rdfs:comment "An increase in the activity of an enzyme, as a result of a variant in the gene that encodes the enzyme or a regulatory region." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0002180 a rdfs:Class ;
  rdfs:label "enzymatic_RNA_gene" ;
  rdfs:comment "A gene that encodes an enzymatic RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0001950 a rdfs:Class ;
  rdfs:label "H4K4_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_1001190 a rdfs:Class ;
  rdfs:label "encodes_different_polypeptides_different_stop" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." ;
  rdfs:subClassOf obo:SO_1001195 .

obo:SO_0001388 a rdfs:Class ;
  rdfs:label "modified_L_asparagine" ;
  rdfs:comment "A post translationally modified asparagine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000390 a rdfs:Class ;
  rdfs:label "telomerase_RNA" ;
  rdfs:comment "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:BS_00151 a rdfs:Class .

obo:SO_0002156 a rdfs:Class ;
  rdfs:label "CArG_box" ;
  rdfs:comment "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002330 a rdfs:Class ;
  rdfs:label "minus_2_translational_frameshift" ;
  rdfs:comment "The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." ;
  rdfs:subClassOf obo:SO_0001210 .

obo:SO_0001190 a rdfs:Class ;
  rdfs:label "TNA" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0000949 a rdfs:Class ;
  rdfs:label "dif_site" ;
  rdfs:comment "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." ;
  rdfs:subClassOf obo:SO_0000947 .

obo:SO_0002373 a rdfs:Class ;
  rdfs:label "H_ACA_box_scaRNA_gene" ;
  rdfs:comment "A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002339 .

obo:SO_0000946 a rdfs:Class ;
  rdfs:label "integration_excision_site" ;
  rdfs:comment "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." ;
  rdfs:subClassOf obo:SO_0000342 .

obo:SO_0002026 a rdfs:Class ;
  rdfs:label "intein_encoding_region" ;
  rdfs:comment "The nucleotide sequence which encodes the intein portion of the precursor gene." ;
  rdfs:subClassOf obo:SO_0000842 .

obo:SO_0001555 a rdfs:Class ;
  rdfs:label "decreased_translational_product_level" ;
  rdfs:comment "A sequence variant which decreases the translational product level with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001553 .

obo:SO_1000021 a rdfs:Class ;
  rdfs:label "T_to_A_transversion" ;
  rdfs:comment "A transversion from T to A." ;
  rdfs:subClassOf obo:SO_1000018 .

obo:SO_0001500 a rdfs:Class ;
  rdfs:label "heritable_phenotypic_marker" ;
  rdfs:comment "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." ;
  rdfs:subClassOf obo:SO_0001645 .

obo:SO_0000364 a rdfs:Class ;
  rdfs:label "transposable_element_flanking_region" ;
  rdfs:comment "The region of sequence surrounding a transposable element." ;
  rdfs:subClassOf obo:SO_0000239 .

obo:SO_0001248 a rdfs:Class ;
  rdfs:label "assembly" ;
  rdfs:comment "A region of the genome of known length that is composed by ordering and aligning two or more different regions." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:BS_00147 a rdfs:Class .

obo:SO_0005851 a rdfs:Class ;
  rdfs:label "gene_array" ;
  rdfs:comment "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0001427 a rdfs:Class ;
  rdfs:label "cis_regulatory_frameshift_element" ;
  rdfs:comment "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0001309 a rdfs:Class ;
  rdfs:label "two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine" ;
  rdfs:comment "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000715 a rdfs:Class ;
  rdfs:label "RNA_motif" ;
  rdfs:comment "A motif that is active in RNA sequence." ;
  rdfs:subClassOf obo:SO_0000714 .

obo:SO_1000144 a rdfs:Class ;
  rdfs:label "free_duplication" ;
  rdfs:comment "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." ;
  rdfs:subClassOf obo:SO_1000037 .

obo:SO_0002299 a rdfs:Class ;
  rdfs:label "complex_operon" ;
  rdfs:comment "An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene." ;
  rdfs:subClassOf obo:SO_0000178 .

obo:SO_0001548 a rdfs:Class ;
  rdfs:label "increased_transcript_stability_variant" ;
  rdfs:comment "A sequence variant that increases transcript stability with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001546 .

obo:SO_0000259 a rdfs:Class ;
  rdfs:label "glutaminyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001791 a rdfs:Class ;
  rdfs:label "exon_variant" ;
  rdfs:comment "A sequence variant that changes exon sequence." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0000404 a rdfs:Class ;
  rdfs:label "vault_RNA" ;
  rdfs:comment "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000567 a rdfs:Class ;
  rdfs:label "inversion_derived_aneuploid_chromosome" ;
  rdfs:comment "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." ;
  rdfs:subClassOf obo:SO_0000550 .

obo:SO_0000241 a rdfs:Class ;
  rdfs:label "internal_UTR" ;
  rdfs:comment "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." ;
  rdfs:subClassOf obo:SO_0000203 .

obo:SO_0001067 a rdfs:Class ;
  rdfs:label "polypeptide_motif" ;
  rdfs:comment "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." ;
  rdfs:subClassOf obo:SO_0100021 .

obo:SO_0001436 a rdfs:Class ;
  rdfs:label "valine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0005856 a rdfs:Class ;
  rdfs:label "selenocysteine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding seryl tRNA (SO:000269)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_1000061 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_nonconservative_missense_codon_change_in_transcript" ;
  rdfs:comment "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." .

obo:SO_0001716 a rdfs:Class ;
  rdfs:label "histone_ubiqitination_site" ;
  rdfs:comment "A histone modification site where ubiquitin may be added." ;
  rdfs:subClassOf obo:SO_0001700 .

obo:SO_0000641 a rdfs:Class ;
  rdfs:label "tetranucleotide_repeat_microsatellite_feature" ;
  rdfs:comment "A region of a repeating tetranucleotide sequence (four bases)." ;
  rdfs:subClassOf obo:SO_0000289 .

obo:SO_1000038 a rdfs:Class ;
  rdfs:label "intrachromosomal_duplication" ;
  rdfs:comment "A duplication that occurred within a chromosome." ;
  rdfs:subClassOf obo:SO_1000028 , obo:SO_1000037 .

obo:SO_0002032 a rdfs:Class ;
  rdfs:label "moR" ;
  rdfs:comment "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0000885 a rdfs:Class ;
  rdfs:label "stop_codon_redefined_as_selenocysteine" ;
  rdfs:comment "A stop codon redefined to be the new amino acid, selenocysteine." ;
  rdfs:subClassOf obo:SO_0000883 .

obo:SO_1001186 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_cryptic_splice_acceptor_activation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000982 a rdfs:Class ;
  rdfs:label "rho_independent_bacterial_terminator" ;
  rdfs:comment "A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure." ;
  rdfs:subClassOf obo:SO_0000614 .

obo:SO_0000480 a rdfs:Class ;
  rdfs:label "tiling_path_clone" ;
  rdfs:comment "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." ;
  rdfs:subClassOf obo:SO_0000151 , obo:SO_0000474 .

obo:SO_0000804 a rdfs:Class ;
  rdfs:label "engineered_region" ;
  rdfs:comment "A region that is engineered." ;
  rdfs:subClassOf obo:SO_0000001 , obo:SO_0001409 .

obo:SO_0002079 a rdfs:Class ;
  rdfs:label "incomplete_transcript_splice_region_variant" ;
  rdfs:comment "A sequence variant that intersects the splice region of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_0000444 a rdfs:Class ;
  rdfs:label "three_prime_noncoding_exon" ;
  rdfs:comment "Non-coding exon in the 3' UTR." ;
  rdfs:subClassOf obo:SO_0000198 .

obo:SO_1000105 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_polypeptide_amino_acid_sequence" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:BS_00226 a rdfs:Class .

obo:SO_0001648 a rdfs:Class ;
  rdfs:label "nested_transposon" ;
  rdfs:comment "A transposon that is disrupted by the insertion of another element." ;
  rdfs:subClassOf obo:SO_0000101 .

obo:SO_0000668 a rdfs:Class ;
  rdfs:label "EST_match" ;
  rdfs:comment "A match against an EST sequence." ;
  rdfs:subClassOf obo:SO_0000102 .

obo:SO_0001711 a rdfs:Class ;
  rdfs:label "H3K79_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001735 .

obo:SO_0000479 a rdfs:Class ;
  rdfs:label "trans_spliced_transcript" ;
  rdfs:comment "A transcript that is trans-spliced." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000740 a rdfs:Class ;
  rdfs:label "plastid_sequence" ;
  rdfs:comment "DNA belonging to the genome of a plastid such as a chloroplast." ;
  rdfs:subClassOf obo:SO_0000736 .

obo:SO_0000074 a rdfs:Class ;
  rdfs:label "five_prime_five_prime_overlap" ;
  rdfs:comment "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_1001280 a rdfs:Class ;
  rdfs:label "five_prime_recoding_site" ;
  rdfs:comment "The recoding stimulatory signal located upstream of the recoding site." ;
  rdfs:subClassOf obo:SO_1001268 .

obo:SO_0001689 a rdfs:Class ;
  rdfs:label "five_prime_restriction_enzyme_junction" ;
  rdfs:comment "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." ;
  rdfs:subClassOf obo:SO_0001694 .

obo:SO_0001044 a rdfs:Class ;
  rdfs:label "nuclear_mt_pseudogene" ;
  rdfs:comment "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_0000500 a rdfs:Class ;
  rdfs:label "Hoogsteen_base_pair" ;
  rdfs:comment "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." ;
  rdfs:subClassOf obo:SO_0000028 .

obo:SO_0002043 a rdfs:Class ;
  rdfs:label "miR_encoding_Y_RNA_primary_transcript" ;
  rdfs:comment "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0002042 .

obo:SO_0001727 a rdfs:Class ;
  rdfs:label "H3K9_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001736 .

obo:SO_0002257 a rdfs:Class ;
  rdfs:label "knob" ;
  rdfs:comment "Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0002086 a rdfs:Class ;
  rdfs:label "bidirectional_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genes, on alternate strands have become joined." ;
  rdfs:subClassOf obo:SO_0001565 .

obo:SO_0001909 a rdfs:Class ;
  rdfs:label "frameshift_elongation" ;
  rdfs:comment "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." ;
  rdfs:subClassOf obo:SO_0001589 , obo:SO_0001908 .

obo:SO_0001690 a rdfs:Class ;
  rdfs:label "three_prime_restriction_enzyme_junction" ;
  rdfs:comment "The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence." ;
  rdfs:subClassOf obo:SO_0001694 .

obo:SO_0000647 a rdfs:Class ;
  rdfs:label "miRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a micro RNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0001742 a rdfs:Class ;
  rdfs:label "copy_number_gain" ;
  rdfs:comment "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." ;
  rdfs:subClassOf obo:SO_0001019 .

obo:SO_0001469 a rdfs:Class ;
  rdfs:label "five_prime_RST" ;
  rdfs:comment "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." ;
  rdfs:subClassOf obo:SO_0001467 .

obo:SO_0000513 a rdfs:Class ;
  rdfs:label "J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_1001262 a rdfs:Class ;
  rdfs:label "minus_1_translationally_frameshifted" ;
  rdfs:comment "An attribute describing a translational frameshift of -1." ;
  rdfs:subClassOf obo:SO_0000887 .

obo:SO_0001097 a rdfs:Class ;
  rdfs:label "polypeptide_iron_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001058 a rdfs:Class ;
  rdfs:label "promoter_targeting_sequence" ;
  rdfs:comment "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0001258 a rdfs:Class ;
  rdfs:label "octamer_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000618 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter_type_2" ;
  rdfs:comment "This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box." ;
  rdfs:subClassOf obo:SO_0000171 .

obo:SO_0002265 a rdfs:Class ;
  rdfs:label "Gypsy_LTR_retrotransposon" ;
  rdfs:comment "LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001246 a rdfs:Class ;
  rdfs:label "miRNA_loop" ;
  rdfs:comment "The loop of the hairpin loop formed by folding of the pre-miRNA." ;
  rdfs:subClassOf obo:SO_0001243 .

obo:SO_0001992 a rdfs:Class ;
  rdfs:label "nonsynonymous_variant" ;
  rdfs:comment "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." ;
  rdfs:subClassOf obo:SO_0001650 .

obo:SO_1000046 a rdfs:Class ;
  rdfs:label "pericentric_inversion" ;
  rdfs:comment "A chromosomal inversion that includes the centromere." ;
  rdfs:subClassOf obo:SO_1000030 .

obo:BS_00128 a rdfs:Class .

obo:SO_0001356 a rdfs:Class ;
  rdfs:label "uridine_five_oxyacetic_acid" ;
  rdfs:comment "Uridine_5_oxyacetic_acid is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000703 a rdfs:Class ;
  rdfs:label "experimental_result_region" ;
  rdfs:comment "A region of sequence implicated in an experimental result." ;
  rdfs:subClassOf obo:SO_0000700 .

obo:SO_0000014 a rdfs:Class ;
  rdfs:label "INR_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000632 a rdfs:Class ;
  rdfs:label "monocistronic_primary_transcript" ;
  rdfs:comment "A primary transcript encoding for one gene product." ;
  rdfs:subClassOf obo:SO_0000185 , obo:SO_0000665 .

obo:SO_0001281 a rdfs:Class ;
  rdfs:label "three_methylcytidine" ;
  rdfs:comment "3-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_1000031 a rdfs:Class ;
  rdfs:label "interchromosomal_mutation" ;
  rdfs:comment "A chromosomal structure variation whereby more than one chromosome is involved." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0002400 a rdfs:Class ;
  rdfs:label "frameshift_unidirectional_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genes, on the same strand have become joined with a disruption of the translational reading frame, because the number of nucleotides between the reading frames of the joined genes is not a multiple of three." ;
  rdfs:subClassOf obo:SO_0002085 .

obo:SO_0005854 a rdfs:Class ;
  rdfs:label "gene_cassette_array" ;
  rdfs:comment "An array of non-functional genes whose members, when captured by recombination form functional genes." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0000149 a rdfs:Class ;
  rdfs:label "contig" ;
  rdfs:comment "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." ;
  rdfs:subClassOf obo:SO_0000143 , obo:SO_0000353 .

obo:BS_0000340 a rdfs:Class .

obo:SO_0002398 a rdfs:Class ;
  rdfs:label "selenocysteine_gain" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon is changed, resulting in a selenocysteine." ;
  rdfs:subClassOf obo:SO_0002008 .

obo:SO_0000003 a rdfs:Class ;
  rdfs:label "G_quartet" ;
  rdfs:comment "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." ;
  rdfs:subClassOf obo:SO_0000002 .

obo:SO_0001345 a rdfs:Class ;
  rdfs:label "two_prime_O_methyluridine" ;
  rdfs:comment "2prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002028 a rdfs:Class ;
  rdfs:label "sORF" ;
  rdfs:comment "An open reading frame that encodes a peptide of less than 100 amino acids." ;
  rdfs:subClassOf obo:SO_0000236 .

obo:SO_0000453 a rdfs:Class ;
  rdfs:label "chromosomal_transposition" ;
  rdfs:comment "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0002254 a rdfs:Class ;
  rdfs:label "loop" ;
  rdfs:comment "The loop portion of a stem loop, which is not folded back upon itself. " ;
  rdfs:subClassOf obo:SO_0002253 .

obo:SO_0001316 a rdfs:Class ;
  rdfs:label "seven_deazaguanosine" ;
  rdfs:comment "7-deazaguanosine is a modified guanosine." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0100008 a rdfs:Class ;
  rdfs:label "alpha_beta_motif" ;
  rdfs:comment "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001952 a rdfs:Class ;
  rdfs:label "promoter_flanking_region" ;
  rdfs:comment "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0001475 a rdfs:Class ;
  rdfs:label "outron" ;
  rdfs:comment "A region of a primary transcript, that is removed via trans splicing." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0001061 a rdfs:Class ;
  rdfs:label "propeptide_cleavage_site" ;
  rdfs:comment "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0001367 a rdfs:Class ;
  rdfs:label "five_carbamoylmethyluridine" ;
  rdfs:comment "5_carbamoylmethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002170 a rdfs:Class ;
  rdfs:label "splice_donor_region_variant" ;
  rdfs:comment "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron)." ;
  rdfs:subClassOf obo:SO_0001630 .

obo:SO_0000528 a rdfs:Class ;
  rdfs:label "V_D_DJ_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001005 a rdfs:Class ;
  rdfs:label "low_complexity_region" ;
  rdfs:comment "A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides." ;
  rdfs:subClassOf obo:SO_0000001 , obo:SO_0001410 .

obo:SO_0001511 a rdfs:Class ;
  rdfs:label "interchromosomal" ;
  rdfs:comment "A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes." ;
  rdfs:subClassOf obo:SO_0001509 .

obo:SO_0000788 a rdfs:Class ;
  rdfs:label "cloned" .

obo:SO_0000350 a rdfs:Class ;
  rdfs:label "FRT_site" ;
  rdfs:comment "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." ;
  rdfs:subClassOf obo:SO_0000948 .

obo:SO_0000894 a rdfs:Class ;
  rdfs:label "silenced_by_DNA_modification" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." ;
  rdfs:subClassOf obo:SO_0000893 .

obo:SO_0001926 a rdfs:Class ;
  rdfs:label "anti_ARRET" ;
  rdfs:comment "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." ;
  rdfs:subClassOf obo:SO_0001927 .

obo:SO_0000868 a rdfs:Class ;
  rdfs:label "plus_1_frameshift" ;
  rdfs:comment "A frameshift caused by inserting one base." ;
  rdfs:subClassOf obo:SO_0000865 .

obo:SO_0000849 a rdfs:Class ;
  rdfs:label "three_prime_LTR_component" ;
  rdfs:comment "A component of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000848 .

obo:BS_00181 a rdfs:Class .

obo:SO_0000166 a rdfs:Class ;
  rdfs:label "enhancer_bound_by_factor" ;
  rdfs:comment "An enhancer bound by a factor." ;
  rdfs:subClassOf obo:SO_0000165 .

obo:SO_0000990 a rdfs:Class ;
  rdfs:label "class_I_RNA" ;
  rdfs:comment "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002387 a rdfs:Class ;
  rdfs:label "5_prime_UTR_uORF_frameshift_variant" ;
  rdfs:comment "A 5' UTR variant which disrupts the translation of an upstream open reading frame because the number of nucleotides inserted or deleted is not a multiple of three." ;
  rdfs:subClassOf obo:SO_0002385 .

obo:SO_0001229 a rdfs:Class ;
  rdfs:label "pseudouridine" ;
  rdfs:comment "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001529 a rdfs:Class ;
  rdfs:label "endosomal_localization_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the endosome." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:BS_00141 a rdfs:Class .

obo:SO_0000337 a rdfs:Class ;
  rdfs:label "RNAi_reagent" ;
  rdfs:comment "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." ;
  rdfs:subClassOf obo:SO_0000442 .

obo:SO_0001718 a rdfs:Class ;
  rdfs:label "H3K18_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0000838 a rdfs:Class ;
  rdfs:label "rRNA_primary_transcript_region" ;
  rdfs:comment "A region of an rRNA primary transcript." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0001026 a rdfs:Class ;
  rdfs:label "genome" ;
  rdfs:comment "A genome is the sum of genetic material within a cell or virion." ;
  rdfs:subClassOf obo:SO_0001260 .

obo:SO_0000777 a rdfs:Class ;
  rdfs:label "pseudogenic_rRNA" ;
  rdfs:comment "A non functional descendant of an rRNA." ;
  rdfs:subClassOf obo:SO_0000516 .

obo:SO_0001175 a rdfs:Class ;
  rdfs:label "CCA_tail" ;
  rdfs:comment "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." ;
  rdfs:subClassOf obo:SO_0001172 .

obo:SO_0000984 a rdfs:Class ;
  rdfs:label "single" ;
  rdfs:comment "When a nucleotide polymer has only one strand." ;
  rdfs:subClassOf obo:SO_0000983 .

obo:SO_0000270 a rdfs:Class ;
  rdfs:label "threonyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000037 a rdfs:Class ;
  rdfs:label "locus_control_region" ;
  rdfs:comment "A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." ;
  rdfs:subClassOf obo:SO_0000727 .

obo:SO_0000260 a rdfs:Class ;
  rdfs:label "glutamyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000081 a rdfs:Class ;
  rdfs:label "gene_array_member" ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0001915 a rdfs:Class ;
  rdfs:label "transcription_start_cluster" ;
  rdfs:comment "A region defined by a cluster of experimentally determined transcription starting sites." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0001269 a rdfs:Class ;
  rdfs:label "SRP_RNA_gene" ;
  rdfs:comment "A gene that encodes a signal recognition particle (SRP) RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0002240 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_5_8S_gene" ;
  rdfs:comment "A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0002186 a rdfs:Class ;
  rdfs:label "mutational_hotspot" ;
  rdfs:comment "A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000184 a rdfs:Class ;
  rdfs:label "U2_intron" ;
  rdfs:comment "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." ;
  rdfs:subClassOf obo:SO_0000662 .

obo:SO_0002344 a rdfs:Class ;
  rdfs:label "mt_SSU_rRNA" ;
  rdfs:comment "Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes." ;
  rdfs:subClassOf obo:SO_0002128 .

obo:SO_1000157 a rdfs:Class ;
  rdfs:label "uninverted_interchromosomal_transposition" ;
  rdfs:comment "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." ;
  rdfs:subClassOf obo:SO_1000155 .

obo:SO_0001947 a rdfs:Class ;
  rdfs:label "H3R2_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0002034 a rdfs:Class ;
  rdfs:label "miR_encoding_snoRNA_primary_transcript" ;
  rdfs:comment "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0001298 a rdfs:Class ;
  rdfs:label "two_prime_O_methyladenosine" ;
  rdfs:comment "2prime_O_methyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001898 a rdfs:Class ;
  rdfs:label "dg_repeat" ;
  rdfs:comment "A repeat region which is part of the regional centromere outer repeat region." ;
  rdfs:subClassOf obo:SO_0001797 .

obo:SO_0001417 a rdfs:Class ;
  rdfs:label "three_prime_flanking_region" ;
  rdfs:comment "A flanking region located three prime of a specific region." ;
  rdfs:subClassOf obo:SO_0000239 .

obo:SO_0001553 a rdfs:Class ;
  rdfs:label "translational_product_level_variant" ;
  rdfs:comment "A functional variant that changes the translational product level with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001539 .

obo:SO_0001395 a rdfs:Class ;
  rdfs:label "modified_L_methionine" ;
  rdfs:comment "A post translationally modified methionine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000967 a rdfs:Class ;
  rdfs:label "circular_double_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." ;
  rdfs:subClassOf obo:SO_0000965 .

obo:SO_0000427 a rdfs:Class ;
  rdfs:label "R_five_prime_LTR_region" ;
  rdfs:comment "The R segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000423 , obo:SO_0000850 .

obo:SO_0000934 a rdfs:Class ;
  rdfs:label "miRNA_target_site" ;
  rdfs:comment "A miRNA target site is a binding site where the molecule is a micro RNA." ;
  rdfs:subClassOf obo:SO_0001655 .

obo:SO_0002338 a rdfs:Class ;
  rdfs:label "U7_snRNA" ;
  rdfs:comment "A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0000789 a rdfs:Class ;
  rdfs:label "validated" ;
  rdfs:comment "An attribute to describe a feature that has been proven." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_1000117 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_polypeptide_function" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000677 a rdfs:Class ;
  rdfs:label "canonical_five_prime_splice_site" ;
  rdfs:comment "The canonical 5' splice site has the sequence \"GT\"." ;
  rdfs:subClassOf obo:SO_0000163 .

obo:SO_0001775 a rdfs:Class ;
  rdfs:label "maternal_variant" ;
  rdfs:comment "A variant in the genetic material inherited from the mother." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_1000020 a rdfs:Class ;
  rdfs:label "C_to_G_transversion" ;
  rdfs:comment "A transversion of a cytidine to a guanine." ;
  rdfs:subClassOf obo:SO_1000018 .

obo:SO_1001251 a rdfs:Class ;
  rdfs:label "CDS_supported_by_sequence_similarity_data" ;
  rdfs:comment "A CDS that is supported by sequence similarity data." ;
  rdfs:subClassOf obo:SO_0000316 , obo:SO_1001254 .

obo:SO_0001112 a rdfs:Class ;
  rdfs:label "antiparallel_beta_strand" ;
  rdfs:comment "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." ;
  rdfs:subClassOf obo:SO_0001111 .

obo:SO_0000468 a rdfs:Class ;
  rdfs:label "golden_path_fragment" ;
  rdfs:comment "One of the pieces of sequence that make up a golden path." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:BS_00153 a rdfs:Class .

obo:SO_0001362 a rdfs:Class ;
  rdfs:label "five_methoxycarbonylmethyl_two_thiouridine" ;
  rdfs:comment "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001191 a rdfs:Class ;
  rdfs:label "TNA_oligo" ;
  rdfs:comment "An oligo composed of TNA residues." ;
  rdfs:subClassOf obo:SO_0001247 .

obo:SO_0001664 a rdfs:Class ;
  rdfs:label "DCE" ;
  rdfs:comment "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_1000057 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_synonymous_codon_change_in_transcript" ;
  rdfs:comment "The changed codon has the same translation product as the original codon." .

obo:SO_0000025 a rdfs:Class ;
  rdfs:label "symmetric_RNA_internal_loop" ;
  rdfs:comment "An internal RNA loop where the extent of the loop on both stands is the same size." ;
  rdfs:subClassOf obo:SO_0000020 .

obo:SO_0001283 a rdfs:Class ;
  rdfs:label "two_prime_O_methylcytidine" ;
  rdfs:comment "2'-O-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0002333 a rdfs:Class ;
  rdfs:label "amber_stop_codon" ;
  rdfs:comment "A stop codon with the DNA sequence TAG." ;
  rdfs:subClassOf obo:SO_0000319 .

obo:SO_0001385 a rdfs:Class ;
  rdfs:label "modified_amino_acid_feature" ;
  rdfs:comment "A post translationally modified amino acid feature." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001338 a rdfs:Class ;
  rdfs:label "N2_7_dimethylguanosine" ;
  rdfs:comment "N2_7_dimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_1000017 a rdfs:Class ;
  rdfs:label "transversion" ;
  rdfs:comment "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." ;
  rdfs:subClassOf obo:SO_0001483 .

obo:SO_0002242 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_25S_gene" ;
  rdfs:comment "A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0002027 a rdfs:Class ;
  rdfs:label "uORF" ;
  rdfs:comment "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." ;
  rdfs:subClassOf obo:SO_0000236 .

obo:SO_0001887 a rdfs:Class ;
  rdfs:label "regulatory_region_fusion" ;
  rdfs:comment "A feature fusion where the deletion brings together regulatory regions." ;
  rdfs:subClassOf obo:SO_0001882 .

obo:SO_0000945 a rdfs:Class ;
  rdfs:label "attR_site" ;
  rdfs:comment "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0000434 a rdfs:Class ;
  rdfs:label "target_site_duplication" ;
  rdfs:comment "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." ;
  rdfs:subClassOf obo:SO_0000314 .

obo:SO_0001937 a rdfs:Class ;
  rdfs:label "H2BK12_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002143 .

obo:SO_0000315 a rdfs:Class ;
  rdfs:label "TSS" ;
  rdfs:comment "The first base where RNA polymerase begins to synthesize the RNA transcript." ;
  rdfs:subClassOf obo:SO_0000835 , obo:SO_0002309 .

obo:SO_0002089 a rdfs:Class ;
  rdfs:label "3_prime_UTR_exon_variant" ;
  rdfs:comment "A UTR variant of exonic sequence of the 3' UTR." ;
  rdfs:subClassOf obo:SO_0001624 .

obo:SO_0002237 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_16S_gene" ;
  rdfs:comment "A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes." ;
  rdfs:subClassOf obo:SO_0002362 .

obo:SO_0001233 a rdfs:Class ;
  rdfs:label "methylinosine" ;
  rdfs:comment "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." ;
  rdfs:subClassOf obo:SO_0001274 .

obo:SO_0000401 a rdfs:Class ;
  rdfs:label "gene_attribute" ;
  rdfs:comment "An attribute describing a gene." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000874 a rdfs:Class ;
  rdfs:label "edited_transcript_by_A_to_I_substitution" ;
  rdfs:comment "A transcript that has been edited by A to I substitution." ;
  rdfs:subClassOf obo:SO_0000873 .

obo:SO_0000123 a rdfs:Class ;
  rdfs:label "transcriptionally_regulated" ;
  rdfs:comment "An attribute describing a gene that is regulated at transcription." ;
  rdfs:subClassOf obo:SO_0000119 .

obo:BS_00077 a rdfs:Class .

obo:SO_0000956 a rdfs:Class ;
  rdfs:label "single_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded DNA molecule." ;
  rdfs:subClassOf obo:SO_0000954 .

obo:SO_0001967 a rdfs:Class ;
  rdfs:label "8_oxoadenine" ;
  rdfs:comment "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." ;
  rdfs:subClassOf obo:SO_0001962 .

obo:SO_0001798 a rdfs:Class ;
  rdfs:label "regional_centromere_inner_repeat_region" ;
  rdfs:comment "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." ;
  rdfs:subClassOf obo:SO_0001797 .

obo:SO_0005843 a rdfs:Class ;
  rdfs:label "rRNA_cleavage_RNA" ;
  rdfs:comment "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001705 a rdfs:Class ;
  rdfs:label "H3K4_monomethylation_site" ;
  rdfs:comment "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001734 .

obo:SO_0000242 a rdfs:Class ;
  rdfs:label "untranslated_region_polycistronic_mRNA" ;
  rdfs:comment "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." ;
  rdfs:subClassOf obo:SO_0000203 .

obo:SO_0002160 a rdfs:Class ;
  rdfs:label "sequence_length_variant" ;
  rdfs:comment "A sequence variant that changes the length of one or more sequence features." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_1000146 a rdfs:Class .

obo:SO_0002403 a rdfs:Class ;
  rdfs:label "unidirectional_intergenic_fusion" ;
  rdfs:comment "A sequence variant whereby two genes on the same strand have become joined such that the 5' breakend is intragenic and the 3' breakend lies proximally upstream of a gene such that it may potentially form a chimeric transcript." ;
  rdfs:subClassOf obo:SO_0001564 , obo:SO_0001882 .

obo:SO_0001047 a rdfs:Class ;
  rdfs:label "IRRinv_site" ;
  rdfs:comment "Component of the inversion site located at the right of a region susceptible to site-specific inversion." ;
  rdfs:subClassOf obo:SO_0001048 .

obo:SO_0001764 a rdfs:Class ;
  rdfs:label "unique_variant" ;
  rdfs:comment "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_1000106 a rdfs:Class ;
  rdfs:label "mutation_causing_inframe_polypeptide_N_terminal_elongation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001016 a rdfs:Class ;
  rdfs:label "internal_guide_sequence" ;
  rdfs:comment "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." ;
  rdfs:subClassOf obo:SO_0001014 .

obo:SO_0001244 a rdfs:Class ;
  rdfs:label "pre_miRNA" ;
  rdfs:comment "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." ;
  rdfs:subClassOf obo:SO_0001243 .

obo:BS_00219 a rdfs:Class .

obo:SO_0001224 a rdfs:Class ;
  rdfs:label "gene_silenced_by_RNA_interference" ;
  rdfs:comment "A gene that is silenced by RNA interference." ;
  rdfs:subClassOf obo:SO_0000127 .

obo:SO_0000138 a rdfs:Class ;
  rdfs:label "gene_rearranged_at_DNA_level" ;
  rdfs:comment "An epigenetically modified gene, rearranged at the DNA level." ;
  rdfs:subClassOf obo:SO_0000898 .

obo:SO_0000503 a rdfs:Class ;
  rdfs:label "alternately_spliced_gene_encodeing_one_transcript" .

obo:SO_1000090 a rdfs:Class .

obo:BS_00223 a rdfs:Class .

obo:SO_1000041 a rdfs:Class ;
  rdfs:label "intrachromosomal_transposition" ;
  rdfs:comment "A chromosome structure variation whereby a transposition occurred within a chromosome." ;
  rdfs:subClassOf obo:SO_0000453 , obo:SO_1000028 , obo:SO_1000038 .

obo:SO_0000282 a rdfs:Class ;
  rdfs:label "mRNA_with_minus_1_frameshift" ;
  rdfs:comment "An mRNA with a minus 1 frameshift." ;
  rdfs:subClassOf obo:SO_0000108 .

obo:SO_0001128 a rdfs:Class ;
  rdfs:label "polypeptide_turn_motif" ;
  rdfs:comment "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0000419 a rdfs:Class ;
  rdfs:label "mature_protein_region" ;
  rdfs:comment "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0002016 a rdfs:Class ;
  rdfs:label "3_prime_UTR_elongation" ;
  rdfs:comment "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001624 .

obo:SO_1001194 a rdfs:Class ;
  rdfs:label "alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping" .

obo:SO_0000546 a rdfs:Class ;
  rdfs:label "designed_sequence" ;
  rdfs:comment "An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence." ;
  rdfs:subClassOf obo:SO_0000351 .

obo:SO_0000995 a rdfs:Class ;
  rdfs:label "consensus_mRNA" ;
  rdfs:comment "An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_0000994 .

obo:SO_0001075 a rdfs:Class ;
  rdfs:label "intramembrane_polypeptide_region" ;
  rdfs:comment "Polypeptide region present in the lipid bilayer." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0002396 a rdfs:Class ;
  rdfs:label "decreased_polypeptide_level" ;
  rdfs:comment "A decrease in polypeptide (i.e. protein) expression, as a consequence of a variant in the gene." ;
  rdfs:subClassOf obo:SO_0001555 .

obo:SO_1000121 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_polypeptide_localization_change" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000163 a rdfs:Class ;
  rdfs:label "five_prime_cis_splice_site" ;
  rdfs:comment "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." ;
  rdfs:subClassOf obo:SO_0001419 .

obo:SO_0000755 a rdfs:Class ;
  rdfs:label "plasmid_vector" ;
  rdfs:comment "A plasmid that has been generated to act as a vector for foreign sequence." ;
  rdfs:subClassOf obo:SO_0000440 , obo:SO_0001235 .

obo:SO_0000051 a rdfs:Class ;
  rdfs:label "probe" ;
  rdfs:comment "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0000800 a rdfs:Class ;
  rdfs:label "assortment_derived_duplication" ;
  rdfs:comment "A multi-chromosome duplication aberration generated by reassortment of other aberration components." ;
  rdfs:subClassOf obo:SO_0001504 .

obo:SO_0001464 a rdfs:Class ;
  rdfs:label "UST" ;
  rdfs:comment "An EST spanning part or all of the untranslated regions of a protein-coding transcript." ;
  rdfs:subClassOf obo:SO_0000345 .

obo:SO_0000883 a rdfs:Class ;
  rdfs:label "stop_codon_read_through" ;
  rdfs:comment "A stop codon redefined to be a new amino acid." ;
  rdfs:subClassOf obo:SO_0000145 .

obo:SO_0001533 a rdfs:Class ;
  rdfs:label "cryptic_splice_site" ;
  rdfs:comment "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." ;
  rdfs:subClassOf obo:SO_0000162 .

obo:SO_0000719 a rdfs:Class ;
  rdfs:label "ultracontig" ;
  rdfs:comment "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." ;
  rdfs:subClassOf obo:SO_0001876 .

obo:SO_0001204 a rdfs:Class ;
  rdfs:label "Phage_RNA_Polymerase_Promoter" ;
  rdfs:comment "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0002311 .

obo:SO_0001560 a rdfs:Class ;
  rdfs:label "inactive_ligand_binding_site" ;
  rdfs:comment "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001559 .

obo:SO_0000214 a rdfs:Class ;
  rdfs:label "aspartic_acid_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding aspartyl tRNA (SO:0000257)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0002272 a rdfs:Class ;
  rdfs:label "L1_LINE_retrotransposon" ;
  rdfs:comment "Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs." ;
  rdfs:subClassOf obo:SO_0000194 .

obo:SO_0001117 a rdfs:Class ;
  rdfs:label "alpha_helix" ;
  rdfs:comment "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." ;
  rdfs:subClassOf obo:SO_0001116 .

obo:SO_0001441 a rdfs:Class ;
  rdfs:label "phenylalanine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000855 a rdfs:Class ;
  rdfs:label "orthologous_region" ;
  rdfs:comment "A homologous_region that is orthologous to another region." ;
  rdfs:subClassOf obo:SO_0000853 .

obo:SO_1000132 a rdfs:Class ;
  rdfs:label "sequence_variant_effect" ;
  rdfs:comment "The effect of a change in nucleotide sequence." .

obo:SO_0000584 a rdfs:Class ;
  rdfs:label "tmRNA" ;
  rdfs:comment "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0001378 a rdfs:Class ;
  rdfs:label "five_taurinomethyluridine" ;
  rdfs:comment "5_taurinomethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002247 a rdfs:Class ;
  rdfs:label "sncRNA" ;
  rdfs:comment "A non-coding RNA less than 200 nucleotides in length." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001219 a rdfs:Class ;
  rdfs:label "retrogene" ;
  rdfs:comment "A gene that has been produced as the product of a reverse transcriptase mediated event." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000193 a rdfs:Class ;
  rdfs:label "RFLP_fragment" ;
  rdfs:comment "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." ;
  rdfs:subClassOf obo:SO_0000412 .

obo:SO_0002153 a rdfs:Class ;
  rdfs:label "genic_upstream_transcript_variant" ;
  rdfs:comment "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." ;
  rdfs:subClassOf obo:SO_0001564 .

obo:SO_0000155 a rdfs:Class ;
  rdfs:label "plasmid" ;
  rdfs:comment "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." ;
  rdfs:subClassOf obo:SO_0001235 .

obo:SO_0001750 a rdfs:Class ;
  rdfs:label "SL5_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0000372 a rdfs:Class ;
  rdfs:label "enzymatic_RNA" ;
  rdfs:comment "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002376 a rdfs:Class ;
  rdfs:label "H_ACA_box_snoRNA_gene" ;
  rdfs:comment "A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." ;
  rdfs:subClassOf obo:SO_0001267 .

obo:SO_0001978 a rdfs:Class ;
  rdfs:label "signature" ;
  rdfs:comment "A region of sequence where developer information is encoded." ;
  rdfs:subClassOf obo:SO_0000804 .

obo:SO_0002349 a rdfs:Class ;
  rdfs:label "fragile_site" ;
  rdfs:comment "A heritable locus on a chromosome that is prone to DNA breakage." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0000070 a rdfs:Class ;
  rdfs:label "inside_intron_antiparallel" ;
  rdfs:comment "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." ;
  rdfs:subClassOf obo:SO_0000069 .

obo:SO_0001656 a rdfs:Class ;
  rdfs:label "metal_binding_site" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:SO_0002321 a rdfs:Class ;
  rdfs:label "stop_gained_NMD_triggering" ;
  rdfs:comment "A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001587 , obo:SO_0002319 .

obo:SO_0000654 a rdfs:Class ;
  rdfs:label "maxicircle_gene" ;
  rdfs:comment "A mitochondrial gene located in a maxicircle." ;
  rdfs:subClassOf obo:SO_0000089 .

obo:SO_0000103 a rdfs:Class ;
  rdfs:label "clone_insert_end" ;
  rdfs:comment "The end of the clone insert." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001310 a rdfs:Class ;
  rdfs:label "two_prime_O_ribosyladenosine_phosphate" ;
  rdfs:comment "2prime_O_ribosyladenosine_phosphate is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000048 a rdfs:Class ;
  rdfs:label "substitute" ;
  rdfs:comment "To substitute a subsection of sequence for another." .

obo:SO_0001634 a rdfs:Class ;
  rdfs:label "500B_downstream_variant" ;
  rdfs:comment "A sequence variant located within a half KB of the end of a gene." ;
  rdfs:subClassOf obo:SO_0001632 .

obo:SO_0001222 a rdfs:Class ;
  rdfs:label "silenced_by_histone_methylation" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." ;
  rdfs:subClassOf obo:SO_0001221 .

obo:SO_0000796 a rdfs:Class ;
  rdfs:label "transgenic_transposable_element" ;
  rdfs:comment "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." ;
  rdfs:subClassOf obo:SO_0000101 .

obo:SO_0000264 a rdfs:Class ;
  rdfs:label "leucyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000253 a rdfs:Class ;
  rdfs:label "tRNA" ;
  rdfs:comment "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." ;
  rdfs:subClassOf obo:SO_0002247 .

obo:SO_0002067 a rdfs:Class ;
  rdfs:label "HERV_deletion" ;
  rdfs:comment "A deletion of the HERV mobile element with respect to a reference." ;
  rdfs:subClassOf obo:SO_0002066 .

obo:SO_0001981 a rdfs:Class ;
  rdfs:label "L_box" ;
  rdfs:comment "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." ;
  rdfs:subClassOf obo:SO_0001678 .

obo:SO_0000361 a rdfs:Class ;
  rdfs:label "FRT_flanked" ;
  rdfs:comment "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." ;
  rdfs:subClassOf obo:SO_0000357 .

obo:SO_0002118 a rdfs:Class ;
  rdfs:label "NMD_polymorphic_pseudogene_transcript" ;
  rdfs:comment "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles." ;
  rdfs:subClassOf obo:SO_0002114 .

obo:SO_0001422 a rdfs:Class ;
  rdfs:label "conformational_switch" ;
  rdfs:comment "A region of a polypeptide, involved in the transition from one conformational state to another." ;
  rdfs:subClassOf obo:SO_0100001 .

obo:SO_0001903 a rdfs:Class .

obo:SO_0000517 a rdfs:Class ;
  rdfs:label "J_spacer" ;
  rdfs:comment "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000563 .

obo:SO_0000394 a rdfs:Class ;
  rdfs:label "U4atac_snRNA" ;
  rdfs:comment "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0001862 a rdfs:Class ;
  rdfs:label "GT_dinucleotide_repeat" ;
  rdfs:comment "A dinucleotide repeat region composed of GT repeating elements." ;
  rdfs:subClassOf obo:SO_0000290 .

obo:SO_0002355 a rdfs:Class ;
  rdfs:label "hpRNA_gene" ;
  rdfs:comment "A gene encoding a hpRNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0002225 a rdfs:Class ;
  rdfs:label "LOZ1_response_element" ;
  rdfs:comment "A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc." ;
  rdfs:subClassOf obo:SO_0002006 .

obo:SO_0002142 a rdfs:Class ;
  rdfs:label "histone_2A_acetylation_site" ;
  rdfs:comment "A histone 2A modification where the modification is the acetylation of the residue." ;
  rdfs:subClassOf obo:SO_0001702 .

obo:SO_0000177 a rdfs:Class ;
  rdfs:label "cross_genome_match" ;
  rdfs:comment "A nucleotide match against a sequence from another organism." ;
  rdfs:subClassOf obo:SO_0000347 .

obo:SO_0002298 a rdfs:Class ;
  rdfs:label "simple_operon" ;
  rdfs:comment "An operon whose transcription is coordinated on a single transcription unit." ;
  rdfs:subClassOf obo:SO_0000178 .

obo:SO_0000010 a rdfs:Class ;
  rdfs:label "protein_coding" ;
  rdfs:comment "A gene which, when transcribed, can be translated into a protein." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0001541 a rdfs:Class ;
  rdfs:label "decreased_transcript_level_variant" ;
  rdfs:comment "A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001540 .

obo:SO_0000782 a rdfs:Class ;
  rdfs:label "natural" ;
  rdfs:comment "An attribute describing a feature that occurs in nature." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0002209 a rdfs:Class ;
  rdfs:label "genomic_DNA_contig" ;
  rdfs:comment "A contig composed of genomic DNA derived sequences." ;
  rdfs:subClassOf obo:SO_0000149 .

obo:SO_0100019 a rdfs:Class ;
  rdfs:label "polypeptide_catalytic_motif" ;
  rdfs:comment "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." ;
  rdfs:subClassOf obo:SO_0100001 .

obo:SO_0001522 a rdfs:Class ;
  rdfs:label "insertional" ;
  rdfs:comment "When a translocation is simply moving genetic material from one chromosome to another." ;
  rdfs:subClassOf obo:SO_0001520 .

obo:SO_0000058 a rdfs:Class ;
  rdfs:label "assortment_derived_aneuploid" .

obo:SO_0002131 a rdfs:Class ;
  rdfs:label "sense_intronic_lncRNA" ;
  rdfs:comment "A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence." ;
  rdfs:subClassOf obo:SO_0001877 .

obo:SO_0001294 a rdfs:Class ;
  rdfs:label "N4_N4_2_prime_O_trimethylcytidine" ;
  rdfs:comment "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0000040 a rdfs:Class ;
  rdfs:label "genomic_clone" ;
  rdfs:comment "A clone of a DNA region of a genome." ;
  rdfs:subClassOf obo:SO_0000151 .

obo:SO_0000410 a rdfs:Class ;
  rdfs:label "protein_binding_site" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:SO_0001332 a rdfs:Class ;
  rdfs:label "wybutosine" ;
  rdfs:comment "Wybutosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000203 a rdfs:Class ;
  rdfs:label "UTR" ;
  rdfs:comment "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001956 a rdfs:Class ;
  rdfs:label "protease_site" ;
  rdfs:comment "A polypeptide_region that codes for a protease cleavage site." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001645 a rdfs:Class ;
  rdfs:label "genetic_marker" ;
  rdfs:comment "A measurable sequence feature that varies within a population." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002293 a rdfs:Class ;
  rdfs:label "mitochondrial_control_region" ;
  rdfs:comment "The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001850 a rdfs:Class ;
  rdfs:label "HSE" ;
  rdfs:comment "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001139 a rdfs:Class ;
  rdfs:label "gamma_turn_classic" ;
  rdfs:comment "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." ;
  rdfs:subClassOf obo:SO_0001138 .

obo:SO_0001101 a rdfs:Class ;
  rdfs:label "polypeptide_nickel_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001486 a rdfs:Class ;
  rdfs:label "standard_draft" ;
  rdfs:comment "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0002197 a rdfs:Class ;
  rdfs:label "processed_pseudogenic_tRNA" ;
  rdfs:comment "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail." ;
  rdfs:subClassOf obo:SO_0000778 .

obo:SO_0000354 a rdfs:Class ;
  rdfs:label "group_1_intron_homing_endonuclease_target_region" ;
  rdfs:comment "A region of intronic nucleotide sequence targeted by a nuclease enzyme." ;
  rdfs:subClassOf obo:SO_0000684 .

obo:SO_0002214 a rdfs:Class ;
  rdfs:label "redundant_inserted_stop_gained" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon is changed, resulting in a stop codon inserted next to an existing stop codon. This leads to a polypeptide of the same length." ;
  rdfs:subClassOf obo:SO_0001992 .

obo:BS_00144 a rdfs:Class .

obo:SO_0000771 a rdfs:Class ;
  rdfs:label "QTL" ;
  rdfs:comment "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001995 a rdfs:Class ;
  rdfs:label "extended_intronic_splice_region_variant" ;
  rdfs:comment "A sequence variant occurring in the intron, within 10 bases of exon." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0001041 a rdfs:Class ;
  rdfs:label "viral_sequence" ;
  rdfs:comment "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." ;
  rdfs:subClassOf obo:SO_0001038 , obo:SO_0001235 .

obo:SO_0000745 a rdfs:Class ;
  rdfs:label "chloroplast_sequence" ;
  rdfs:comment "DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_0001772 a rdfs:Class ;
  rdfs:label "disease_causing_variant" ;
  rdfs:comment "A variant that has been found to cause disease." ;
  rdfs:subClassOf obo:SO_0001769 .

obo:SO_0002250 a rdfs:Class ;
  rdfs:label "propeptide_region_of_CDS" ;
  rdfs:comment "A CDS region corresponding to a propeptide of a polypeptide." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0100004 a rdfs:Class ;
  rdfs:label "catmat_left_handed_three" ;
  rdfs:comment "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001022 a rdfs:Class ;
  rdfs:label "inversion_breakpoint" ;
  rdfs:comment "The point within a chromosome where an inversion begins or ends." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0000663 a rdfs:Class ;
  rdfs:label "tRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a transfer RNA (tRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0000174 a rdfs:Class ;
  rdfs:label "TATA_box" ;
  rdfs:comment "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000442 a rdfs:Class ;
  rdfs:label "ds_oligo" ;
  rdfs:comment "A double stranded oligonucleotide." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0002045 a rdfs:Class ;
  rdfs:label "pheromone_response_element" ;
  rdfs:comment "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." ;
  rdfs:subClassOf obo:SO_0000235 , obo:SO_0001659 .

obo:SO_0000293 a rdfs:Class ;
  rdfs:label "engineered_foreign_repetitive_element" ;
  rdfs:comment "A repetitive element that is engineered and foreign." ;
  rdfs:subClassOf obo:SO_0000657 , obo:SO_0000805 .

obo:SO_0001802 a rdfs:Class ;
  rdfs:label "increased_polyadenylation_variant" ;
  rdfs:comment "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." ;
  rdfs:subClassOf obo:SO_0001545 .

obo:BS_00208 a rdfs:Class .

obo:SO_0002284 a rdfs:Class ;
  rdfs:label "PIF_Harbinger_TIR_transposon" ;
  rdfs:comment "Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCC…GGC/GCC' or 'GA/GGCA…TGCC/TC'." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0000681 a rdfs:Class ;
  rdfs:label "aberrant_processed_transcript" ;
  rdfs:comment "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000412 a rdfs:Class ;
  rdfs:label "restriction_fragment" ;
  rdfs:comment "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_0001262 a rdfs:Class ;
  rdfs:label "overlapping_EST_set" ;
  rdfs:comment "A continous experimental result region extending the length of multiple overlapping EST's." ;
  rdfs:subClassOf obo:SO_0001261 .

obo:SO_0000145 a rdfs:Class ;
  rdfs:label "recoded_codon" ;
  rdfs:comment "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." ;
  rdfs:subClassOf obo:SO_0000360 .

obo:SO_0000908 a rdfs:Class ;
  rdfs:label "supported_by_domain_match" ;
  rdfs:comment "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." ;
  rdfs:subClassOf obo:SO_0000907 .

obo:SO_0000565 a rdfs:Class ;
  rdfs:label "V_VDJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_1000113 a rdfs:Class .

obo:SO_0001761 a rdfs:Class ;
  rdfs:label "variant_quality" ;
  rdfs:comment "A dependent entity that inheres in a bearer, a sequence variant." ;
  rdfs:subClassOf obo:SO_0000400 .

obo:SO_0001078 a rdfs:Class ;
  rdfs:label "polypeptide_secondary_structure" ;
  rdfs:comment "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0000923 a rdfs:Class ;
  rdfs:label "insert_G" ;
  rdfs:comment "An edit to insert a G." .

obo:SO_0000978 a rdfs:Class ;
  rdfs:label "template_region" ;
  rdfs:comment "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." ;
  rdfs:subClassOf obo:SO_0000930 .

obo:SO_0001255 a rdfs:Class ;
  rdfs:label "autopolyploid" ;
  rdfs:comment "A polyploid where the multiple chromosome set was derived from the same organism." ;
  rdfs:subClassOf obo:SO_0001254 .

obo:SO_0000643 a rdfs:Class ;
  rdfs:label "minisatellite" ;
  rdfs:comment "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." ;
  rdfs:subClassOf obo:SO_0000005 .

obo:SO_0001086 a rdfs:Class ;
  rdfs:label "sequence_uncertainty" ;
  rdfs:comment "Describes the positions in a sequence where the authors are unsure about the sequence assignment." ;
  rdfs:subClassOf obo:SO_0001082 .

obo:SO_0001733 a rdfs:Class ;
  rdfs:label "H3K36_methylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0001321 a rdfs:Class ;
  rdfs:label "seven_cyano_seven_deazaguanosine" ;
  rdfs:comment "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0000930 a rdfs:Class ;
  rdfs:label "guide_RNA_region" ;
  rdfs:comment "A region of guide RNA." ;
  rdfs:subClassOf obo:SO_0000834 .

obo:SO_0001430 a rdfs:Class .

obo:SO_0001235 a rdfs:Class ;
  rdfs:label "replicon" ;
  rdfs:comment "A region containing at least one unique origin of replication and a unique termination site." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002038 a rdfs:Class ;
  rdfs:label "shRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding an shRNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0002363 a rdfs:Class ;
  rdfs:label "mt_rRNA_gene" ;
  rdfs:comment "A gene that codes for mitochondrial rRNA." ;
  rdfs:subClassOf obo:SO_0000088 , obo:SO_0001637 .

obo:SO_0001143 a rdfs:Class ;
  rdfs:label "st_turn_left_handed_type_two" ;
  rdfs:comment "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0001141 .

obo:SO_0001813 a rdfs:Class ;
  rdfs:label "vacuolar_sorting_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the vacuole." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0001729 a rdfs:Class ;
  rdfs:label "H4K16_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001972 .

obo:SO_0002107 a rdfs:Class ;
  rdfs:label "transcribed_unprocessed_pseudogene" ;
  rdfs:comment "A unprocessed pseudogene supported by locus-specific evidence of transcription." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_0002261 a rdfs:Class ;
  rdfs:label "TRIM" ;
  rdfs:comment "TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100–300 bp. TRIMs lack coding domains and thus do not encode proteins." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001943 a rdfs:Class ;
  rdfs:label "H3K4_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0001839 a rdfs:Class ;
  rdfs:label "CSL_response_element" ;
  rdfs:comment "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001406 a rdfs:Class ;
  rdfs:label "modified_L_arginine" ;
  rdfs:comment "A post translationally modified arginine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000345 a rdfs:Class ;
  rdfs:label "EST" ;
  rdfs:comment "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." ;
  rdfs:subClassOf obo:SO_0000324 .

obo:SO_0000134 a rdfs:Class ;
  rdfs:label "genomically_imprinted" ;
  rdfs:comment "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." ;
  rdfs:subClassOf obo:SO_0000119 , obo:SO_0000133 .

obo:SO_0002374 a rdfs:Class ;
  rdfs:label "C-D_H_ACA_box_scaRNA_gene" ;
  rdfs:comment "A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002339 .

obo:SO_0000941 a rdfs:Class ;
  rdfs:label "recombinationally_rearranged_vertebrate_immune_system_gene" ;
  rdfs:comment "A recombinationally rearranged gene of the vertebrate immune system." ;
  rdfs:subClassOf obo:SO_0000456 .

obo:SO_0001198 a rdfs:Class ;
  rdfs:label "ds_DNA_viral_sequence" ;
  rdfs:comment "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." ;
  rdfs:subClassOf obo:SO_0001041 .

obo:SO_0001327 a rdfs:Class ;
  rdfs:label "two_prime_O_methylguanosine" ;
  rdfs:comment "2prime_O_methylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_1000171 a rdfs:Class ;
  rdfs:label "deficient_inversion" ;
  rdfs:comment "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." ;
  rdfs:subClassOf obo:SO_1000029 , obo:SO_1000030 .

obo:SO_0000587 a rdfs:Class ;
  rdfs:label "group_I_intron" ;
  rdfs:comment "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." ;
  rdfs:subClassOf obo:SO_0000588 .

obo:SO_0000508 a rdfs:Class ;
  rdfs:label "D_DJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000670 a rdfs:Class ;
  rdfs:label "chromosome_breakage_sequence" ;
  rdfs:comment "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." ;
  rdfs:subClassOf obo:SO_0000669 .

obo:SO_0000268 a rdfs:Class ;
  rdfs:label "prolyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:BS_00212 a rdfs:Class .

obo:SO_0001747 a rdfs:Class ;
  rdfs:label "open_chromatin_region" ;
  rdfs:comment "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000208 a rdfs:Class ;
  rdfs:label "terminal_inverted_repeat_element" ;
  rdfs:comment "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." ;
  rdfs:subClassOf obo:SO_0000182 .

obo:SO_1000125 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_gain_of_function_of_polypeptide" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000699 a rdfs:Class ;
  rdfs:label "junction" ;
  rdfs:comment "A sequence_feature with an extent of zero." ;
  rdfs:subClassOf obo:SO_0000110 .

obo:SO_0002023 a rdfs:Class ;
  rdfs:label "multiplexing_sequence_identifier" ;
  rdfs:comment "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." ;
  rdfs:subClassOf obo:SO_0000324 .

obo:SO_0001660 a rdfs:Class ;
  rdfs:label "core_eukaryotic_promoter_element" ;
  rdfs:comment "An element that only exists within the promoter region of a eukaryotic gene." ;
  rdfs:subClassOf obo:SO_0002309 .

obo:SO_0001963 a rdfs:Class ;
  rdfs:label "modified_cytosine" ;
  rdfs:comment "A modified cytosine DNA base feature." ;
  rdfs:subClassOf obo:SO_0000305 .

obo:SO_0000152 a rdfs:Class ;
  rdfs:label "YAC" ;
  rdfs:comment "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0002175 a rdfs:Class ;
  rdfs:label "insertion_artifact" ;
  rdfs:comment "An insertion that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002172 .

obo:SO_0000330 a rdfs:Class ;
  rdfs:label "conserved_region" ;
  rdfs:comment "Region of sequence similarity by descent from a common ancestor." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0002283 a rdfs:Class ;
  rdfs:label "piggyBac_TIR_transposon" ;
  rdfs:comment "Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0001300 a rdfs:Class ;
  rdfs:label "N6_isopentenyladenosine" ;
  rdfs:comment "N6_isopentenyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001598 a rdfs:Class ;
  rdfs:label "translational_product_structure_variant" ;
  rdfs:comment "A sequence variant within the transcript that changes the structure of the translational product." ;
  rdfs:subClassOf obo:SO_0001564 .

obo:SO_0001571 a rdfs:Class ;
  rdfs:label "cryptic_splice_donor" ;
  rdfs:comment "A sequence variant whereby a new splice site is created due to the activation of a new donor." ;
  rdfs:subClassOf obo:SO_0001569 .

obo:SO_0001492 a rdfs:Class ;
  rdfs:label "intronic_regulatory_region" ;
  rdfs:comment "A regulatory region that is part of an intron." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0001518 a rdfs:Class ;
  rdfs:label "pericentric" ;
  rdfs:comment "An inversion event that includes the centromere." ;
  rdfs:subClassOf obo:SO_0001517 .

obo:SO_0000021 a rdfs:Class ;
  rdfs:label "asymmetric_RNA_internal_loop" ;
  rdfs:comment "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." ;
  rdfs:subClassOf obo:SO_0000020 .

obo:SO_0002012 a rdfs:Class ;
  rdfs:label "start_lost" ;
  rdfs:comment "A codon variant that changes at least one base of the canonical start codon." ;
  rdfs:subClassOf obo:SO_0001582 , obo:SO_0001992 .

obo:SO_0001588 a rdfs:Class .

obo:SO_1001187 a rdfs:Class ;
  rdfs:label "alternatively_spliced_transcript" ;
  rdfs:comment "A transcript that is alternatively spliced." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_1000102 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_level_of_translational_product" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001876 a rdfs:Class ;
  rdfs:label "partial_genomic_sequence_assembly" ;
  rdfs:comment "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." ;
  rdfs:subClassOf obo:SO_0000353 .

obo:SO_0000607 a rdfs:Class ;
  rdfs:label "unedited_region" ;
  rdfs:comment "The region of an edited transcript that will not be edited." ;
  rdfs:subClassOf obo:SO_0000579 .

obo:SO_1001273 a rdfs:Class ;
  rdfs:label "CTG_start_codon" ;
  rdfs:comment "A non-canonical start codon of sequence CTG." ;
  rdfs:subClassOf obo:SO_0000680 .

obo:SO_0000211 a rdfs:Class ;
  rdfs:label "alanine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding alanyl tRNA." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0001134 a rdfs:Class ;
  rdfs:label "beta_turn_left_handed_type_one" ;
  rdfs:comment "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:SO_0001340 a rdfs:Class ;
  rdfs:label "one_two_prime_O_dimethylguanosine" ;
  rdfs:comment "1_2prime_O_dimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000326 a rdfs:Class ;
  rdfs:label "SAGE_tag" ;
  rdfs:comment "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." ;
  rdfs:subClassOf obo:SO_0000324 .

obo:SO_1000013 a rdfs:Class ;
  rdfs:label "T_to_C_transition" ;
  rdfs:comment "A transition of a thymine to a cytidine." ;
  rdfs:subClassOf obo:SO_1000010 .

obo:SO_0000759 a rdfs:Class ;
  rdfs:label "plasmid_clone" .

obo:SO_0000626 a rdfs:Class ;
  rdfs:label "chromosomal_regulatory_element" ;
  rdfs:comment "Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0000068 a rdfs:Class ;
  rdfs:label "overlapping" ;
  rdfs:comment "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." ;
  rdfs:subClassOf obo:SO_0000067 .

obo:SO_0001507 a rdfs:Class ;
  rdfs:label "variant_collection" ;
  rdfs:comment "A collection of one or more sequences of an individual." ;
  rdfs:subClassOf obo:SO_0001260 .

obo:SO_0000692 a rdfs:Class ;
  rdfs:label "gene_with_dicistronic_transcript" ;
  rdfs:comment "A gene that encodes a dicistronic transcript." ;
  rdfs:subClassOf obo:SO_0000690 .

obo:SO_0000987 a rdfs:Class ;
  rdfs:label "linear" ;
  rdfs:comment "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." ;
  rdfs:subClassOf obo:SO_0000986 .

obo:SO_0000912 a rdfs:Class ;
  rdfs:label "asx_turn" ;
  rdfs:comment "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." ;
  rdfs:subClassOf obo:SO_0001128 .

obo:SO_0002259 a rdfs:Class ;
  rdfs:label "polyA_site_cluster" ;
  rdfs:comment "A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000112 a rdfs:Class ;
  rdfs:label "primer" ;
  rdfs:comment "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." ;
  rdfs:subClassOf obo:SO_0000441 .

obo:SO_0002091 a rdfs:Class ;
  rdfs:label "5_prime_UTR_intron_variant" ;
  rdfs:comment "A UTR variant of intronic sequence of the 5' UTR." ;
  rdfs:subClassOf obo:SO_0001623 , obo:SO_0001969 .

obo:SO_0000187 a rdfs:Class ;
  rdfs:label "repeat_family" ;
  rdfs:comment "A group of characterized repeat sequences." .

obo:SO_0001036 a rdfs:Class ;
  rdfs:label "arginyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000639 a rdfs:Class ;
  rdfs:label "internal_transcribed_spacer_region" ;
  rdfs:comment "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." ;
  rdfs:subClassOf obo:SO_0000638 .

obo:SO_0000108 a rdfs:Class ;
  rdfs:label "mRNA_with_frameshift" ;
  rdfs:comment "An mRNA with a frameshift." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_0000540 a rdfs:Class ;
  rdfs:label "DJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001351 a rdfs:Class ;
  rdfs:label "five_methyl_2_thiouridine" ;
  rdfs:comment "5_methyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1001267 a rdfs:Class ;
  rdfs:label "stop_codon_readthrough" .

obo:SO_0001497 a rdfs:Class ;
  rdfs:label "X_element" ;
  rdfs:comment "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0000127 a rdfs:Class ;
  rdfs:label "silenced_gene" ;
  rdfs:comment "A gene that is silenced." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001052 a rdfs:Class ;
  rdfs:label "nested_repeat" .

obo:SO_0000760 a rdfs:Class ;
  rdfs:label "YAC_clone" .

obo:SO_0000721 a rdfs:Class ;
  rdfs:label "gene_with_dicistronic_primary_transcript" ;
  rdfs:comment "A gene that encodes a dicistronic primary transcript." ;
  rdfs:subClassOf obo:SO_0000692 .

obo:SO_0001260 a rdfs:Class ;
  rdfs:label "sequence_collection" ;
  rdfs:comment "A collection of discontinuous sequences." .

obo:SO_0002124 a rdfs:Class ;
  rdfs:label "IG_D_gene" ;
  rdfs:comment "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene." ;
  rdfs:subClassOf obo:SO_0002122 .

obo:SO_0001564 a rdfs:Class ;
  rdfs:label "gene_variant" ;
  rdfs:comment "A sequence variant where the structure of the gene is changed." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0000844 a rdfs:Class ;
  rdfs:label "RNApol_II_promoter_region" ;
  rdfs:comment "A region of sequence which is a promoter for RNA polymerase II." .

obo:SO_0001272 a rdfs:Class ;
  rdfs:label "tRNA_gene" ;
  rdfs:comment "A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA." ;
  rdfs:subClassOf obo:SO_0002342 .

obo:SO_0001153 a rdfs:Class ;
  rdfs:label "beta_turn_type_six_a_two" ;
  rdfs:comment "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees." ;
  rdfs:subClassOf obo:SO_0001151 .

obo:SO_0001020 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_copy_number" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000766 a rdfs:Class ;
  rdfs:label "pyrrolysyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001820 a rdfs:Class ;
  rdfs:label "inframe_indel" ;
  rdfs:comment "A coding sequence variant where the change does not alter the frame of the transcript." ;
  rdfs:subClassOf obo:SO_0001650 .

obo:SO_0002113 a rdfs:Class ;
  rdfs:label "lncRNA_with_retained_intron" ;
  rdfs:comment "A lncRNA transcript containing a retained intron." ;
  rdfs:subClassOf obo:SO_0002035 .

obo:SO_0001215 a rdfs:Class ;
  rdfs:label "coding_region_of_exon" ;
  rdfs:comment "The region of an exon that encodes for protein sequence." ;
  rdfs:subClassOf obo:SO_0000852 .

obo:SO_0002385 a rdfs:Class ;
  rdfs:label "5_prime_UTR_uORF_variant" ;
  rdfs:comment "A 5' UTR variant within an upstream open reading frame." ;
  rdfs:subClassOf obo:SO_0001623 .

obo:SO_0000387 a rdfs:Class ;
  rdfs:label "RprA_RNA" ;
  rdfs:comment "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_1000136 a rdfs:Class ;
  rdfs:label "autosynaptic_chromosome" ;
  rdfs:comment "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0000431 a rdfs:Class ;
  rdfs:label "U3_three_prime_LTR_region" ;
  rdfs:comment "The U3 segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000849 .

obo:SO_1001249 a rdfs:Class ;
  rdfs:label "CDS_supported_by_domain_match_data" ;
  rdfs:comment "A CDS that is supported by domain similarity." ;
  rdfs:subClassOf obo:SO_1001251 .

obo:SO_0000658 a rdfs:Class ;
  rdfs:label "dispersed_repeat" ;
  rdfs:comment "A repeat that is located at dispersed sites in the genome." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0001974 a rdfs:Class ;
  rdfs:label "CTCF_binding_site" ;
  rdfs:comment "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000554 a rdfs:Class ;
  rdfs:label "assortment_derived_deficiency_plus_duplication" .

obo:SO_0000226 a rdfs:Class ;
  rdfs:label "serine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding seryl tRNA (SO:000269)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000539 a rdfs:Class ;
  rdfs:label "DJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000039 a rdfs:Class ;
  rdfs:label "match_part" ;
  rdfs:comment "A part of a match, for example an hsp from blast is a match_part." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0000065 a rdfs:Class ;
  rdfs:label "free_chromosome_arm" ;
  rdfs:comment "A chromosome structure variation whereby an arm exists as an individual chromosome element." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0000811 a rdfs:Class ;
  rdfs:label "genomically_contaminated_cDNA_clone" ;
  rdfs:comment "A cDNA clone invalidated by genomic contamination." ;
  rdfs:subClassOf obo:SO_0000809 .

obo:SO_0001701 a rdfs:Class ;
  rdfs:label "histone_methylation_site" ;
  rdfs:comment "A histone modification site where the modification is the methylation of the residue." ;
  rdfs:subClassOf obo:SO_0001700 .

obo:SO_0002276 a rdfs:Class ;
  rdfs:label "5S_SINE_retrotransposon" ;
  rdfs:comment "Short interspersed elements that originated from 5S rRNAs." ;
  rdfs:subClassOf obo:SO_0000206 .

obo:SO_0000793 a rdfs:Class ;
  rdfs:label "engineered_DNA" .

obo:SO_0000289 a rdfs:Class ;
  rdfs:label "microsatellite" ;
  rdfs:comment "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." ;
  rdfs:subClassOf obo:SO_0000005 .

obo:SO_0002039 a rdfs:Class ;
  rdfs:label "miR_encoding_shRNA_primary_transcript" ;
  rdfs:comment "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0002038 .

obo:SO_0002146 a rdfs:Class ;
  rdfs:label "H2AZK7_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002144 .

obo:SO_1000124 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_partial_loss_of_function_of_polypeptide" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001629 a rdfs:Class ;
  rdfs:label "splice_site_variant" ;
  rdfs:comment "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." ;
  rdfs:subClassOf obo:SO_0001568 , obo:SO_0001627 .

obo:SO_0001123 a rdfs:Class ;
  rdfs:label "schellmann_loop" ;
  rdfs:comment "A motif of six or seven consecutive residues that contains two H-bonds." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0000822 a rdfs:Class ;
  rdfs:label "cyanelle_chromosome" ;
  rdfs:comment "A chromosome originating in a cyanelle." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001844 a rdfs:Class ;
  rdfs:label "CuRE" ;
  rdfs:comment "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002232 a rdfs:Class ;
  rdfs:label "selection_marker" ;
  rdfs:comment "A genetic feature that encodes a trait used for artificial selection of a subpopulation." ;
  rdfs:subClassOf obo:SO_0001645 .

obo:SO_0001482 a rdfs:Class ;
  rdfs:label "shadow_enhancer" ;
  rdfs:comment "An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene." ;
  rdfs:subClassOf obo:SO_0000165 .

obo:SO_0001914 a rdfs:Class ;
  rdfs:label "rDNA_replication_fork_barrier" ;
  rdfs:comment "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000591 a rdfs:Class ;
  rdfs:label "pseudoknot" ;
  rdfs:comment "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." ;
  rdfs:subClassOf obo:SO_0000002 .

obo:SO_0001679 a rdfs:Class ;
  rdfs:label "transcription_regulatory_region" ;
  rdfs:comment "A regulatory region that is involved in the control of the process of transcription." .

obo:BS_00148 a rdfs:Class .

obo:SO_1001285 a rdfs:Class ;
  rdfs:label "UGA_stop_codon_signal" ;
  rdfs:comment "A stop codon signal for a UGA stop codon redefinition." ;
  rdfs:subClassOf obo:SO_1001288 .

obo:SO_1000143 a rdfs:Class ;
  rdfs:label "laevosynaptic_chromosome" ;
  rdfs:comment "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." ;
  rdfs:subClassOf obo:SO_1000136 .

obo:SO_0000710 a rdfs:Class ;
  rdfs:label "gene_with_stop_codon_redefined_as_selenocysteine" ;
  rdfs:comment "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." ;
  rdfs:subClassOf obo:SO_0000697 .

obo:SO_0000833 a rdfs:Class ;
  rdfs:label "transcript_region" ;
  rdfs:comment "A region of a transcript." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000267 a rdfs:Class ;
  rdfs:label "phenylalanyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000568 a rdfs:Class ;
  rdfs:label "bidirectional_promoter" ;
  rdfs:comment "A promoter that can allow for transcription in both directions." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0000398 a rdfs:Class ;
  rdfs:label "U11_snRNA" ;
  rdfs:comment "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0000054 a rdfs:Class ;
  rdfs:label "aneuploid" ;
  rdfs:comment "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." ;
  rdfs:subClassOf obo:SO_1000182 .

obo:SO_0001614 a rdfs:Class ;
  rdfs:label "elongated_in_frame_polypeptide_N_terminal_elongation" ;
  rdfs:comment "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." ;
  rdfs:subClassOf obo:SO_0001611 .

obo:SO_1000039 a rdfs:Class ;
  rdfs:label "direct_tandem_duplication" ;
  rdfs:comment "A tandem duplication where the individual regions are in the same orientation." ;
  rdfs:subClassOf obo:SO_1000173 .

obo:SO_0000006 a rdfs:Class ;
  rdfs:label "PCR_product" ;
  rdfs:comment "A region amplified by a PCR reaction." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0000484 a rdfs:Class ;
  rdfs:label "three_prime_coding_exon_noncoding_region" ;
  rdfs:comment "The sequence of the 3' exon that is not coding." ;
  rdfs:subClassOf obo:SO_0001214 .

obo:SO_0000365 a rdfs:Class ;
  rdfs:label "integron" ;
  rdfs:comment "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_0000687 a rdfs:Class ;
  rdfs:label "deletion_junction" ;
  rdfs:comment "The space between two bases in a sequence which marks the position where a deletion has occurred." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001855 a rdfs:Class ;
  rdfs:label "MCB" ;
  rdfs:comment "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000999 a rdfs:Class ;
  rdfs:label "BAC_end" ;
  rdfs:comment "A region of sequence from the end of a BAC clone that may provide a highly specific marker." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0002135 a rdfs:Class ;
  rdfs:label "TR_D_Gene" ;
  rdfs:comment "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0002133 .

obo:SO_0100012 a rdfs:Class ;
  rdfs:label "peptide_coil" ;
  rdfs:comment "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001090 a rdfs:Class ;
  rdfs:label "covalent_binding_site" ;
  rdfs:comment "Binding involving a covalent bond." .

obo:SO_0000886 a rdfs:Class ;
  rdfs:label "recoded_by_translational_bypass" ;
  rdfs:comment "Recoded mRNA where a block of nucleotides is not translated." ;
  rdfs:subClassOf obo:SO_0000881 .

obo:SO_0001649 a rdfs:Class ;
  rdfs:label "nested_repeat" ;
  rdfs:comment "A repeat that is disrupted by the insertion of another element." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_1000158 a rdfs:Class ;
  rdfs:label "inverted_intrachromosomal_transposition" ;
  rdfs:comment "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." ;
  rdfs:subClassOf obo:SO_1000030 , obo:SO_1000041 .

obo:SO_0002306 a rdfs:Class ;
  rdfs:label "chromatin_regulatory_region" ;
  rdfs:comment "A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0000129 a rdfs:Class ;
  rdfs:label "gene_silenced_by_DNA_methylation" ;
  rdfs:comment "A gene that is silenced by DNA methylation." ;
  rdfs:subClassOf obo:SO_0000128 .

obo:SO_0000092 a rdfs:Class ;
  rdfs:label "ct_gene" ;
  rdfs:comment "A gene from chloroplast sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0001599 a rdfs:Class ;
  rdfs:label "3D_polypeptide_structure_variant" ;
  rdfs:comment "A sequence variant that changes the resulting polypeptide structure." ;
  rdfs:subClassOf obo:SO_0001539 .

obo:SO_0002310 a rdfs:Class ;
  rdfs:label "cryptic_promoter" ;
  rdfs:comment "The promoter of a cryptic gene." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0000928 a rdfs:Class ;
  rdfs:label "insert_AA" ;
  rdfs:comment "An edit to insert a AA dinucleotide." .

obo:SO_0002339 a rdfs:Class ;
  rdfs:label "scaRNA_gene" ;
  rdfs:comment "A gene that encodes for a scaRNA (small Cajal body-specific RNA)." ;
  rdfs:subClassOf obo:SO_0001267 .

obo:SO_0002210 a rdfs:Class ;
  rdfs:label "presence_absence_variation" ;
  rdfs:comment "A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome." ;
  rdfs:subClassOf obo:SO_0001019 .

obo:SO_0001011 a rdfs:Class ;
  rdfs:label "PNA_oligo" ;
  rdfs:comment "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." ;
  rdfs:subClassOf obo:SO_0001247 .

obo:SO_1000118 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_loss_of_function_of_polypeptide" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_1000028 a rdfs:Class ;
  rdfs:label "intrachromosomal_mutation" ;
  rdfs:comment "A chromosomal structure variation within a single chromosome." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0001999 a rdfs:Class ;
  rdfs:label "mating_type_region_motif" ;
  rdfs:comment "DNA motif that is a component of a mating type region." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001587 a rdfs:Class ;
  rdfs:label "stop_gained" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide." ;
  rdfs:subClassOf obo:SO_0001906 , obo:SO_0001992 .

obo:SO_0000456 a rdfs:Class ;
  rdfs:label "recombinationally_rearranged_gene" ;
  rdfs:comment "A gene that is recombinationally rearranged." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0002080 a rdfs:Class ;
  rdfs:label "incomplete_transcript_exonic_variant" ;
  rdfs:comment "A sequence variant that intersects the exon of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_0001891 a rdfs:Class ;
  rdfs:label "regulatory_region_amplification" ;
  rdfs:comment "A feature amplification of a region containing a regulatory region." ;
  rdfs:subClassOf obo:SO_0001880 .

obo:SO_0002248 a rdfs:Class ;
  rdfs:label "spurious_protein" ;
  rdfs:comment "A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0002001 a rdfs:Class ;
  rdfs:label "Y_region" ;
  rdfs:comment "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." ;
  rdfs:subClassOf obo:SO_0001999 .

obo:SO_0001491 a rdfs:Class ;
  rdfs:label "finished_genome" ;
  rdfs:comment "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0000416 a rdfs:Class ;
  rdfs:label "invalidated_by_partial_processing" ;
  rdfs:comment "An attribute to describe a feature that is invalidated due to partial processing." ;
  rdfs:subClassOf obo:SO_0000790 .

obo:SO_0000478 a rdfs:Class ;
  rdfs:label "C_gene_segment" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." ;
  rdfs:subClassOf obo:SO_0000460 .

obo:SO_0000974 a rdfs:Class .

obo:SO_0001251 a rdfs:Class ;
  rdfs:label "STS_map" ;
  rdfs:comment "An STS map is a physical map organized by the unique STS landmarks." ;
  rdfs:subClassOf obo:SO_0001249 .

obo:SO_1000084 a rdfs:Class ;
  rdfs:label "sequence_variant_decreasing_transcript_stability" ;
  rdfs:comment "Sequence variant decreases the stability (half-life) of the transcript." .

obo:SO_0000309 a rdfs:Class ;
  rdfs:label "computed_feature" .

obo:SO_0002049 a rdfs:Class ;
  rdfs:label "H3K27_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0000573 a rdfs:Class ;
  rdfs:label "rRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a ribosomal RNA (rRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0001856 a rdfs:Class ;
  rdfs:label "CCAAT_motif" ;
  rdfs:comment "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002215 a rdfs:Class ;
  rdfs:label "Zas1_recognition_motif" ;
  rdfs:comment "A DNA motif to which the S. pombe Zas1 protein binds. The consensus sequence is 5'-(Y)CCCCAY-3'." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000199 a rdfs:Class ;
  rdfs:label "translocation" ;
  rdfs:comment "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." ;
  rdfs:subClassOf obo:SO_0001785 .

obo:SO_0000141 a rdfs:Class ;
  rdfs:label "terminator" ;
  rdfs:comment "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0001869 a rdfs:Class ;
  rdfs:label "functional_candidate_gene" ;
  rdfs:comment "A candidate gene whose function has something in common biologically with the trait under investigation." ;
  rdfs:subClassOf obo:SO_0001867 .

obo:SO_0001210 a rdfs:Class ;
  rdfs:label "translational_frameshift" ;
  rdfs:comment "The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0000602 a rdfs:Class ;
  rdfs:label "guide_RNA" ;
  rdfs:comment "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000130 a rdfs:Class ;
  rdfs:label "post_translationally_regulated" ;
  rdfs:comment "An attribute describing a gene that is regulated after it has been translated." ;
  rdfs:subClassOf obo:SO_0000119 .

obo:BS_00040 a rdfs:Class .

obo:SO_0000043 a rdfs:Class ;
  rdfs:label "processed_pseudogene" ;
  rdfs:comment "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." ;
  rdfs:subClassOf obo:SO_0000336 .

obo:SO_0001737 a rdfs:Class ;
  rdfs:label "histone_acylation_region" ;
  rdfs:comment "A histone modification, whereby the histone protein is acylated at multiple sites in a region." ;
  rdfs:subClassOf obo:SO_0001700 .

obo:SO_0002205 a rdfs:Class ;
  rdfs:label "response_element" ;
  rdfs:comment "A regulatory element that acts in response to a stimulus, usually via transcription factor binding." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0002221 a rdfs:Class ;
  rdfs:label "eukaryotic_promoter" ;
  rdfs:comment "A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0000917 a rdfs:Class ;
  rdfs:label "insert_U" ;
  rdfs:comment "An edit to insert a U." .

obo:SO_0002130 a rdfs:Class ;
  rdfs:label "NSD_transcript" ;
  rdfs:comment "A transcript that contains a CDS but has no stop codon before the polyA site is reached." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_0001683 a rdfs:Class ;
  rdfs:label "sequence_motif" ;
  rdfs:comment "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000297 a rdfs:Class ;
  rdfs:label "D_loop" ;
  rdfs:comment "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000095 a rdfs:Class ;
  rdfs:label "leucoplast_gene" ;
  rdfs:comment "A plastid gene from leucoplast sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0000613 a rdfs:Class ;
  rdfs:label "bacterial_RNApol_promoter" ;
  rdfs:comment "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0002222 .

obo:SO_0001064 a rdfs:Class ;
  rdfs:label "active_peptide" ;
  rdfs:comment "Active peptides are proteins which are biologically active, released from a precursor molecule." ;
  rdfs:subClassOf obo:SO_0000419 .

obo:SO_0000349 a rdfs:Class ;
  rdfs:label "protein_match" ;
  rdfs:comment "A match against a protein sequence." ;
  rdfs:subClassOf obo:SO_0000343 .

obo:SO_0001266 a rdfs:Class ;
  rdfs:label "scRNA_gene" ;
  rdfs:comment "A gene encoding a small noncoding RNA that is generally found only in the cytoplasm." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_1000095 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_nonconservative_amino_acid_substitution" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001624 a rdfs:Class ;
  rdfs:label "3_prime_UTR_variant" ;
  rdfs:comment "A UTR variant of the 3' UTR." ;
  rdfs:subClassOf obo:SO_0001622 .

obo:SO_0001575 a rdfs:Class ;
  rdfs:label "splice_donor_variant" ;
  rdfs:comment "A splice variant that changes the 2 base pair region at the 5' end of an intron." ;
  rdfs:subClassOf obo:SO_0001629 .

obo:SO_0001530 a rdfs:Class ;
  rdfs:label "lysosomal_localization_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the lysosome." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_1000073 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_splice_acceptor" ;
  rdfs:comment "A sequence_variant_effect that changes the splice acceptor sequence." .

obo:SO_0000383 a rdfs:Class ;
  rdfs:label "MicF_RNA" ;
  rdfs:comment "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." ;
  rdfs:subClassOf obo:SO_0000644 .

obo:SO_0000840 a rdfs:Class ;
  rdfs:label "repeat_component" ;
  rdfs:comment "A region of a repeated sequence." ;
  rdfs:subClassOf obo:SO_0001412 .

obo:SO_0001170 a rdfs:Class ;
  rdfs:label "polinton" ;
  rdfs:comment "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0000543 a rdfs:Class ;
  rdfs:label "alternately_spliced_gene_encoding_greater_than_one_transcript" .

obo:SO_0000970 a rdfs:Class ;
  rdfs:label "theta_replication" ;
  rdfs:comment "This has been obsoleted as it represents a process. replaced_by: GO:0070582" .

obo:SO_0000292 a rdfs:Class ;
  rdfs:label "repetitive_element" .

obo:SO_0000685 a rdfs:Class ;
  rdfs:label "DNaseI_hypersensitive_site" ;
  rdfs:comment "DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I." ;
  rdfs:subClassOf obo:SO_0000322 .

obo:SO_1000049 a rdfs:Class ;
  rdfs:label "sequence_variation_affecting_transcript" ;
  rdfs:comment "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." .

obo:SO_0000596 a rdfs:Class ;
  rdfs:label "H_ACA_box_snoRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0001313 a rdfs:Class ;
  rdfs:label "N6_N6_2_prime_O_trimethyladenosine" ;
  rdfs:comment "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001753 a rdfs:Class ;
  rdfs:label "SL8_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0000774 a rdfs:Class ;
  rdfs:label "metabolic_island" ;
  rdfs:comment "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_0000449 a rdfs:Class ;
  rdfs:label "random_sequence" ;
  rdfs:comment "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." ;
  rdfs:subClassOf obo:SO_0000351 .

obo:SO_0000816 a rdfs:Class ;
  rdfs:label "rescue_gene" ;
  rdfs:comment "A gene that rescues." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0002202 a rdfs:Class ;
  rdfs:label "repeat_instability_region" ;
  rdfs:comment "A repeat region that is prone to expansions and/or contractions." ;
  rdfs:subClassOf obo:SO_0000705 .

obo:SO_0001051 a rdfs:Class ;
  rdfs:label "nested_region" .

obo:SO_0000860 a rdfs:Class ;
  rdfs:label "syntenic" ;
  rdfs:comment "Attribute describing sequence regions occurring in same order on chromosome of different species." ;
  rdfs:subClassOf obo:SO_0000856 .

obo:SO_0001000 a rdfs:Class ;
  rdfs:label "cytosolic_16S_rRNA" ;
  rdfs:comment "Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes." ;
  rdfs:subClassOf obo:SO_0000650 .

obo:SO_0000059 a rdfs:Class ;
  rdfs:label "nuclease_binding_site" ;
  rdfs:comment "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." ;
  rdfs:subClassOf obo:SO_0001654 .

obo:SO_0001790 a rdfs:Class ;
  rdfs:label "paired_end_fragment" ;
  rdfs:comment "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_0000465 a rdfs:Class ;
  rdfs:label "inversion_derived_deficiency_plus_duplication" ;
  rdfs:comment "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." ;
  rdfs:subClassOf obo:SO_1000029 , obo:SO_1000038 .

obo:SO_0001783 a rdfs:Class .

obo:SO_0002108 a rdfs:Class ;
  rdfs:label "transcribed_unitary_pseudogene" ;
  rdfs:comment "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species." ;
  rdfs:subClassOf obo:SO_0001759 .

obo:SO_0000275 a rdfs:Class ;
  rdfs:label "snoRNA" ;
  rdfs:comment "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." ;
  rdfs:subClassOf obo:SO_0002247 .

obo:SO_1000160 a rdfs:Class ;
  rdfs:label "unoriented_insertional_duplication" ;
  rdfs:comment "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." ;
  rdfs:subClassOf obo:SO_1000154 .

obo:SO_0001710 a rdfs:Class ;
  rdfs:label "H3K79_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." ;
  rdfs:subClassOf obo:SO_0001735 .

obo:SO_0001594 a rdfs:Class ;
  rdfs:label "plus_1_frameshift_variant" ;
  rdfs:comment "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." ;
  rdfs:subClassOf obo:SO_0001589 .

obo:SO_0001271 a rdfs:Class ;
  rdfs:label "tmRNA_gene" ;
  rdfs:comment "A bacterial RNA with both tRNA and mRNA like properties." ;
  rdfs:subClassOf obo:SO_0002342 .

obo:SO_0001880 a rdfs:Class ;
  rdfs:label "feature_amplification" ;
  rdfs:comment "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_0002380 a rdfs:Class ;
  rdfs:label "pseudouridylation_guide_snoRNA_gene" ;
  rdfs:comment "A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." ;
  rdfs:subClassOf obo:SO_0002376 .

obo:SO_1000180 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_gene_structure" ;
  rdfs:comment "A sequence_variant_effect that changes the gene structure." .

obo:SO_0001480 a rdfs:Class ;
  rdfs:label "PAC_end" ;
  rdfs:comment "A region of sequence from the end of a PAC clone that may provide a highly specific marker." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0000156 a rdfs:Class ;
  rdfs:label "cosmid" ;
  rdfs:comment "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0001121 a rdfs:Class ;
  rdfs:label "polypeptide_nest_left_right_motif" ;
  rdfs:comment "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0001120 .

obo:SO_0001411 a rdfs:Class ;
  rdfs:label "biological_region" ;
  rdfs:comment "A region defined by its disposition to be involved in a biological process." ;
  rdfs:subClassOf obo:SO_0000001 .

obo:SO_0002129 a rdfs:Class ;
  rdfs:label "mt_tRNA" ;
  rdfs:comment "Mitochondrial transfer RNA." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_1000089 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_no_change_of_translational_product" ;
  rdfs:comment "The sequence variant at RNA level does not lead to any change in polypeptide." .

obo:SO_0000064 a rdfs:Class ;
  rdfs:label "gene_by_transcript_attribute" ;
  rdfs:comment "This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004." .

obo:SO_0000622 a rdfs:Class ;
  rdfs:label "C_box" ;
  rdfs:comment "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000032 a rdfs:Class ;
  rdfs:label "DNA_aptamer" ;
  rdfs:comment "DNA molecules that have been selected from random pools based on their ability to bind other molecules." ;
  rdfs:subClassOf obo:SO_0000031 .

obo:SO_0000902 a rdfs:Class ;
  rdfs:label "transgene" ;
  rdfs:comment "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_1000175 a rdfs:Class ;
  rdfs:label "partially_characterized_chromosomal_mutation" ;
  rdfs:comment "A chromosome structure variant that has not been characterized fully." ;
  rdfs:subClassOf obo:SO_1000170 .

obo:BS_00178 a rdfs:Class .

obo:SO_0001932 a rdfs:Class ;
  rdfs:label "restriction_enzyme_five_prime_single_strand_overhang" ;
  rdfs:comment "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." ;
  rdfs:subClassOf obo:SO_0001695 .

obo:SO_0002120 a rdfs:Class ;
  rdfs:label "three_prime_overlapping_ncrna" ;
  rdfs:comment "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_1001259 a rdfs:Class ;
  rdfs:label "CDS_supported_by_EST_or_cDNA_data" ;
  rdfs:comment "A CDS that is supported by similarity to EST or cDNA data." ;
  rdfs:subClassOf obo:SO_1001251 .

obo:SO_0001236 a rdfs:Class ;
  rdfs:label "base" ;
  rdfs:comment "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:BS_00125 a rdfs:Class .

obo:SO_0000736 a rdfs:Class ;
  rdfs:label "organelle_sequence" ;
  rdfs:comment "A sequence of DNA that originates from a an organelle." ;
  rdfs:subClassOf obo:SO_0000735 .

obo:SO_0001984 a rdfs:Class ;
  rdfs:label "silent_mating_type_cassette_array" ;
  rdfs:comment "A gene cassette array that corresponds to a silenced version of a mating type region." ;
  rdfs:subClassOf obo:SO_0005854 .

obo:SO_0000009 a rdfs:Class ;
  rdfs:label "gene_class" .

obo:SO_0002168 a rdfs:Class ;
  rdfs:label "RNA_thermometer" ;
  rdfs:comment "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001145 a rdfs:Class ;
  rdfs:label "st_turn_right_handed_type_two" ;
  rdfs:comment "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0001141 .

obo:SO_0001578 a rdfs:Class ;
  rdfs:label "stop_lost" ;
  rdfs:comment "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." ;
  rdfs:subClassOf obo:SO_0001590 , obo:SO_0001907 , obo:SO_0001992 .

obo:SO_0001400 a rdfs:Class ;
  rdfs:label "modified_L_lysine" ;
  rdfs:comment "A post translationally modified lysine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000118 a rdfs:Class ;
  rdfs:label "transcript_with_translational_frameshift" ;
  rdfs:comment "A transcript with a translational frameshift." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000725 a rdfs:Class ;
  rdfs:label "transit_peptide" ;
  rdfs:comment "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0000408 a rdfs:Class ;
  rdfs:label "site" ;
  rdfs:comment "The interbase position where something (eg an aberration) occurred." .

obo:SO_0001276 a rdfs:Class ;
  rdfs:label "modified_guanosine" ;
  rdfs:comment "A guanosine base that has been modified." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_0001795 a rdfs:Class ;
  rdfs:label "regional_centromere" ;
  rdfs:comment "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." ;
  rdfs:subClassOf obo:SO_0000577 .

obo:SO_0000889 a rdfs:Class ;
  rdfs:label "paternally_imprinted_gene" ;
  rdfs:comment "A gene that is paternally imprinted." ;
  rdfs:subClassOf obo:SO_0000704 , obo:SO_0000898 .

obo:SO_1000154 a rdfs:Class ;
  rdfs:label "insertional_duplication" ;
  rdfs:comment "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." ;
  rdfs:subClassOf obo:SO_1000037 .

obo:SO_0001921 a rdfs:Class ;
  rdfs:label "mitochondrial_contig" ;
  rdfs:comment "A contig of mitochondria derived sequences." ;
  rdfs:subClassOf obo:SO_0000149 .

obo:SO_0001715 a rdfs:Class ;
  rdfs:label "ISRE" ;
  rdfs:comment "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." ;
  rdfs:subClassOf obo:SO_0000235 .

obo:SO_0001824 a rdfs:Class ;
  rdfs:label "disruptive_inframe_insertion" ;
  rdfs:comment "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." ;
  rdfs:subClassOf obo:SO_0001821 .

obo:SO_0002192 a rdfs:Class ;
  rdfs:label "flanking_repeat" ;
  rdfs:comment "A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites)." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0002179 a rdfs:Class ;
  rdfs:label "MNV_artifact" ;
  rdfs:comment "An MNV that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002176 .

obo:SO_0001493 a rdfs:Class ;
  rdfs:label "centromere_DNA_Element_I" ;
  rdfs:comment "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0000808 a rdfs:Class ;
  rdfs:label "validated_cDNA_clone" ;
  rdfs:comment "A cDNA clone that has been validated." ;
  rdfs:subClassOf obo:SO_0000317 .

obo:SO_0001904 a rdfs:Class ;
  rdfs:label "antisense_lncRNA" ;
  rdfs:comment "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." ;
  rdfs:subClassOf obo:SO_0000644 , obo:SO_0001877 .

obo:SO_0002296 a rdfs:Class ;
  rdfs:label "TFRS_module" ;
  rdfs:comment "The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. " ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_1001274 a rdfs:Class ;
  rdfs:label "SECIS_element" ;
  rdfs:comment "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." ;
  rdfs:subClassOf obo:SO_1001268 .

obo:SO_0000489 a rdfs:Class ;
  rdfs:label "VJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001040 a rdfs:Class ;
  rdfs:label "integrated_plasmid" ;
  rdfs:comment "A plasmid sequence that is integrated within the host chromosome." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_0001544 a rdfs:Class ;
  rdfs:label "editing_variant" ;
  rdfs:comment "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." ;
  rdfs:subClassOf obo:SO_0001543 .

obo:SO_0002329 a rdfs:Class ;
  rdfs:label "minus_1_translational_frameshift" ;
  rdfs:comment "The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." ;
  rdfs:subClassOf obo:SO_0001210 .

obo:SO_0000875 a rdfs:Class ;
  rdfs:label "bound_by_protein" ;
  rdfs:comment "An attribute describing a sequence that is bound by a protein." ;
  rdfs:subClassOf obo:SO_0000277 .

obo:SO_0001631 a rdfs:Class ;
  rdfs:label "upstream_gene_variant" ;
  rdfs:comment "A sequence variant located 5' of a gene." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0000535 a rdfs:Class ;
  rdfs:label "V_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0002226 a rdfs:Class ;
  rdfs:label "group_IIC_intron" ;
  rdfs:comment "A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA." ;
  rdfs:subClassOf obo:SO_0000603 .

obo:SO_0001072 a rdfs:Class ;
  rdfs:label "extramembrane_polypeptide_region" ;
  rdfs:comment "Polypeptide region that is localized outside of a lipid bilayer." ;
  rdfs:subClassOf obo:SO_0001070 .

obo:SO_0000423 a rdfs:Class ;
  rdfs:label "R_LTR_region" ;
  rdfs:comment "The R segment of the long terminal repeats." ;
  rdfs:subClassOf obo:SO_0000848 .

obo:SO_0002258 a rdfs:Class ;
  rdfs:label "teb1_recognition_motif" ;
  rdfs:comment "A binding motif with the consensus sequence TTAGGG to which Teb1 binds." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001726 a rdfs:Class ;
  rdfs:label "H3K27_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001732 .

obo:SO_0000963 a rdfs:Class ;
  rdfs:label "linear_single_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." ;
  rdfs:subClassOf obo:SO_0000962 .

obo:SO_0000562 a rdfs:Class ;
  rdfs:label "nonamer_of_recombination_feature_of_vertebrate_immune_system_gene" ;
  rdfs:comment "Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000939 .

obo:SO_0000666 a rdfs:Class ;
  rdfs:label "mobile_intron" ;
  rdfs:comment "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." ;
  rdfs:subClassOf obo:SO_0000188 , obo:SO_0001037 .

obo:SO_0000714 a rdfs:Class ;
  rdfs:label "nucleotide_motif" ;
  rdfs:comment "A region of nucleotide sequence corresponding to a known motif." ;
  rdfs:subClassOf obo:SO_0001683 .

obo:SO_0000636 a rdfs:Class ;
  rdfs:label "spliced_leader_RNA" ;
  rdfs:comment "Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0001556 a rdfs:Class ;
  rdfs:label "increased_translational_product_level" ;
  rdfs:comment "A sequence variant which increases the translational product level with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001553 .

obo:SO_0000897 a rdfs:Class ;
  rdfs:label "allelically_excluded_gene" ;
  rdfs:comment "A gene that is allelically_excluded." ;
  rdfs:subClassOf obo:SO_0000898 .

obo:SO_0000050 a rdfs:Class ;
  rdfs:label "gene_part" ;
  rdfs:comment "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." .

obo:SO_1001281 a rdfs:Class ;
  rdfs:label "flanking_three_prime_quadruplet_recoding_signal" ;
  rdfs:comment "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." ;
  rdfs:subClassOf obo:SO_1001277 .

obo:SO_0001501 a rdfs:Class ;
  rdfs:label "peptide_collection" ;
  rdfs:comment "A collection of peptide sequences." ;
  rdfs:subClassOf obo:SO_0001260 .

obo:SO_0001910 a rdfs:Class ;
  rdfs:label "frameshift_truncation" ;
  rdfs:comment "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." ;
  rdfs:subClassOf obo:SO_0001589 , obo:SO_0001906 .

obo:SO_0001009 a rdfs:Class ;
  rdfs:label "DNA_constraint_sequence" ;
  rdfs:comment "A double-stranded DNA used to control macromolecular structure and function." ;
  rdfs:subClassOf obo:SO_0000442 .

obo:SO_0001306 a rdfs:Class ;
  rdfs:label "two_methylthio_N6_threonyl_carbamoyladenosine" ;
  rdfs:comment "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001721 a rdfs:Class ;
  rdfs:label "H3K27_acylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." .

obo:SO_0002236 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_18S_gene" ;
  rdfs:comment "A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes." ;
  rdfs:subClassOf obo:SO_0002362 .

obo:SO_0000223 a rdfs:Class ;
  rdfs:label "methionine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding methionyl tRNA (SO:0000266)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0005857 a rdfs:Class ;
  rdfs:label "selenocysteinyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0002269 a rdfs:Class ;
  rdfs:label "R2_LINE_retrotransposon" ;
  rdfs:comment "R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes." ;
  rdfs:subClassOf obo:SO_0000194 .

obo:SO_0000342 a rdfs:Class ;
  rdfs:label "site_specific_recombination_target_region" ;
  rdfs:comment "A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis." ;
  rdfs:subClassOf obo:SO_0000299 .

obo:SO_0001653 a rdfs:Class ;
  rdfs:label "retinoic_acid_responsive_element" ;
  rdfs:comment "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." ;
  rdfs:subClassOf obo:SO_0000235 .

obo:SO_0100014 a rdfs:Class ;
  rdfs:label "n_terminal_region" ;
  rdfs:comment "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0000524 a rdfs:Class ;
  rdfs:label "V_VJ_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001694 a rdfs:Class ;
  rdfs:label "single_strand_restriction_enzyme_cleavage_site" ;
  rdfs:comment "A restriction enzyme cleavage site whereby only one strand is cut." ;
  rdfs:subClassOf obo:SO_0001688 .

obo:SO_0001471 a rdfs:Class ;
  rdfs:label "RST_match" ;
  rdfs:comment "A match against an RST sequence." ;
  rdfs:subClassOf obo:SO_0000102 .

obo:SO_0001409 a rdfs:Class ;
  rdfs:label "biomaterial_region" ;
  rdfs:comment "A region which is intended for use in an experiment." ;
  rdfs:subClassOf obo:SO_0000001 .

obo:SO_1000016 a rdfs:Class ;
  rdfs:label "G_to_A_transition" ;
  rdfs:comment "A transition of a guanine to an adenine." ;
  rdfs:subClassOf obo:SO_1000014 .

obo:SO_0002163 a rdfs:Class ;
  rdfs:label "short_tandem_repeat_contraction" ;
  rdfs:comment "A short tandem repeat variant containing fewer repeat units than the reference sequence." ;
  rdfs:subClassOf obo:SO_0002161 .

obo:SO_0000557 a rdfs:Class ;
  rdfs:label "three_prime_clip" ;
  rdfs:comment "3'-most region of a precursor transcript that is clipped off during processing." ;
  rdfs:subClassOf obo:SO_0000303 .

obo:SO_0001094 a rdfs:Class ;
  rdfs:label "polypeptide_calcium_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0000890 a rdfs:Class ;
  rdfs:label "post_translationally_regulated_gene" ;
  rdfs:comment "A gene that is post translationally regulated." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000473 a rdfs:Class ;
  rdfs:label "negatively_autoregulated" ;
  rdfs:comment "The gene product is involved in its own transcriptional regulation where it decreases transcription." ;
  rdfs:subClassOf obo:SO_0000126 , obo:SO_0000471 .

obo:SO_0000017 a rdfs:Class ;
  rdfs:label "PSE_motif" ;
  rdfs:comment "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000026 a rdfs:Class ;
  rdfs:label "RNA_junction_loop" ;
  rdfs:subClassOf obo:SO_0000715 .

obo:SO_0001363 a rdfs:Class ;
  rdfs:label "five_aminomethyl_two_thiouridine" ;
  rdfs:comment "5_aminomethyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:BS_00156 a rdfs:Class .

obo:SO_0001567 a rdfs:Class ;
  rdfs:label "stop_retained_variant" ;
  rdfs:comment "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." ;
  rdfs:subClassOf obo:SO_0001590 , obo:SO_0001819 .

obo:SO_0000805 a rdfs:Class ;
  rdfs:label "engineered_foreign_region" ;
  rdfs:comment "A region that is engineered and foreign." ;
  rdfs:subClassOf obo:SO_0000001 , obo:SO_0000804 .

obo:SO_0001015 a rdfs:Class ;
  rdfs:label "wobble_base_pair" ;
  rdfs:comment "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." ;
  rdfs:subClassOf obo:SO_0000028 .

obo:SO_0001779 a rdfs:Class ;
  rdfs:label "pedigree_specific_variant" ;
  rdfs:comment "A variant that is found only by individuals that belong to the same pedigree." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0001106 a rdfs:Class ;
  rdfs:label "asx_motif" ;
  rdfs:comment "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:BS_00234 a rdfs:Class .

obo:SO_0002005 a rdfs:Class ;
  rdfs:label "DSR_motif" ;
  rdfs:comment "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0002119 a rdfs:Class ;
  rdfs:label "allelic_frequency" ;
  rdfs:comment "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_0001786 a rdfs:Class ;
  rdfs:label "loss_of_heterozygosity" ;
  rdfs:comment "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:BS_00055 a rdfs:Class .

obo:SO_0001583 a rdfs:Class ;
  rdfs:label "missense_variant" ;
  rdfs:comment "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." ;
  rdfs:subClassOf obo:SO_0001992 .

obo:SO_0000617 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter_type_1" ;
  rdfs:comment "This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species." ;
  rdfs:subClassOf obo:SO_0000171 .

obo:SO_0002251 a rdfs:Class ;
  rdfs:label "signal_peptide_region_of_CDS" ;
  rdfs:comment "A CDS region corresponding to a signal peptide of a polypeptide." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0001282 a rdfs:Class ;
  rdfs:label "five_methylcytidine" ;
  rdfs:comment "5-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0001642 a rdfs:Class ;
  rdfs:label "mathematically_defined_repeat" ;
  rdfs:comment "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0000674 a rdfs:Class ;
  rdfs:label "non_canonical_splice_site" ;
  rdfs:comment "A splice site where the donor and acceptor sites differ from the canonical form." .

obo:SO_0002219 a rdfs:Class ;
  rdfs:label "functionally_normal" ;
  rdfs:comment "A sequence variant in which the function of a gene product is retained with respect to a reference." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:SO_0000304 a rdfs:Class ;
  rdfs:label "type_II_enzyme_restriction_site" ;
  rdfs:comment "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." .

obo:SO_0001030 a rdfs:Class ;
  rdfs:label "forward" ;
  rdfs:comment "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." ;
  rdfs:subClassOf obo:SO_0001029 .

obo:SO_0001132 a rdfs:Class ;
  rdfs:label "asx_turn_right_handed_type_one" ;
  rdfs:comment "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0000912 .

obo:SO_0001225 a rdfs:Class ;
  rdfs:label "gene_silenced_by_histone_modification" ;
  rdfs:comment "A gene that is silenced by histone modification." ;
  rdfs:subClassOf obo:SO_0000127 .

obo:SO_0001293 a rdfs:Class ;
  rdfs:label "five_formyl_two_prime_O_methylcytidine" ;
  rdfs:comment "5-formyl-2'-O-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0001425 a rdfs:Class ;
  rdfs:label "ligation_based_read" ;
  rdfs:comment "A read produced by ligation based sequencing technologies." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:BS_00072 a rdfs:Class .

obo:SO_0000785 a rdfs:Class ;
  rdfs:label "cloned_region" ;
  rdfs:comment "The region of sequence that has been inserted and is being propagated by the clone." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:BS_00136 a rdfs:Class .

obo:SO_0001399 a rdfs:Class ;
  rdfs:label "modified_L_serine" ;
  rdfs:comment "A post translationally modified serine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001865 a rdfs:Class ;
  rdfs:label "CDRE_motif" ;
  rdfs:comment "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002391 a rdfs:Class ;
  rdfs:label "abolished_transcription_level_variant" ;
  rdfs:comment "Complete lack of transcription of a gene, as a consequence of a variant in the gene or a regulatory region." ;
  rdfs:subClassOf obo:SO_0001541 .

obo:SO_0000580 a rdfs:Class ;
  rdfs:label "methylation_guide_snoRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a methylation guide small nucleolar RNA." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0000708 a rdfs:Class ;
  rdfs:label "SL1_acceptor_site" ;
  rdfs:comment "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." ;
  rdfs:subClassOf obo:SO_0000706 .

obo:SO_0001379 a rdfs:Class ;
  rdfs:label "five_taurinomethyl_two_thiouridine" ;
  rdfs:comment "5_taurinomethyl_2_thiouridineis a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0100005 a rdfs:Class ;
  rdfs:label "catmat_left_handed_four" ;
  rdfs:comment "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_1000067 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_minus_1_frameshift" ;
  rdfs:comment "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." .

obo:SO_1001193 a rdfs:Class ;
  rdfs:label "encodes_overlapping_polypeptides_different_start_and_stop" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." ;
  rdfs:subClassOf obo:SO_1001195 .

obo:SO_0001359 a rdfs:Class ;
  rdfs:label "five_carboxyhydroxymethyl_uridine_methyl_ester" ;
  rdfs:comment "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001346 a rdfs:Class ;
  rdfs:label "five_two_prime_O_dimethyluridine" ;
  rdfs:comment "5_2_prime_O_dimethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:BS_00331 a rdfs:Class .

obo:SO_0000047 a rdfs:Class ;
  rdfs:label "invert" ;
  rdfs:comment "To invert a subsection of sequence." .

obo:SO_0001873 a rdfs:Class ;
  rdfs:label "interchromosomal_breakpoint" ;
  rdfs:comment "A rearrangement breakpoint between two different chromosomes." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0000640 a rdfs:Class ;
  rdfs:label "external_transcribed_spacer_region" ;
  rdfs:comment "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." ;
  rdfs:subClassOf obo:SO_0000638 .

obo:SO_0002243 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_23S_gene" ;
  rdfs:comment "A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0002017 a rdfs:Class ;
  rdfs:label "conserved_intergenic_variant" ;
  rdfs:comment "A sequence variant located in a conserved intergenic region, between genes." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0001925 a rdfs:Class ;
  rdfs:label "ARIA" ;
  rdfs:comment "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." ;
  rdfs:subClassOf obo:SO_0001927 .

obo:SO_0001757 a rdfs:Class ;
  rdfs:label "SL12_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0001164 a rdfs:Class ;
  rdfs:label "DPE1_motif" ;
  rdfs:comment "A promoter motif with consensus sequence CGGACGT." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001620 a rdfs:Class ;
  rdfs:label "mature_miRNA_variant" ;
  rdfs:comment "A transcript variant located with the sequence of the mature miRNA." ;
  rdfs:subClassOf obo:SO_0001619 .

obo:SO_0001428 a rdfs:Class ;
  rdfs:label "expressed_sequence_assembly" ;
  rdfs:comment "A sequence assembly derived from expressed sequences." ;
  rdfs:subClassOf obo:SO_0000353 .

obo:SO_0000100 a rdfs:Class ;
  rdfs:label "endogenous_retroviral_gene" ;
  rdfs:comment "A proviral gene with origin endogenous retrovirus." ;
  rdfs:subClassOf obo:SO_0000099 .

obo:SO_0001452 a rdfs:Class ;
  rdfs:label "histidine" ;
  rdfs:comment "A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000405 a rdfs:Class ;
  rdfs:label "Y_RNA" ;
  rdfs:comment "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000084 a rdfs:Class ;
  rdfs:label "micronuclear_sequence" ;
  rdfs:comment "DNA belonging to the micronuclei of a cell." ;
  rdfs:subClassOf obo:SO_0000736 .

obo:SO_0001357 a rdfs:Class ;
  rdfs:label "uridine_five_oxyacetic_acid_methyl_ester" ;
  rdfs:comment "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001083 a rdfs:Class ;
  rdfs:label "non_adjacent_residues" ;
  rdfs:comment "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." ;
  rdfs:subClassOf obo:SO_0001082 .

obo:SO_1000179 a rdfs:Class .

obo:SO_0001247 a rdfs:Class ;
  rdfs:label "synthetic_oligo" ;
  rdfs:comment "An oligo composed of synthetic nucleotides." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0002273 a rdfs:Class ;
  rdfs:label "I_LINE_retrotransposon" ;
  rdfs:comment "Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain." ;
  rdfs:subClassOf obo:SO_0000194 .

obo:BS_0000339 a rdfs:Class .

obo:SO_0000015 a rdfs:Class ;
  rdfs:label "DPE_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_1000062 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_nonsense_codon_change_in_transcript" ;
  rdfs:comment "The nucleotide change in the codon triplet creates a terminator codon." .

obo:SO_0001004 a rdfs:Class ;
  rdfs:label "low_complexity" ;
  rdfs:comment "When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0001110 a rdfs:Class ;
  rdfs:label "beta_bulge_loop_six" ;
  rdfs:comment "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." ;
  rdfs:subClassOf obo:SO_0001108 .

obo:SO_0000939 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_gene_recombination_signal_feature" ;
  rdfs:comment "Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0000231 a rdfs:Class ;
  rdfs:label "snRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a small nuclear RNA (SO:0000274)." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000060 a rdfs:Class ;
  rdfs:label "compound_chromosome_arm" ;
  rdfs:comment "One arm of a compound chromosome." ;
  rdfs:subClassOf obo:SO_1000042 .

obo:SO_0000696 a rdfs:Class ;
  rdfs:label "oligo" ;
  rdfs:comment "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0000763 a rdfs:Class ;
  rdfs:label "fosmid_clone" .

obo:SO_0000445 a rdfs:Class ;
  rdfs:label "five_prime_noncoding_exon" ;
  rdfs:comment "Non-coding exon in the 5' UTR." ;
  rdfs:subClassOf obo:SO_0000198 .

obo:SO_0000952 a rdfs:Class ;
  rdfs:label "oriV" ;
  rdfs:comment "An origin of vegetative replication in plasmids and phages." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0000669 a rdfs:Class ;
  rdfs:label "sequence_rearrangement_feature" ;
  rdfs:comment "A feature where a segment of DNA has been rearranged from what it was in the parent cell." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:SO_0001895 a rdfs:Class ;
  rdfs:label "TFBS_ablation" ;
  rdfs:comment "A feature ablation whereby the deleted region includes a transcription factor binding site." ;
  rdfs:subClassOf obo:SO_0001894 .

obo:SO_0001833 a rdfs:Class ;
  rdfs:label "V_region" ;
  rdfs:comment "The variable region of an immunoglobulin polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0001832 .

obo:SO_0001768 a rdfs:Class ;
  rdfs:label "fixed_variant" ;
  rdfs:comment "When a variant has become fixed in the population so that it is now the only variant." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_0002286 a rdfs:Class ;
  rdfs:label "YR_retrotransposon" ;
  rdfs:comment "Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs)." ;
  rdfs:subClassOf obo:SO_0000189 .

obo:SO_0000073 a rdfs:Class ;
  rdfs:label "five_prime_three_prime_overlap" ;
  rdfs:comment "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_0001368 a rdfs:Class ;
  rdfs:label "five_carbamoylmethyl_two_prime_O_methyluridine" ;
  rdfs:comment "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002365 a rdfs:Class ;
  rdfs:label "mt_SSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for mitochondrial SSU rRNA." ;
  rdfs:subClassOf obo:SO_0002363 .

obo:SO_0000286 a rdfs:Class ;
  rdfs:label "long_terminal_repeat" ;
  rdfs:comment "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0002006 a rdfs:Class ;
  rdfs:label "zinc_repressed_element" ;
  rdfs:comment "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000438 a rdfs:Class ;
  rdfs:label "gene_not_polyadenylated" .

obo:SO_0000271 a rdfs:Class ;
  rdfs:label "tryptophanyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001708 a rdfs:Class ;
  rdfs:label "H3K27_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001732 .

obo:SO_0001287 a rdfs:Class ;
  rdfs:label "five_two_prime_O_dimethylcytidine" ;
  rdfs:comment "5,2'-O-dimethylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0001257 a rdfs:Class ;
  rdfs:label "homing_endonuclease_binding_site" ;
  rdfs:comment "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." ;
  rdfs:subClassOf obo:SO_0000059 .

obo:BS_00033 a rdfs:Class .

obo:SO_1000045 a rdfs:Class ;
  rdfs:label "ring_chromosome" ;
  rdfs:comment "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." ;
  rdfs:subClassOf obo:SO_1000028 .

obo:SO_0000878 a rdfs:Class ;
  rdfs:label "monocistronic" ;
  rdfs:comment "An attribute describing a sequence that contains the code for one gene product." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0000799 a rdfs:Class ;
  rdfs:label "engineered_foreign_transposable_element" ;
  rdfs:comment "A transposable_element that is engineered and foreign." ;
  rdfs:subClassOf obo:SO_0000101 , obo:SO_0000720 , obo:SO_0000798 , obo:SO_0000805 .

obo:SO_0000698 a rdfs:Class ;
  rdfs:label "gene_with_stop_codon_redefined_as_pyrrolysine" ;
  rdfs:comment "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." ;
  rdfs:subClassOf obo:SO_0000693 , obo:SO_0000697 .

obo:SO_0001208 a rdfs:Class ;
  rdfs:label "five_prime_EST" ;
  rdfs:comment "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." ;
  rdfs:subClassOf obo:SO_0000345 .

obo:SO_0000236 a rdfs:Class ;
  rdfs:label "ORF" ;
  rdfs:comment "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." ;
  rdfs:subClassOf obo:SO_0000717 .

obo:SO_0000871 a rdfs:Class ;
  rdfs:label "polyadenylated_mRNA" ;
  rdfs:comment "An mRNA that is polyadenylated." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_0000036 a rdfs:Class ;
  rdfs:label "matrix_attachment_site" ;
  rdfs:comment "A DNA region that is required for the binding of chromatin to the nuclear matrix." ;
  rdfs:subClassOf obo:SO_0000626 .

obo:SO_0001884 a rdfs:Class ;
  rdfs:label "regulatory_region_translocation" ;
  rdfs:comment "A feature translocation where the region contains a regulatory region." ;
  rdfs:subClassOf obo:SO_0001881 .

obo:SO_0001603 a rdfs:Class ;
  rdfs:label "polypeptide_sequence_variant" ;
  rdfs:comment "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0001598 .

obo:SO_0001460 a rdfs:Class ;
  rdfs:label "insulator_binding_site" ;
  rdfs:comment "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." ;
  rdfs:subClassOf obo:SO_0001654 .

obo:SO_0001537 a rdfs:Class ;
  rdfs:label "structural_variant" ;
  rdfs:comment "A sequence variant that changes one or more structural features." ;
  rdfs:subClassOf obo:SO_0001060 .

obo:SO_0001374 a rdfs:Class ;
  rdfs:label "five_carboxymethyluridine" ;
  rdfs:comment "5_carboxymethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001027 a rdfs:Class ;
  rdfs:label "genotype" ;
  rdfs:comment "A genotype is a variant genome, complete or incomplete." ;
  rdfs:subClassOf obo:SO_0001507 .

obo:SO_0002262 a rdfs:Class ;
  rdfs:label "Watson_strand" ;
  rdfs:comment "An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_1000005 a rdfs:Class ;
  rdfs:label "complex_substitution" ;
  rdfs:comment "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." ;
  rdfs:subClassOf obo:SO_1000002 .

obo:SO_0001268 a rdfs:Class ;
  rdfs:label "snRNA_gene" ;
  rdfs:comment "A gene that encodes a small nuclear RNA." ;
  rdfs:subClassOf obo:SO_0002342 .

obo:SO_0000028 a rdfs:Class ;
  rdfs:label "base_pair" ;
  rdfs:comment "Two bases paired opposite each other by hydrogen bonds creating a secondary structure." ;
  rdfs:subClassOf obo:SO_0000002 .

obo:SO_0000551 a rdfs:Class ;
  rdfs:label "polyA_signal_sequence" ;
  rdfs:comment "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0000461 a rdfs:Class ;
  rdfs:label "inversion_derived_bipartite_deficiency" ;
  rdfs:comment "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." ;
  rdfs:subClassOf obo:SO_1000029 .

obo:SO_1000056 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_amino_acid_coding_codon_change_in_transcript" ;
  rdfs:comment "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." .

obo:SO_0000200 a rdfs:Class ;
  rdfs:label "five_prime_coding_exon" ;
  rdfs:comment "The 5' most coding exon." ;
  rdfs:subClassOf obo:SO_0000195 .

obo:SO_0001348 a rdfs:Class ;
  rdfs:label "two_prime_O_methylpseudouridine" ;
  rdfs:comment "2prime_O_methylpseudouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1000110 a rdfs:Class ;
  rdfs:label "frame_restoring_sequence_variant" ;
  rdfs:comment "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." .

obo:SO_0000729 a rdfs:Class ;
  rdfs:label "intein_containing" ;
  rdfs:comment "An attribute of protein-coding genes where the initial protein product contains an intein." ;
  rdfs:subClassOf obo:SO_0000010 .

obo:SO_0000420 a rdfs:Class ;
  rdfs:label "five_prime_terminal_inverted_repeat" ;
  rdfs:comment "An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon." ;
  rdfs:subClassOf obo:SO_0000481 .

obo:SO_0000281 a rdfs:Class ;
  rdfs:label "engineered_foreign_gene" ;
  rdfs:comment "A gene that is engineered and foreign." ;
  rdfs:subClassOf obo:SO_0000280 , obo:SO_0000285 , obo:SO_0000805 .

obo:SO_1000185 a rdfs:Class ;
  rdfs:label "sequence_variant_causes_intron_gain" ;
  rdfs:comment "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." .

obo:SO_1001270 a rdfs:Class ;
  rdfs:label "stop_codon_redefinition_as_pyrrolysine" .

obo:SO_0001672 a rdfs:Class ;
  rdfs:label "bacterial_RNApol_promoter_sigma54_element" ;
  rdfs:comment "A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0000613 .

obo:SO_0000827 a rdfs:Class .

obo:SO_0001988 a rdfs:Class ;
  rdfs:label "5_prime_UTR_premature_start_codon_gain_variant" ;
  rdfs:comment "A 5' UTR variant where a premature start codon is gained." ;
  rdfs:subClassOf obo:SO_0001983 .

obo:SO_0001948 a rdfs:Class ;
  rdfs:label "H3R2_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0000376 a rdfs:Class ;
  rdfs:label "RNA_6S" ;
  rdfs:comment "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0001809 a rdfs:Class ;
  rdfs:label "signal_anchor" ;
  rdfs:comment "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." ;
  rdfs:subClassOf obo:SO_0000418 .

obo:SO_0002102 a rdfs:Class ;
  rdfs:label "IG_V_pseudogene" ;
  rdfs:comment "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002098 .

obo:SO_0000851 a rdfs:Class ;
  rdfs:label "CDS_region" ;
  rdfs:comment "A region of a CDS." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_1000150 a rdfs:Class ;
  rdfs:label "cyclic_translocation" ;
  rdfs:comment "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." ;
  rdfs:subClassOf obo:SO_0002060 .

obo:SO_0000819 a rdfs:Class ;
  rdfs:label "mitochondrial_chromosome" ;
  rdfs:comment "A chromosome originating in a mitochondria." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0000732 a rdfs:Class ;
  rdfs:label "predicted" ;
  rdfs:comment "An attribute describing an unverified region." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0000495 a rdfs:Class ;
  rdfs:label "three_prime_D_spacer" ;
  rdfs:comment "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." ;
  rdfs:subClassOf obo:SO_0000563 .

obo:SO_0002317 a rdfs:Class ;
  rdfs:label "absent_gene_product" ;
  rdfs:comment "A sequence variant that results in no gene product." ;
  rdfs:subClassOf obo:SO_0002055 , obo:SO_0002316 .

obo:SO_1000078 a rdfs:Class ;
  rdfs:label "sequence_variant_decreasing_rate_of_transcription" ;
  rdfs:comment "A sequence variation that decreases the rate a which transcription of the sequence occurs." .

obo:SO_0001389 a rdfs:Class ;
  rdfs:label "modified_L_aspartic_acid" ;
  rdfs:comment "A post translationally modified aspartic acid amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001187 a rdfs:Class ;
  rdfs:label "pseudouridylation_guide_snoRNA" ;
  rdfs:comment "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." ;
  rdfs:subClassOf obo:SO_0000594 .

obo:SO_0001667 a rdfs:Class ;
  rdfs:label "DCE_SIII" ;
  rdfs:comment "A sub element of the DCE core promoter element with consensus sequence AGC." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001936 a rdfs:Class ;
  rdfs:label "H3K36_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0000579 a rdfs:Class ;
  rdfs:label "edited_transcript_feature" ;
  rdfs:comment "A locatable feature on a transcript that is edited." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0002181 a rdfs:Class ;
  rdfs:label "ribozyme_gene" ;
  rdfs:comment "A gene that encodes a ribozyme." ;
  rdfs:subClassOf obo:SO_0002180 .

obo:SO_0002157 a rdfs:Class ;
  rdfs:label "Mat2P" ;
  rdfs:comment "A gene cassette array containing H+ mating type specific information." ;
  rdfs:subClassOf obo:SO_0001984 .

obo:BS_00152 a rdfs:Class .

obo:SO_0000004 a rdfs:Class ;
  rdfs:label "interior_coding_exon" ;
  rdfs:comment "A coding exon that is not the most 3-prime or the most 5-prime in a given transcript." ;
  rdfs:subClassOf obo:SO_0000195 .

obo:BS_00140 a rdfs:Class .

obo:SO_0001563 a rdfs:Class ;
  rdfs:label "copy_number_change" ;
  rdfs:comment "A sequence variant where copies of a feature (CNV) are either increased or decreased." ;
  rdfs:subClassOf obo:SO_0002160 .

obo:SO_0001176 a rdfs:Class ;
  rdfs:label "DHU_loop" ;
  rdfs:comment "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." ;
  rdfs:subClassOf obo:SO_0001172 .

obo:SO_0005853 a rdfs:Class ;
  rdfs:label "gene_cassette" ;
  rdfs:comment "A gene that can be substituted for a related gene at a different site in the genome." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000301 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_gene_recombination_feature" ;
  rdfs:comment "A feature where recombination has occurred for the purpose of generating a diversity in the immune system." ;
  rdfs:subClassOf obo:SO_0000300 .

obo:SO_0001602 a rdfs:Class ;
  rdfs:label "complex_change_of_translational_product_variant" ;
  rdfs:comment "A variant that changes the translational product with respect to the reference." ;
  rdfs:subClassOf obo:SO_0001539 .

obo:SO_0000958 a rdfs:Class ;
  rdfs:label "circular_double_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." ;
  rdfs:subClassOf obo:SO_0000955 .

obo:SO_0001201 a rdfs:Class ;
  rdfs:label "positive_sense_ssRNA_viral_sequence" ;
  rdfs:comment "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." ;
  rdfs:subClassOf obo:SO_0001199 .

obo:SO_0002271 a rdfs:Class ;
  rdfs:label "Jockey_LINE_retrotransposon" ;
  rdfs:comment "Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT)." ;
  rdfs:subClassOf obo:SO_0000194 .

obo:SO_0000109 a rdfs:Class ;
  rdfs:label "sequence_variant_obs" ;
  rdfs:comment "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." .

obo:SO_0000093 a rdfs:Class ;
  rdfs:label "chromoplast_gene" ;
  rdfs:comment "A gene from chromoplast_sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0001263 a rdfs:Class ;
  rdfs:label "ncRNA_gene" ;
  rdfs:comment "A gene that encodes a non-coding RNA." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001498 a rdfs:Class ;
  rdfs:label "YAC_end" ;
  rdfs:comment "A region of sequence from the end of a YAC clone that may provide a highly specific marker." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0002218 a rdfs:Class ;
  rdfs:label "functionally_abnormal" ;
  rdfs:comment "A sequence variant in which the function of a gene product is altered with respect to a reference." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:SO_0001671 a rdfs:Class ;
  rdfs:label "bacterial_RNApol_promoter_sigma_70_element" ;
  rdfs:comment "A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0000613 .

obo:SO_0001085 a rdfs:Class ;
  rdfs:label "sequence_conflict" ;
  rdfs:comment "Different sources report differing sequences." ;
  rdfs:subClassOf obo:SO_0001082 .

obo:SO_0000983 a rdfs:Class ;
  rdfs:label "strand_attribute" ;
  rdfs:comment "The attribute of how many strands are present in a nucleotide polymer." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001641 a rdfs:Class ;
  rdfs:label "lincRNA_gene" ;
  rdfs:comment "A gene that encodes a long, intervening non-coding RNA." ;
  rdfs:subClassOf obo:SO_0002127 .

obo:SO_0000341 a rdfs:Class ;
  rdfs:label "chromosome_band" ;
  rdfs:comment "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0000413 a rdfs:Class ;
  rdfs:label "sequence_difference" ;
  rdfs:comment "A region where the sequence differs from that of a specified sequence." ;
  rdfs:subClassOf obo:SO_0000700 .

obo:SO_0002185 a rdfs:Class ;
  rdfs:label "bidirectional_promoter_lncRNA_gene" ;
  rdfs:comment "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand." ;
  rdfs:subClassOf obo:SO_0002127 .

obo:SO_0002229 a rdfs:Class ;
  rdfs:label "CDS_three_prime_extension" ;
  rdfs:comment "A sequence variant extending the CDS at the 3' end, that causes elongation of the resulting polypeptide sequence at the C terminus." ;
  rdfs:subClassOf obo:SO_0002227 .

obo:SO_0000521 a rdfs:Class ;
  rdfs:label "V_VDJ_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001418 a rdfs:Class ;
  rdfs:label "transcribed_fragment" ;
  rdfs:comment "An experimental region, defined by a tiling array experiment to be transcribed at some level." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0002241 a rdfs:Class ;
  rdfs:label "rRNA_21S_gene" ;
  rdfs:comment "A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria." .

obo:SO_1000186 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_cryptic_splice_donor_activation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001866 a rdfs:Class ;
  rdfs:label "BAC_read_contig" ;
  rdfs:comment "A contig of BAC reads." ;
  rdfs:subClassOf obo:SO_0000149 .

obo:SO_0001717 a rdfs:Class ;
  rdfs:label "H2B_ubiquitination_site" ;
  rdfs:comment "A histone modification site on H2B where ubiquitin may be added." ;
  rdfs:subClassOf obo:SO_0001716 .

obo:SO_0001942 a rdfs:Class ;
  rdfs:label "H2BK20_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002143 .

obo:SO_0000300 a rdfs:Class ;
  rdfs:label "recombination_feature_of_rearranged_gene" ;
  rdfs:comment "A location where a gene is rearranged due to recombination during mitosis or meiosis." ;
  rdfs:subClassOf obo:SO_0000299 .

obo:SO_0001396 a rdfs:Class ;
  rdfs:label "modified_L_isoleucine" ;
  rdfs:comment "A post translationally modified isoleucine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000532 a rdfs:Class ;
  rdfs:label "V_D_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001657 a rdfs:Class ;
  rdfs:label "ligand_binding_site" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:SO_0000071 a rdfs:Class ;
  rdfs:label "inside_intron_parallel" ;
  rdfs:comment "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." ;
  rdfs:subClassOf obo:SO_0000069 .

obo:SO_0001977 a rdfs:Class ;
  rdfs:label "ribonuclease_site" ;
  rdfs:comment "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0000044 a rdfs:Class ;
  rdfs:label "pseudogene_by_unequal_crossing_over" ;
  rdfs:comment "A pseudogene caused by unequal crossing over at recombination." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_0000250 a rdfs:Class ;
  rdfs:label "modified_RNA_base_feature" ;
  rdfs:comment "A post_transcriptionally modified base." ;
  rdfs:subClassOf obo:SO_0001236 .

obo:SO_0001776 a rdfs:Class ;
  rdfs:label "paternal_variant" ;
  rdfs:comment "A variant in the genetic material inherited from the father." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0000814 a rdfs:Class ;
  rdfs:label "rescue" ;
  rdfs:comment "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0002324 a rdfs:Class ;
  rdfs:label "frameshift_variant_NMD_escaping" ;
  rdfs:comment "A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001589 , obo:SO_0002320 .

obo:SO_0002318 a rdfs:Class ;
  rdfs:label "altered_gene_product_sequence" ;
  rdfs:comment "A sequence variant that alters the sequence of a gene product." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:SO_0000377 a rdfs:Class ;
  rdfs:label "CsrB_RsmB_RNA" ;
  rdfs:comment "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_3000000 a rdfs:Class ;
  rdfs:label "gene_segment" ;
  rdfs:comment "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." ;
  rdfs:subClassOf obo:SO_0000842 .

obo:SO_0000280 a rdfs:Class ;
  rdfs:label "engineered_gene" ;
  rdfs:comment "A gene that is engineered." ;
  rdfs:subClassOf obo:SO_0000704 , obo:SO_0000804 .

obo:SO_0000346 a rdfs:Class ;
  rdfs:label "loxP_site" ;
  rdfs:comment "Cre-Recombination target sequence." ;
  rdfs:subClassOf obo:SO_0000947 .

obo:SO_0000062 a rdfs:Class ;
  rdfs:label "deficient_intrachromosomal_transposition" ;
  rdfs:comment "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." ;
  rdfs:subClassOf obo:SO_1000029 , obo:SO_1000041 .

obo:SO_0000741 a rdfs:Class ;
  rdfs:label "kinetoplast" ;
  rdfs:comment "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." ;
  rdfs:subClassOf obo:SO_0001026 , obo:SO_0001260 .

obo:SO_0001192 a rdfs:Class ;
  rdfs:label "GNA" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0000738 a rdfs:Class ;
  rdfs:label "nuclear_sequence" ;
  rdfs:comment "DNA belonging to the nuclear genome of cell." ;
  rdfs:subClassOf obo:SO_0000735 .

obo:SO_0000588 a rdfs:Class ;
  rdfs:label "autocatalytically_spliced_intron" ;
  rdfs:comment "A self spliced intron." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0001902 a rdfs:Class ;
  rdfs:label "splice_region" ;
  rdfs:comment "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_1000071 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_splicing" ;
  rdfs:comment "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." .

obo:SO_0001421 a rdfs:Class ;
  rdfs:label "splice_junction" ;
  rdfs:comment "The boundary between an intron and an exon." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001096 a rdfs:Class ;
  rdfs:label "polypeptide_copper_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0002356 a rdfs:Class ;
  rdfs:label "hpRNA" ;
  rdfs:comment "An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs)." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001658 a rdfs:Class ;
  rdfs:label "nested_tandem_repeat" ;
  rdfs:comment "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." ;
  rdfs:subClassOf obo:SO_0001649 .

obo:SO_0002088 a rdfs:Class ;
  rdfs:label "non_coding_transcript_splice_region_variant" ;
  rdfs:comment "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript." ;
  rdfs:subClassOf obo:SO_0001619 , obo:SO_0001630 .

obo:SO_0000569 a rdfs:Class ;
  rdfs:label "retrotransposed" ;
  rdfs:comment "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000825 a rdfs:Class ;
  rdfs:label "micronuclear_chromosome" ;
  rdfs:comment "A chromosome originating in a micronucleus." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001487 a rdfs:Class ;
  rdfs:label "high_quality_draft" ;
  rdfs:comment "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0001861 a rdfs:Class ;
  rdfs:label "sterol_regulatory_element" ;
  rdfs:comment "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000362 a rdfs:Class ;
  rdfs:label "invalidated_by_chimeric_cDNA" ;
  rdfs:comment "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." ;
  rdfs:subClassOf obo:SO_0000790 .

obo:SO_0002359 a rdfs:Class ;
  rdfs:label "Y_RNA_gene" ;
  rdfs:comment "A gene that encodes a Y RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0002143 a rdfs:Class ;
  rdfs:label "histone_2B_acetylation_site" ;
  rdfs:comment "A histone 2B modification where the modification is the acetylation of the residue." ;
  rdfs:subClassOf obo:SO_0001702 .

obo:SO_0000312 a rdfs:Class ;
  rdfs:label "experimentally_determined" ;
  rdfs:comment "Attribute to describe a feature that has been experimentally verified." ;
  rdfs:subClassOf obo:SO_0000789 .

obo:SO_0000153 a rdfs:Class ;
  rdfs:label "BAC" ;
  rdfs:comment "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0001451 a rdfs:Class ;
  rdfs:label "arginine" ;
  rdfs:comment "A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0002297 a rdfs:Class ;
  rdfs:label "TFRS_collection" ;
  rdfs:comment "The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0000148 a rdfs:Class ;
  rdfs:label "supercontig" ;
  rdfs:comment "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." ;
  rdfs:subClassOf obo:SO_0001876 .

obo:SO_0001938 a rdfs:Class ;
  rdfs:label "H2AK5_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002142 .

obo:SO_0002307 a rdfs:Class ;
  rdfs:label "DNA_loop" ;
  rdfs:comment "A region of DNA between two loop anchor positions that are held in close physical proximity." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0000904 a rdfs:Class ;
  rdfs:label "rearranged_at_DNA_level" ;
  rdfs:comment "An attribute to describe the sequence of a feature, where the DNA is rearranged." ;
  rdfs:subClassOf obo:SO_0000133 .

obo:SO_0100015 a rdfs:Class ;
  rdfs:label "c_terminal_region" ;
  rdfs:comment "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_1001272 a rdfs:Class ;
  rdfs:label "tRNA_intron" ;
  rdfs:comment "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." ;
  rdfs:subClassOf obo:SO_0001216 .

obo:SO_0000770 a rdfs:Class ;
  rdfs:label "tmRNA_acceptor_piece" ;
  rdfs:comment "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." ;
  rdfs:subClassOf obo:SO_0000847 .

obo:SO_0000113 a rdfs:Class ;
  rdfs:label "proviral_region" ;
  rdfs:comment "A viral sequence which has integrated into a host genome." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_0001646 a rdfs:Class ;
  rdfs:label "DArT_marker" ;
  rdfs:comment "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." ;
  rdfs:subClassOf obo:SO_0001645 .

obo:SO_0000470 a rdfs:Class ;
  rdfs:label "J_gene_segment" ;
  rdfs:comment "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." ;
  rdfs:subClassOf obo:SO_0000460 .

obo:SO_0001991 a rdfs:Class ;
  rdfs:label "consensus_AFLP_fragment" ;
  rdfs:comment "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." ;
  rdfs:subClassOf obo:SO_0000994 .

obo:SO_0000126 a rdfs:Class ;
  rdfs:label "transcriptionally_repressed" ;
  rdfs:comment "A repressor molecule is required for transcription to stop." ;
  rdfs:subClassOf obo:SO_0000123 .

obo:SO_0000178 a rdfs:Class ;
  rdfs:label "operon" ;
  rdfs:comment "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0001765 a rdfs:Class ;
  rdfs:label "rare_variant" ;
  rdfs:comment "When a variant from the genomic sequence is rarely found in the general population. The threshold for 'rare' varies between studies." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_0000662 a rdfs:Class ;
  rdfs:label "spliceosomal_intron" ;
  rdfs:comment "An intron which is spliced by the spliceosome." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0001102 a rdfs:Class ;
  rdfs:label "polypeptide_tungsten_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001512 a rdfs:Class ;
  rdfs:label "insertion_attribute" ;
  rdfs:comment "A quality of a chromosomal insertion,." ;
  rdfs:subClassOf obo:SO_0001508 .

obo:SO_0002077 a rdfs:Class ;
  rdfs:label "incomplete_transcript_5UTR_variant" ;
  rdfs:comment "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_0000128 a rdfs:Class ;
  rdfs:label "gene_silenced_by_DNA_modification" ;
  rdfs:comment "A gene that is silenced by DNA modification." ;
  rdfs:subClassOf obo:SO_0000127 , obo:SO_0000704 .

obo:SO_0000752 a rdfs:Class ;
  rdfs:label "gene_group_regulatory_region" ;
  rdfs:comment "A region that is involved in the regulation of transcription of a group of regulated genes." .

obo:SO_0002009 a rdfs:Class ;
  rdfs:label "selenocysteine_loss" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid." ;
  rdfs:subClassOf obo:SO_0002008 .

obo:SO_0000593 a rdfs:Class ;
  rdfs:label "C_D_box_snoRNA" ;
  rdfs:comment "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." ;
  rdfs:subClassOf obo:SO_0000275 .

obo:SO_0000867 a rdfs:Class ;
  rdfs:label "minus_2_frameshift" ;
  rdfs:comment "A frameshift caused by deleting two bases." ;
  rdfs:subClassOf obo:SO_0000865 .

obo:SO_0001074 a rdfs:Class ;
  rdfs:label "non_cytoplasmic_polypeptide_region" ;
  rdfs:comment "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." ;
  rdfs:subClassOf obo:SO_0001072 .

obo:SO_0001216 a rdfs:Class ;
  rdfs:label "endonuclease_spliced_intron" ;
  rdfs:comment "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0001299 a rdfs:Class ;
  rdfs:label "two_methylthio_N6_methyladenosine" ;
  rdfs:comment "2_methylthio_N6_methyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001239 a rdfs:Class ;
  rdfs:label "minor_TSS" ;
  rdfs:comment "A tanscription start site that is not the most frequently used for transcription of a gene." ;
  rdfs:subClassOf obo:SO_0000315 .

obo:SO_0000104 a rdfs:Class ;
  rdfs:label "polypeptide" ;
  rdfs:comment "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001407 a rdfs:Class ;
  rdfs:label "peptidyl" ;
  rdfs:comment "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." ;
  rdfs:subClassOf obo:SO_0000443 .

obo:SO_0005836 a rdfs:Class ;
  rdfs:label "regulatory_region" ;
  rdfs:comment "A region of sequence that is involved in the control of a biological process." ;
  rdfs:subClassOf obo:SO_0000831 .

obo:SO_0002139 a rdfs:Class ;
  rdfs:label "unconfirmed_transcript" ;
  rdfs:comment "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies." ;
  rdfs:subClassOf obo:SO_0002138 .

obo:SO_0000441 a rdfs:Class ;
  rdfs:label "ss_oligo" ;
  rdfs:comment "A single stranded oligonucleotide." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0001375 a rdfs:Class ;
  rdfs:label "three_two_prime_O_dimethyluridine" ;
  rdfs:comment "3_2prime_O_dimethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1001283 a rdfs:Class ;
  rdfs:label "UAA_stop_codon_signal" ;
  rdfs:comment "A stop codon signal for a UAA stop codon redefinition." ;
  rdfs:subClassOf obo:SO_1001288 .

obo:SO_0000839 a rdfs:Class ;
  rdfs:label "polypeptide_region" ;
  rdfs:comment "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000215 a rdfs:Class ;
  rdfs:label "cysteine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding cysteinyl tRNA (SO:0000258)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_1000097 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_amino_acid_deletion" ;
  rdfs:comment "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." .

obo:SO_0002388 a rdfs:Class ;
  rdfs:label "5_prime_UTR_uORF_stop_codon_gain_variant" ;
  rdfs:comment "A 5' UTR variant where a premature stop codon is gained in an upstream open reading frame." ;
  rdfs:subClassOf obo:SO_0002386 .

obo:SO_0002128 a rdfs:Class ;
  rdfs:label "mt_rRNA" ;
  rdfs:comment "Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes." ;
  rdfs:subClassOf obo:SO_0000252 .

obo:SO_0000655 a rdfs:Class ;
  rdfs:label "ncRNA" ;
  rdfs:comment "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." ;
  rdfs:subClassOf obo:SO_0000233 .

obo:SO_0001743 a rdfs:Class ;
  rdfs:label "copy_number_loss" ;
  rdfs:comment "A sequence alteration whereby the copy number of a given region is less than the reference sequence." ;
  rdfs:subClassOf obo:SO_0001019 .

obo:SO_0001584 a rdfs:Class .

obo:SO_0000322 a rdfs:Class ;
  rdfs:label "nuclease_hypersensitive_site" ;
  rdfs:comment "A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance." ;
  rdfs:subClassOf obo:SO_0000684 , obo:SO_0002331 .

obo:SO_0000716 a rdfs:Class ;
  rdfs:label "dicistronic_mRNA" ;
  rdfs:comment "An mRNA that has the quality dicistronic." ;
  rdfs:subClassOf obo:SO_0000079 , obo:SO_0000234 , obo:SO_0000634 .

obo:SO_0000583 a rdfs:Class ;
  rdfs:label "pre_edited_region" ;
  rdfs:comment "The region of a transcript that will be edited." ;
  rdfs:subClassOf obo:SO_0000579 .

obo:SO_0001916 a rdfs:Class ;
  rdfs:label "CAGE_tag" ;
  rdfs:comment "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." ;
  rdfs:subClassOf obo:SO_0000324 .

obo:SO_0002002 a rdfs:Class ;
  rdfs:label "Z1_region" ;
  rdfs:comment "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." ;
  rdfs:subClassOf obo:SO_0001999 .

obo:SO_0000644 a rdfs:Class ;
  rdfs:label "antisense_RNA" ;
  rdfs:comment "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000490 a rdfs:Class ;
  rdfs:label "VJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001256 a rdfs:Class ;
  rdfs:label "allopolyploid" ;
  rdfs:comment "A polyploid where the multiple chromosome set was derived from a different organism." ;
  rdfs:subClassOf obo:SO_0001254 .

obo:SO_0001732 a rdfs:Class ;
  rdfs:label "H3K27_methylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0000847 a rdfs:Class ;
  rdfs:label "tmRNA_region" ;
  rdfs:comment "A region of a tmRNA." ;
  rdfs:subClassOf obo:SO_0000834 .

obo:SO_0002377 a rdfs:Class ;
  rdfs:label "U14_snoRNA_gene" ;
  rdfs:comment "A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." ;
  rdfs:subClassOf obo:SO_0002375 .

obo:SO_0000612 a rdfs:Class ;
  rdfs:label "polypyrimidine_tract" ;
  rdfs:comment "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." ;
  rdfs:subClassOf obo:SO_0000841 .

obo:SO_0000190 a rdfs:Class ;
  rdfs:label "five_prime_intron" ;
  rdfs:comment "An intron that is the most 5-prime in a given transcript." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0001899 a rdfs:Class ;
  rdfs:label "dh_repeat" ;
  rdfs:comment "A repeat region which is part of the regional centromere outer repeat region." ;
  rdfs:subClassOf obo:SO_0001797 .

obo:SO_0000966 a rdfs:Class ;
  rdfs:label "circular_single_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." ;
  rdfs:subClassOf obo:SO_0000962 .

obo:SO_0000265 a rdfs:Class ;
  rdfs:label "lysyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001440 a rdfs:Class ;
  rdfs:label "tryptophan" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codon TGG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000509 a rdfs:Class ;
  rdfs:label "D_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0001059 a rdfs:Class ;
  rdfs:label "sequence_alteration" ;
  rdfs:comment "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." ;
  rdfs:subClassOf obo:SO_0002072 .

obo:SO_0001888 a rdfs:Class ;
  rdfs:label "TFBS_fusion" ;
  rdfs:comment "A fusion where the deletion brings together transcription factor binding sites." ;
  rdfs:subClassOf obo:SO_0001887 .

obo:SO_0000510 a rdfs:Class ;
  rdfs:label "VD_gene_segment" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." ;
  rdfs:subClassOf obo:SO_0000936 .

obo:SO_0000124 a rdfs:Class ;
  rdfs:label "transcriptionally_constitutive" ;
  rdfs:comment "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." ;
  rdfs:subClassOf obo:SO_0000123 .

obo:SO_0001676 a rdfs:Class ;
  rdfs:label "A_box_type_2" ;
  rdfs:comment "An A box within an RNA polymerase III type 2 promoter." ;
  rdfs:subClassOf obo:SO_0000619 .

obo:SO_0002117 a rdfs:Class ;
  rdfs:label "<new term>" .

obo:SO_0000069 a rdfs:Class ;
  rdfs:label "inside_intron" ;
  rdfs:comment "An attribute to describe a gene when it is located within the intron of another gene." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_0001111 a rdfs:Class ;
  rdfs:label "beta_strand" ;
  rdfs:comment "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001966 a rdfs:Class ;
  rdfs:label "5_carboxylcytosine" ;
  rdfs:comment "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." ;
  rdfs:subClassOf obo:SO_0001963 .

obo:SO_1001277 a rdfs:Class ;
  rdfs:label "three_prime_recoding_site" ;
  rdfs:comment "The recoding stimulatory signal located downstream of the recoding site." ;
  rdfs:subClassOf obo:SO_1001268 .

obo:SO_0000481 a rdfs:Class ;
  rdfs:label "terminal_inverted_repeat" ;
  rdfs:comment "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." ;
  rdfs:subClassOf obo:SO_0000294 .

obo:BS_00076 a rdfs:Class .

obo:SO_0000115 a rdfs:Class ;
  rdfs:label "transcript_feature" .

obo:BS_0000341 a rdfs:Class .

obo:SO_0000000 a rdfs:Class ;
  rdfs:label "Sequence_Ontology" .

obo:SO_1000126 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_transcript_secondary_structure" ;
  rdfs:comment "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." .

obo:SO_0001223 a rdfs:Class ;
  rdfs:label "silenced_by_histone_deacetylation" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." ;
  rdfs:subClassOf obo:SO_0001221 .

obo:BS_00026 a rdfs:Class .

obo:SO_0001704 a rdfs:Class ;
  rdfs:label "H3K14_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0001019 a rdfs:Class ;
  rdfs:label "copy_number_variation" ;
  rdfs:comment "A variation that increases or decreases the copy number of a given region." ;
  rdfs:subClassOf obo:SO_0000248 .

obo:SO_0001570 a rdfs:Class ;
  rdfs:label "cryptic_splice_acceptor" ;
  rdfs:comment "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." ;
  rdfs:subClassOf obo:SO_0001569 .

obo:SO_0000575 a rdfs:Class ;
  rdfs:label "scRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a small cytoplasmic RNA (scRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0000049 a rdfs:Class ;
  rdfs:label "translocate" ;
  rdfs:comment "To translocate a subsection of sequence." .

obo:SO_0000499 a rdfs:Class ;
  rdfs:label "virtual_sequence" ;
  rdfs:comment "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." ;
  rdfs:subClassOf obo:SO_0000353 .

obo:SO_0001663 a rdfs:Class ;
  rdfs:label "BREd_motif" ;
  rdfs:comment "A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000395 a rdfs:Class ;
  rdfs:label "U5_snRNA" ;
  rdfs:comment "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0000232 a rdfs:Class ;
  rdfs:label "snoRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding one or more small nucleolar RNAs (SO:0000275)." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000204 a rdfs:Class ;
  rdfs:label "five_prime_UTR" ;
  rdfs:comment "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." ;
  rdfs:subClassOf obo:SO_0000203 .

obo:SO_0001364 a rdfs:Class ;
  rdfs:label "five_methylaminomethyluridine" ;
  rdfs:comment "5_methylaminomethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1000060 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_conservative_missense_codon_change_in_transcript" ;
  rdfs:comment "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." .

obo:SO_0001062 a rdfs:Class ;
  rdfs:label "propeptide" ;
  rdfs:comment "Part of a peptide chain which is cleaved off during the formation of the mature protein." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0000969 a rdfs:Class ;
  rdfs:label "rolling_circle" ;
  rdfs:comment "This has been obsoleted as it represents a process. replaced_by: GO:0070581." .

obo:SO_0001245 a rdfs:Class ;
  rdfs:label "miRNA_stem" ;
  rdfs:comment "The stem of the hairpin loop formed by folding of the pre-miRNA." ;
  rdfs:subClassOf obo:SO_0001243 .

obo:SO_0001951 a rdfs:Class ;
  rdfs:label "H3K23_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:BS_00337 a rdfs:Class .

obo:SO_0001138 a rdfs:Class ;
  rdfs:label "gamma_turn" ;
  rdfs:comment "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." ;
  rdfs:subClassOf obo:SO_0001128 .

obo:SO_0001135 a rdfs:Class ;
  rdfs:label "beta_turn_left_handed_type_two" ;
  rdfs:comment "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:SO_0000558 a rdfs:Class ;
  rdfs:label "C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0000272 a rdfs:Class ;
  rdfs:label "tyrosyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001048 a rdfs:Class ;
  rdfs:label "inversion_site_part" ;
  rdfs:comment "A region located within an inversion site." ;
  rdfs:subClassOf obo:SO_0000342 .

obo:SO_0001693 a rdfs:Class ;
  rdfs:label "blunt_end_restriction_enzyme_cleavage_junction" ;
  rdfs:comment "A restriction enzyme cleavage site where both strands are cut at the same position." ;
  rdfs:subClassOf obo:SO_0001688 .

obo:SO_1000012 a rdfs:Class ;
  rdfs:label "C_to_T_transition_at_pCpG_site" ;
  rdfs:comment "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." ;
  rdfs:subClassOf obo:SO_1000011 .

obo:SO_0002171 a rdfs:Class ;
  rdfs:label "telomeric_D_loop" ;
  rdfs:comment "A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001284 a rdfs:Class ;
  rdfs:label "two_thiocytidine" ;
  rdfs:comment "2-thiocytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0002397 a rdfs:Class ;
  rdfs:label "cellular_mislocalization_variant" ;
  rdfs:comment "Trafficking of a polypeptide (i.e. protein) sequence to the wrong cellular location, as a consequence of a variant in the gene." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:SO_0000911 a rdfs:Class ;
  rdfs:label "predicted_by_ab_initio_computation" ;
  rdfs:comment "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." ;
  rdfs:subClassOf obo:SO_0000732 .

obo:SO_0001008 a rdfs:Class ;
  rdfs:label "tetraloop" ;
  rdfs:comment "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." ;
  rdfs:subClassOf obo:SO_0000313 .

obo:SO_0000355 a rdfs:Class ;
  rdfs:label "haplotype_block" ;
  rdfs:comment "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:BS_00036 a rdfs:Class .

obo:SO_0000625 a rdfs:Class ;
  rdfs:label "silencer" ;
  rdfs:comment "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." ;
  rdfs:subClassOf obo:SO_0000727 .

obo:SO_0001197 a rdfs:Class ;
  rdfs:label "S_GNA_oligo" ;
  rdfs:comment "An oligo composed of (S)-GNA residues." ;
  rdfs:subClassOf obo:SO_0001193 .

obo:SO_0001127 a rdfs:Class ;
  rdfs:label "serine_threonine_staple_motif" ;
  rdfs:comment "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001437 a rdfs:Class ;
  rdfs:label "leucine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000164 a rdfs:Class ;
  rdfs:label "three_prime_cis_splice_site" ;
  rdfs:comment "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." ;
  rdfs:subClassOf obo:SO_0001419 .

obo:SO_0000294 a rdfs:Class ;
  rdfs:label "inverted_repeat" ;
  rdfs:comment "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0000464 a rdfs:Class ;
  rdfs:label "decayed_exon" ;
  rdfs:comment "A non-functional descendant of an exon." ;
  rdfs:subClassOf obo:SO_0000462 .

obo:BS_00145 a rdfs:Class .

obo:SO_1001261 a rdfs:Class ;
  rdfs:label "recoded_mRNA" ;
  rdfs:comment "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_0001851 a rdfs:Class ;
  rdfs:label "iron_repressed_GATA_element" ;
  rdfs:comment "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." ;
  rdfs:subClassOf obo:SO_0001840 .

obo:SO_0001116 a rdfs:Class ;
  rdfs:label "right_handed_peptide_helix" ;
  rdfs:comment "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." ;
  rdfs:subClassOf obo:SO_0001114 .

obo:SO_0001037 a rdfs:Class ;
  rdfs:label "mobile_genetic_element" ;
  rdfs:comment "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." ;
  rdfs:subClassOf obo:SO_0000001 , obo:SO_0001411 .

obo:SO_0001840 a rdfs:Class ;
  rdfs:label "GATA_box" ;
  rdfs:comment "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." ;
  rdfs:subClassOf obo:SO_0000235 .

obo:SO_0001205 a rdfs:Class ;
  rdfs:label "SP6_RNA_Polymerase_Promoter" ;
  rdfs:comment "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0001204 .

obo:SO_0002314 a rdfs:Class ;
  rdfs:label "altered_gene_product_level" ;
  rdfs:comment "A sequence variant that alters the level or amount of gene product produced. This high level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed." ;
  rdfs:subClassOf obo:SO_0001536 .

obo:SO_0001133 a rdfs:Class ;
  rdfs:label "beta_turn" ;
  rdfs:comment "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." ;
  rdfs:subClassOf obo:SO_0001128 .

obo:SO_0001352 a rdfs:Class ;
  rdfs:label "two_thio_two_prime_O_methyluridine" ;
  rdfs:comment "2_thio_2prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000033 a rdfs:Class ;
  rdfs:label "RNA_aptamer" ;
  rdfs:comment "RNA molecules that have been selected from random pools based on their ability to bind other molecules." ;
  rdfs:subClassOf obo:SO_0000031 .

obo:SO_0000977 a rdfs:Class ;
  rdfs:label "anchor_binding_site" ;
  rdfs:comment "Part of an edited transcript only." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0000601 a rdfs:Class ;
  rdfs:label "edited_by_G_addition" .

obo:SO_0000680 a rdfs:Class ;
  rdfs:label "non_canonical_start_codon" ;
  rdfs:comment "A start codon that is not the usual AUG sequence." ;
  rdfs:subClassOf obo:SO_0000318 .

obo:SO_0000907 a rdfs:Class ;
  rdfs:label "supported_by_sequence_similarity" ;
  rdfs:comment "An attribute to describe a feature that has been predicted using sequence similarity techniques." ;
  rdfs:subClassOf obo:SO_0000732 .

obo:SO_0002285 a rdfs:Class ;
  rdfs:label "CACTA_TIR_transposon" ;
  rdfs:comment "This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/G…C/TAGTG'." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_1001266 a rdfs:Class ;
  rdfs:label "stop_codon_redefinition_as_selenocysteine" .

obo:BS_00231 a rdfs:Class .

obo:SO_0000858 a rdfs:Class ;
  rdfs:label "orthologous" ;
  rdfs:comment "An attribute describing a kind of homology where divergence occurred after a speciation event." ;
  rdfs:subClassOf obo:SO_0000857 .

obo:BS_00207 a rdfs:Class .

obo:SO_0001053 a rdfs:Class ;
  rdfs:label "nested_transposon" .

obo:SO_0000082 a rdfs:Class ;
  rdfs:label "processed_transcript_attribute" .

obo:SO_0001878 a rdfs:Class ;
  rdfs:label "feature_variant" ;
  rdfs:comment "A sequence variant that falls entirely or partially within a genomic feature." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_0002260 a rdfs:Class ;
  rdfs:label "LARD" ;
  rdfs:comment "Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001812 a rdfs:Class ;
  rdfs:label "transmembrane_helix" ;
  rdfs:comment "A region that traverses the lipid bilayer and adopts a helical secondary structure." ;
  rdfs:subClassOf obo:SO_0001114 .

obo:SO_1000182 a rdfs:Class ;
  rdfs:label "chromosome_number_variation" ;
  rdfs:comment "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." ;
  rdfs:subClassOf obo:SO_0000240 .

obo:SO_0001273 a rdfs:Class ;
  rdfs:label "modified_adenosine" ;
  rdfs:comment "A modified adenine is an adenine base feature that has been altered." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_1000064 a rdfs:Class ;
  rdfs:label "sequence_variation_affecting_reading_frame" ;
  rdfs:comment "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." .

obo:SO_0002386 a rdfs:Class ;
  rdfs:label "5_prime_UTR_uORF_stop_codon_variant" ;
  rdfs:comment "A 5' UTR variant where a stop codon in an upstream open reading frame is introduced, moved or lost." ;
  rdfs:subClassOf obo:SO_0002385 .

obo:SO_0000305 a rdfs:Class ;
  rdfs:label "modified_DNA_base" ;
  rdfs:comment "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." ;
  rdfs:subClassOf obo:SO_0001236 , obo:SO_0001720 .

obo:SO_1000153 a rdfs:Class ;
  rdfs:label "inverted_insertional_duplication" ;
  rdfs:comment "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." ;
  rdfs:subClassOf obo:SO_1000154 .

obo:SO_0000810 a rdfs:Class ;
  rdfs:label "chimeric_cDNA_clone" ;
  rdfs:comment "A cDNA clone invalidated because it is chimeric." ;
  rdfs:subClassOf obo:SO_0000809 .

obo:SO_0002106 a rdfs:Class ;
  rdfs:label "translated_unprocessed_pseudogene" ;
  rdfs:comment "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_0000075 a rdfs:Class ;
  rdfs:label "three_prime_three_prime_overlap" ;
  rdfs:comment "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_0000373 a rdfs:Class ;
  rdfs:label "recombinationally_inverted_gene" ;
  rdfs:comment "A recombinationally rearranged gene by inversion." ;
  rdfs:subClassOf obo:SO_0000456 .

obo:SO_1001246 a rdfs:Class ;
  rdfs:label "CDS_independently_known" ;
  rdfs:comment "A CDS with the evidence status of being independently known." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:BS_00185 a rdfs:Class .

obo:SO_0000254 a rdfs:Class ;
  rdfs:label "alanyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000536 a rdfs:Class ;
  rdfs:label "V_nonamer" ;
  rdfs:comment "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000562 .

obo:SO_0000488 a rdfs:Class ;
  rdfs:label "VDJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001682 a rdfs:Class ;
  rdfs:label "replication_regulatory_region" ;
  rdfs:comment "A regulatory region that is involved in the control of the process of nucleotide replication." ;
  rdfs:subClassOf obo:SO_0005836 .

obo:SO_0000797 a rdfs:Class ;
  rdfs:label "natural_transposable_element" ;
  rdfs:comment "TE that exists (or existed) in nature." ;
  rdfs:subClassOf obo:SO_0000101 , obo:SO_0001038 .

obo:SO_0001392 a rdfs:Class ;
  rdfs:label "modified_L_threonine" ;
  rdfs:comment "A post translationally modified threonine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000185 a rdfs:Class ;
  rdfs:label "primary_transcript" ;
  rdfs:comment "A transcript that in its initial state requires modification to be functional." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_1000075 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_editing" ;
  rdfs:comment "Sequence variant affects the editing of the transcript." .

obo:SO_0001509 a rdfs:Class ;
  rdfs:label "chromosomal_variation_attribute" ;
  rdfs:comment "An attribute of a change in the structure or number of a chromosomes." ;
  rdfs:subClassOf obo:SO_0001508 .

obo:SO_0001973 a rdfs:Class ;
  rdfs:label "histone_3_acetylation_site" ;
  rdfs:comment "A histone 3 modification where the modification is the acetylation of the residue." ;
  rdfs:subClassOf obo:SO_0001702 .

obo:SO_0000864 a rdfs:Class ;
  rdfs:label "exemplar" ;
  rdfs:comment "An attribute describing a sequence is representative of a class of similar sequences." ;
  rdfs:subClassOf obo:SO_0000863 .

obo:SO_0001724 a rdfs:Class ;
  rdfs:label "H3K36_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001733 .

obo:SO_0000951 a rdfs:Class ;
  rdfs:label "eukaryotic_terminator" ;
  rdfs:comment "A signal for RNA polymerase to terminate transcription." ;
  rdfs:subClassOf obo:SO_0000141 .

obo:SO_0001353 a rdfs:Class ;
  rdfs:label "three_three_amino_three_carboxypropyl_uridine" ;
  rdfs:comment "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000633 a rdfs:Class ;
  rdfs:label "monocistronic_mRNA" ;
  rdfs:comment "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_0000665 .

obo:SO_0001303 a rdfs:Class ;
  rdfs:label "two_methylthio_N6_cis_hydroxyisopentenyl_adenosine" ;
  rdfs:comment "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000243 a rdfs:Class ;
  rdfs:label "internal_ribosome_entry_site" ;
  rdfs:comment "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." ;
  rdfs:subClassOf obo:SO_0000139 .

obo:SO_1000142 a rdfs:Class ;
  rdfs:label "dextrosynaptic_chromosome" ;
  rdfs:comment "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." ;
  rdfs:subClassOf obo:SO_1000136 .

obo:SO_0000713 a rdfs:Class ;
  rdfs:label "DNA_motif" ;
  rdfs:comment "A motif that is active in the DNA form of the sequence." ;
  rdfs:subClassOf obo:SO_0000714 .

obo:SO_0001234 a rdfs:Class ;
  rdfs:label "mobile" ;
  rdfs:comment "An attribute describing a feature that has either intra-genome or intracellular mobility." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000597 a rdfs:Class ;
  rdfs:label "transcript_edited_by_U_insertion/deletion" ;
  rdfs:comment "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." .

obo:SO_0000402 a rdfs:Class ;
  rdfs:label "enhancer_attribute" .

obo:SO_0002399 a rdfs:Class ;
  rdfs:label "inframe_unidirectional_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genes, on the same strand have become joined without a disruption of the translational reading frame, because the number of nucleotides between the reading frames of the joined genes is a multiple of three." ;
  rdfs:subClassOf obo:SO_0002085 .

obo:SO_1000147 a rdfs:Class ;
  rdfs:label "deficient_translocation" ;
  rdfs:comment "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." ;
  rdfs:subClassOf obo:SO_1000029 , obo:SO_1000044 .

obo:SO_0002174 a rdfs:Class ;
  rdfs:label "deletion_artifact" ;
  rdfs:comment "A deletion that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002172 .

obo:SO_0001625 a rdfs:Class .

obo:SO_0000452 a rdfs:Class ;
  rdfs:label "transgene_attribute" .

obo:SO_0000366 a rdfs:Class ;
  rdfs:label "insertion_site" ;
  rdfs:comment "The junction where an insertion occurred." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0002070 a rdfs:Class ;
  rdfs:label "Alu_deletion" ;
  rdfs:comment "A deletion of an Alu mobile element with respect to a reference." ;
  rdfs:subClassOf obo:SO_0002066 .

obo:SO_0005858 a rdfs:Class ;
  rdfs:label "syntenic_region" ;
  rdfs:comment "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0001331 a rdfs:Class ;
  rdfs:label "two_prime_O_ribosylguanosine_phosphate" ;
  rdfs:comment "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000727 a rdfs:Class ;
  rdfs:label "cis_regulatory_module" ;
  rdfs:comment "A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_1000035 a rdfs:Class ;
  rdfs:label "duplication" ;
  rdfs:comment "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." ;
  rdfs:subClassOf obo:SO_0000667 .

obo:SO_1001188 a rdfs:Class ;
  rdfs:label "encodes_1_polypeptide" ;
  rdfs:comment "A gene that is alternately spliced, but encodes only one polypeptide." ;
  rdfs:subClassOf obo:SO_0000463 .

obo:SO_1000107 a rdfs:Class ;
  rdfs:label "mutation_causing_out_of_frame_polypeptide_N_terminal_elongation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001877 a rdfs:Class ;
  rdfs:label "lncRNA" ;
  rdfs:comment "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002404 a rdfs:Class ;
  rdfs:label "five_prime_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genomic features have become joined with one breakend within the 5' end of a gene." ;
  rdfs:subClassOf obo:SO_0001564 , obo:SO_0001882 .

obo:BS_00224 a rdfs:Class .

obo:SO_0001181 a rdfs:Class ;
  rdfs:label "Bruno_response_element" ;
  rdfs:comment "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." ;
  rdfs:subClassOf obo:SO_0000837 .

obo:SO_0000333 a rdfs:Class ;
  rdfs:label "exon_junction" ;
  rdfs:comment "The boundary between two exons in a processed transcript." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0000117 a rdfs:Class ;
  rdfs:label "transcript_with_readthrough_stop_codon" .

obo:SO_0001687 a rdfs:Class ;
  rdfs:label "restriction_enzyme_recognition_site" ;
  rdfs:comment "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." ;
  rdfs:subClassOf obo:SO_0001954 .

obo:SO_0000283 a rdfs:Class ;
  rdfs:label "engineered_foreign_transposable_element_gene" ;
  rdfs:comment "A transposable_element that is engineered and foreign." ;
  rdfs:subClassOf obo:SO_0000111 , obo:SO_0000281 .

obo:SO_0005848 a rdfs:Class ;
  rdfs:label "gene_cassette_member" ;
  rdfs:comment "A gene that is a member of a gene cassette, which is a mobile genetic element." ;
  rdfs:subClassOf obo:SO_0000081 .

obo:SO_0000188 a rdfs:Class ;
  rdfs:label "intron" ;
  rdfs:comment "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0002211 a rdfs:Class ;
  rdfs:label "circular_plasmid" ;
  rdfs:comment "A self replicating circular nucleic acid molecule that is distinct from a chromosome in the organism." ;
  rdfs:subClassOf obo:SO_0000155 .

obo:SO_0001455 a rdfs:Class ;
  rdfs:label "selenocysteine" ;
  rdfs:comment "A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_1000120 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_inactive_catalytic_site" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000137 a rdfs:Class ;
  rdfs:label "allelically_excluded" ;
  rdfs:comment "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." ;
  rdfs:subClassOf obo:SO_0000133 .

obo:SO_0001771 a rdfs:Class ;
  rdfs:label "disease_associated_variant" ;
  rdfs:comment "A variant that has been found to be associated with disease." ;
  rdfs:subClassOf obo:SO_0001769 .

obo:SO_1000024 a rdfs:Class ;
  rdfs:label "A_to_C_transversion" ;
  rdfs:comment "A transversion from adenine to cytidine." ;
  rdfs:subClassOf obo:SO_1000023 .

obo:SO_0001919 a rdfs:Class ;
  rdfs:label "4_methylcytosine" ;
  rdfs:comment "A cytosine methylated at the 4 nitrogen." ;
  rdfs:subClassOf obo:SO_0000114 .

obo:SO_0001996 a rdfs:Class ;
  rdfs:label "extended_intronic_splice_region" ;
  rdfs:comment "Region of intronic sequence within 10 bases of an exon." ;
  rdfs:subClassOf obo:SO_0001014 .

obo:SO_1001255 a rdfs:Class ;
  rdfs:label "status_of_coding_sequence" .

obo:SO_0000821 a rdfs:Class ;
  rdfs:label "chromoplast_chromosome" ;
  rdfs:comment "A chromosome originating in a chromoplast." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001122 a rdfs:Class ;
  rdfs:label "polypeptide_nest_right_left_motif" ;
  rdfs:comment "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0001120 .

obo:SO_0000994 a rdfs:Class ;
  rdfs:label "consensus_region" ;
  rdfs:comment "A region that has a known consensus sequence." ;
  rdfs:subClassOf obo:SO_0000001 , obo:SO_0001410 .

obo:SO_0001927 a rdfs:Class ;
  rdfs:label "telomeric_transcript" ;
  rdfs:comment "A non-coding transcript derived from the transcript of the telomere." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001719 a rdfs:Class ;
  rdfs:label "H3K23_acetylation_site" ;
  rdfs:comment "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0001468 a rdfs:Class ;
  rdfs:label "three_prime_RST" ;
  rdfs:comment "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." ;
  rdfs:subClassOf obo:SO_0001467 .

obo:SO_0005837 a rdfs:Class ;
  rdfs:label "U14_snoRNA_primary_transcript" ;
  rdfs:comment "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0002066 a rdfs:Class ;
  rdfs:label "mobile_element_deletion" ;
  rdfs:comment "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." ;
  rdfs:subClassOf obo:SO_0000159 .

obo:SO_0000469 a rdfs:Class ;
  rdfs:label "post_translationally_regulated_by_protein_modification" ;
  rdfs:comment "An attribute describing a gene sequence where the resulting protein is modified to regulate it." ;
  rdfs:subClassOf obo:SO_0000130 .

obo:SO_0001618 a rdfs:Class ;
  rdfs:label "inactive_catalytic_site" ;
  rdfs:comment "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001560 .

obo:SO_0001836 a rdfs:Class ;
  rdfs:label "S_region" ;
  rdfs:comment "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0000279 a rdfs:Class ;
  rdfs:label "transcript_bound_by_protein" ;
  rdfs:comment "A transcript that is bound by a protein." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0002092 a rdfs:Class ;
  rdfs:label "5_prime_UTR_exon_variant" ;
  rdfs:comment "A UTR variant of exonic sequence of the 5' UTR." ;
  rdfs:subClassOf obo:SO_0001623 .

obo:SO_0000803 a rdfs:Class ;
  rdfs:label "assortment_derived_aneuploid" ;
  rdfs:comment "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." ;
  rdfs:subClassOf obo:SO_0001504 .

obo:SO_1000093 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_amino_acid_substitution" ;
  rdfs:comment "The replacement of a single amino acid by another." .

obo:SO_0001801 a rdfs:Class ;
  rdfs:label "tasiRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a tasiRNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000651 a rdfs:Class ;
  rdfs:label "cytosolic_LSU_rRNA" ;
  rdfs:comment "Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes." ;
  rdfs:subClassOf obo:SO_0002343 .

obo:SO_0005847 a rdfs:Class ;
  rdfs:label "cassette_array_member" ;
  rdfs:comment "A gene that is a member of a gene cassette, which is a mobile genetic element." ;
  rdfs:subClassOf obo:SO_0005848 .

obo:SO_0001320 a rdfs:Class ;
  rdfs:label "mannosyl_queuosine" ;
  rdfs:comment "Mannosyl_queuosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0000882 a rdfs:Class ;
  rdfs:label "codon_redefined" ;
  rdfs:comment "An attribute describing the alteration of codon meaning." ;
  rdfs:subClassOf obo:SO_0000881 .

obo:SO_0001534 a rdfs:Class ;
  rdfs:label "nuclear_rim_localization_signal" ;
  rdfs:comment "A polypeptide region that targets a polypeptide to the nuclear rim." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0000239 a rdfs:Class ;
  rdfs:label "flanking_region" ;
  rdfs:comment "The sequences extending on either side of a specific region." ;
  rdfs:subClassOf obo:SO_0001412 .

obo:SO_0002348 a rdfs:Class ;
  rdfs:label "plastid_LSU_rRNA" ;
  rdfs:comment "Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes." ;
  rdfs:subClassOf obo:SO_0002346 .

obo:SO_0000249 a rdfs:Class ;
  rdfs:label "six_cutter_restriction_site" .

obo:SO_0001140 a rdfs:Class ;
  rdfs:label "gamma_turn_inverse" ;
  rdfs:comment "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." ;
  rdfs:subClassOf obo:SO_0001138 .

obo:SO_0001444 a rdfs:Class ;
  rdfs:label "serine" ;
  rdfs:comment "A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000940 a rdfs:Class ;
  rdfs:label "recombinationally_rearranged" ;
  rdfs:comment "A gene that is recombinationally rearranged." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001760 a rdfs:Class ;
  rdfs:label "non_processed_pseudogene" ;
  rdfs:comment "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations." ;
  rdfs:subClassOf obo:SO_0000336 .

obo:SO_0002125 a rdfs:Class ;
  rdfs:label "IG_J_gene" ;
  rdfs:comment "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002122 .

obo:SO_0001240 a rdfs:Class ;
  rdfs:label "TSS_region" ;
  rdfs:comment "The region of a gene from the 5' most TSS to the 3' TSS." .

obo:SO_0000792 a rdfs:Class ;
  rdfs:label "cloned_cDNA" .

obo:SO_0001021 a rdfs:Class ;
  rdfs:label "chromosome_breakpoint" ;
  rdfs:comment "A chromosomal region that may sustain a double-strand break, resulting in a recombination event." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001433 a rdfs:Class ;
  rdfs:label "three_prime_RACE_clone" ;
  rdfs:comment "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." ;
  rdfs:subClassOf obo:SO_0000317 .

obo:SO_0002364 a rdfs:Class ;
  rdfs:label "mt_LSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for mitochondrial LSU rRNA." ;
  rdfs:subClassOf obo:SO_0002363 .

obo:SO_0000428 a rdfs:Class ;
  rdfs:label "U5_five_prime_LTR_region" ;
  rdfs:comment "The U5 segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000422 , obo:SO_0000850 .

obo:SO_0002337 a rdfs:Class ;
  rdfs:label "cytosolic_2S_rRNA" ;
  rdfs:comment "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_0000492 a rdfs:Class ;
  rdfs:label "D_gene_recombination_feature" ;
  rdfs:comment "Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence." ;
  rdfs:subClassOf obo:SO_0000939 .

obo:SO_0000388 a rdfs:Class ;
  rdfs:label "RRE_RNA" ;
  rdfs:comment "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0002345 a rdfs:Class ;
  rdfs:label "mt_LSU_rRNA" ;
  rdfs:comment "Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes." ;
  rdfs:subClassOf obo:SO_0002128 .

obo:SO_0000430 a rdfs:Class ;
  rdfs:label "R_three_prime_LTR_region" ;
  rdfs:comment "The R segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000849 .

obo:SO_0001700 a rdfs:Class ;
  rdfs:label "histone_modification" ;
  rdfs:comment "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." ;
  rdfs:subClassOf obo:SO_0001089 , obo:SO_0001720 .

obo:SO_1000014 a rdfs:Class ;
  rdfs:label "purine_transition" ;
  rdfs:comment "A substitution of a purine, A or G, for another purine." ;
  rdfs:subClassOf obo:SO_1000009 .

obo:SO_0000038 a rdfs:Class ;
  rdfs:label "match_set" ;
  rdfs:comment "A collection of match parts." .

obo:SO_0000167 a rdfs:Class ;
  rdfs:label "promoter" ;
  rdfs:comment "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0000842 , obo:SO_0001055 .

obo:SO_0000291 a rdfs:Class ;
  rdfs:label "trinucleotide_repeat_microsatellite_feature" ;
  rdfs:comment "A region of a repeating trinucleotide sequence (three bases)." ;
  rdfs:subClassOf obo:SO_0000289 .

obo:SO_0001728 a rdfs:Class ;
  rdfs:label "H3K9_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." ;
  rdfs:subClassOf obo:SO_0001736 .

obo:SO_0001635 a rdfs:Class ;
  rdfs:label "5KB_upstream_variant" ;
  rdfs:comment "A sequence variant located within 5KB 5' of a gene." ;
  rdfs:subClassOf obo:SO_0001631 .

obo:SO_0001980 a rdfs:Class ;
  rdfs:label "G_box" ;
  rdfs:comment "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." ;
  rdfs:subClassOf obo:SO_0001678 .

obo:BS_00213 a rdfs:Class .

obo:SO_0001799 a rdfs:Class ;
  rdfs:label "regional_centromere_outer_repeat_region" ;
  rdfs:comment "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." ;
  rdfs:subClassOf obo:SO_0001797 .

obo:SO_0001754 a rdfs:Class ;
  rdfs:label "SL9_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0002233 a rdfs:Class ;
  rdfs:label "homologous_chromosome_recognition_and_pairing_locus" ;
  rdfs:comment "A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:SO_1001288 a rdfs:Class ;
  rdfs:label "stop_codon_signal" ;
  rdfs:comment "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." ;
  rdfs:subClassOf obo:SO_1001268 .

obo:BS_0000338 a rdfs:Class .

obo:SO_0100018 a rdfs:Class ;
  rdfs:label "polypeptide_binding_motif" ;
  rdfs:comment "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." ;
  rdfs:subClassOf obo:SO_0100001 .

obo:SO_0000955 a rdfs:Class ;
  rdfs:label "double_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded DNA molecule." ;
  rdfs:subClassOf obo:SO_0000954 .

obo:SO_0000055 a rdfs:Class ;
  rdfs:label "hyperploid" ;
  rdfs:comment "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." ;
  rdfs:subClassOf obo:SO_0000054 .

obo:SO_0000139 a rdfs:Class ;
  rdfs:label "ribosome_entry_site" ;
  rdfs:comment "Region in mRNA where ribosome assembles." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001962 a rdfs:Class ;
  rdfs:label "modified_adenine" ;
  rdfs:comment "A modified adenine DNA base feature." ;
  rdfs:subClassOf obo:SO_0000305 .

obo:SO_0001100 a rdfs:Class ;
  rdfs:label "polypeptide_molybdenum_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001748 a rdfs:Class ;
  rdfs:label "SL3_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0001280 a rdfs:Class ;
  rdfs:label "two_prime_O_methylinosine" ;
  rdfs:comment "2'-O-methylinosine is a modified inosine." ;
  rdfs:subClassOf obo:SO_0001274 .

obo:SO_0000209 a rdfs:Class ;
  rdfs:label "rRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a ribosomal RNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0002222 a rdfs:Class ;
  rdfs:label "prokaryotic_promoter" ;
  rdfs:comment "A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:BS_00229 a rdfs:Class .

obo:SO_1000030 a rdfs:Class ;
  rdfs:label "chromosomal_inversion" ;
  rdfs:comment "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." ;
  rdfs:subClassOf obo:SO_1000028 .

obo:SO_0001476 a rdfs:Class ;
  rdfs:label "natural_plasmid" ;
  rdfs:comment "A plasmid that occurs naturally." ;
  rdfs:subClassOf obo:SO_0000155 , obo:SO_0001038 .

obo:SO_0001613 a rdfs:Class ;
  rdfs:label "elongated_out_of_frame_polypeptide_C_terminal" ;
  rdfs:comment "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." ;
  rdfs:subClassOf obo:SO_0001610 .

obo:SO_0001540 a rdfs:Class ;
  rdfs:label "level_of_transcript_variant" ;
  rdfs:comment "A sequence variant which alters the level of a transcript." ;
  rdfs:subClassOf obo:SO_0001538 .

obo:SO_0001523 a rdfs:Class ;
  rdfs:label "duplication_attribute" ;
  rdfs:comment "An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." ;
  rdfs:subClassOf obo:SO_0001508 .

obo:SO_0001295 a rdfs:Class ;
  rdfs:label "one_methyladenosine" ;
  rdfs:comment "1_methyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0001595 a rdfs:Class ;
  rdfs:label "plus_2_frameshift_variant" ;
  rdfs:comment "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward." ;
  rdfs:subClassOf obo:SO_0001589 .

obo:SO_1000040 a rdfs:Class ;
  rdfs:label "inverted_tandem_duplication" ;
  rdfs:comment "A tandem duplication where the individual regions are not in the same orientation." ;
  rdfs:subClassOf obo:SO_1000173 .

obo:SO_0000893 a rdfs:Class ;
  rdfs:label "silenced" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." ;
  rdfs:subClassOf obo:SO_0000126 .

obo:SO_0001341 a rdfs:Class ;
  rdfs:label "four_demethylwyosine" ;
  rdfs:comment "4_demethylwyosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001955 a rdfs:Class ;
  rdfs:label "protein_stability_element" ;
  rdfs:comment "A polypeptide region that proves structure in a protein that affects the stability of the protein." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001697 a rdfs:Class ;
  rdfs:label "ChIP_seq_region" ;
  rdfs:comment "A region of sequence identified by CHiP seq technology to contain a protein binding site." ;
  rdfs:subClassOf obo:SO_0001696 .

obo:SO_0001739 a rdfs:Class ;
  rdfs:label "gene_with_non_canonical_start_codon" ;
  rdfs:comment "A gene with a start codon other than AUG." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001012 a rdfs:Class ;
  rdfs:label "DNAzyme" ;
  rdfs:comment "A DNA sequence with catalytic activity." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_1000086 a rdfs:Class ;
  rdfs:label "sequence_variation_decreasing_level_of_transcript" ;
  rdfs:comment "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." .

obo:SO_0000648 a rdfs:Class .

obo:SO_0001479 a rdfs:Class ;
  rdfs:label "enhancer_trap_construct" ;
  rdfs:comment "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." ;
  rdfs:subClassOf obo:SO_0000637 .

obo:SO_0000748 a rdfs:Class ;
  rdfs:label "proplastid_sequence" ;
  rdfs:comment "DNA belonging to the genome of a proplastid such as an immature chloroplast." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_1000029 a rdfs:Class ;
  rdfs:label "chromosomal_deletion" ;
  rdfs:comment "An incomplete chromosome." ;
  rdfs:subClassOf obo:SO_1000028 .

obo:BS_00159 a rdfs:Class .

obo:SO_0002196 a rdfs:Class ;
  rdfs:label "allelic_pseudogenic_rRNA" ;
  rdfs:comment "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." ;
  rdfs:subClassOf obo:SO_0000777 .

obo:SO_0000933 a rdfs:Class ;
  rdfs:label "intermediate" ;
  rdfs:comment "An attribute to describe a feature between stages of processing." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_1000103 a rdfs:Class ;
  rdfs:label "sequence_variant_decreasing_level_of_translation_product" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0100013 a rdfs:Class ;
  rdfs:label "hydrophobic_region_of_peptide" ;
  rdfs:comment "Hydrophobic regions are regions with a low affinity for water." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001270 a rdfs:Class .

obo:SO_0001209 a rdfs:Class ;
  rdfs:label "three_prime_EST" ;
  rdfs:comment "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." ;
  rdfs:subClassOf obo:SO_0000345 .

obo:SO_0001698 a rdfs:Class ;
  rdfs:label "ASPE_primer" ;
  rdfs:comment "\"A primer containing an SNV at the 3' end for accurate genotyping." ;
  rdfs:subClassOf obo:SO_0000112 .

obo:SO_0001931 a rdfs:Class ;
  rdfs:label "consensus_gDNA" ;
  rdfs:comment "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." ;
  rdfs:subClassOf obo:SO_0000994 .

obo:SO_0000506 a rdfs:Class ;
  rdfs:label "D_DJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:BS_00003 a rdfs:Class .

obo:BS_00235 a rdfs:Class .

obo:SO_0001490 a rdfs:Class ;
  rdfs:label "noncontiguous_finished" ;
  rdfs:comment "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0001159 a rdfs:Class ;
  rdfs:label "DMv5_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001985 a rdfs:Class ;
  rdfs:label "Okazaki_fragment" ;
  rdfs:comment "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001023 a rdfs:Class ;
  rdfs:label "allele" ;
  rdfs:comment "An allele is one of a set of coexisting sequence variants of a gene." ;
  rdfs:subClassOf obo:SO_0001507 .

obo:SO_0000298 a rdfs:Class ;
  rdfs:label "recombination_feature" ;
  rdfs:comment "A feature where there has been exchange of genetic material in the event of mitosis or meiosis" ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000460 a rdfs:Class ;
  rdfs:label "vertebrate_immunoglobulin_T_cell_receptor_segment" ;
  rdfs:comment "Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0000477 a rdfs:Class ;
  rdfs:label "polycistronic_gene" ;
  rdfs:comment "A gene that is polycistronic." .

obo:SO_0000027 a rdfs:Class ;
  rdfs:label "RNA_hook_turn" ;
  rdfs:subClassOf obo:SO_0000026 .

obo:SO_0001277 a rdfs:Class ;
  rdfs:label "modified_uridine" ;
  rdfs:comment "A uridine base that has been modified." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_0000572 a rdfs:Class ;
  rdfs:label "DJ_gene_segment" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." ;
  rdfs:subClassOf obo:SO_0000936 .

obo:SO_0001105 a rdfs:Class ;
  rdfs:label "polypeptide_ligand_contact" ;
  rdfs:comment "Residues which interact with a ligand." ;
  rdfs:subClassOf obo:SO_0001657 , obo:SO_0100002 .

obo:SO_1000055 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_initiator_codon_change_in_transcript" ;
  rdfs:comment "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." .

obo:SO_0001010 a rdfs:Class ;
  rdfs:label "i_motif" ;
  rdfs:comment "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." ;
  rdfs:subClassOf obo:SO_0000142 .

obo:SO_0001552 a rdfs:Class ;
  rdfs:label "decreased_transcription_rate_variant" ;
  rdfs:comment "A sequence variant that decreases the rate of transcription with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001550 .

obo:SO_0001823 a rdfs:Class ;
  rdfs:label "conservative_inframe_insertion" ;
  rdfs:comment "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." ;
  rdfs:subClassOf obo:SO_0001821 .

obo:SO_0001854 a rdfs:Class ;
  rdfs:label "smFISH_probe" ;
  rdfs:comment "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." ;
  rdfs:subClassOf obo:SO_0000051 .

obo:SO_0001113 a rdfs:Class ;
  rdfs:label "parallel_beta_strand" ;
  rdfs:comment "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." ;
  rdfs:subClassOf obo:SO_0001111 .

obo:SO_0002193 a rdfs:Class ;
  rdfs:label "processed_pseudogenic_rRNA" ;
  rdfs:comment "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail." ;
  rdfs:subClassOf obo:SO_0000777 .

obo:SO_0000605 a rdfs:Class ;
  rdfs:label "intergenic_region" ;
  rdfs:comment "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002178 a rdfs:Class ;
  rdfs:label "SNV_artifact" ;
  rdfs:comment "An SNV that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002176 .

obo:SO_0000257 a rdfs:Class ;
  rdfs:label "aspartyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000724 a rdfs:Class ;
  rdfs:label "oriT" ;
  rdfs:comment "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_1000068 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_plus_2_frameshift" ;
  rdfs:comment "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." .

obo:SO_0000854 a rdfs:Class ;
  rdfs:label "paralogous_region" ;
  rdfs:comment "A homologous_region that is paralogous to another region." ;
  rdfs:subClassOf obo:SO_0000853 .

obo:SO_0000550 a rdfs:Class ;
  rdfs:label "aneuploid_chromosome" ;
  rdfs:comment "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:BS_00073 a rdfs:Class .

obo:SO_0001180 a rdfs:Class ;
  rdfs:label "AU_rich_element" ;
  rdfs:comment "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." ;
  rdfs:subClassOf obo:SO_0000837 .

obo:BS_00069 a rdfs:Class .

obo:SO_0001686 a rdfs:Class ;
  rdfs:label "quality_value" ;
  rdfs:comment "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." ;
  rdfs:subClassOf obo:SO_0001684 .

obo:SO_0000809 a rdfs:Class ;
  rdfs:label "invalidated_cDNA_clone" ;
  rdfs:comment "A cDNA clone that is invalid." ;
  rdfs:subClassOf obo:SO_0000317 .

obo:SO_0002390 a rdfs:Class ;
  rdfs:label "pseudoexon_variant" ;
  rdfs:comment "Inclusion of a non-conserved, unannotated exon in the spliced transcript, as a consequence of a variant in the gene." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0100020 a rdfs:Class ;
  rdfs:label "polypeptide_DNA_contact" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." ;
  rdfs:subClassOf obo:SO_0001429 , obo:SO_0100002 .

obo:SO_0001545 a rdfs:Class ;
  rdfs:label "polyadenylation_variant" ;
  rdfs:comment "A sequence variant that changes polyadenylation with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001543 .

obo:SO_0001630 a rdfs:Class ;
  rdfs:label "splice_region_variant" ;
  rdfs:comment "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0000628 a rdfs:Class ;
  rdfs:label "chromosomal_structural_element" ;
  rdfs:comment "Regions of the chromosome that are important for structural elements." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0002375 a rdfs:Class ;
  rdfs:label "C_D_box_snoRNA_gene" ;
  rdfs:comment "A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." ;
  rdfs:subClassOf obo:SO_0001267 .

obo:SO_1000023 a rdfs:Class ;
  rdfs:label "purine_to_pyrimidine_transversion" ;
  rdfs:comment "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." ;
  rdfs:subClassOf obo:SO_1000017 .

obo:SO_0001073 a rdfs:Class ;
  rdfs:label "cytoplasmic_polypeptide_region" ;
  rdfs:comment "Polypeptide region that is localized inside the cytoplasm." ;
  rdfs:subClassOf obo:SO_0001072 .

obo:SO_0002035 a rdfs:Class ;
  rdfs:label "lncRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a lncRNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000971 a rdfs:Class ;
  rdfs:label "DNA_replication_mode" ;
  rdfs:comment "This has been obsoleted as it represents a process. replaced_by: GO:0006260." .

obo:SO_0000561 a rdfs:Class ;
  rdfs:label "heptamer_of_recombination_feature_of_vertebrate_immune_system_gene" ;
  rdfs:comment "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000939 .

obo:SO_1000079 a rdfs:Class ;
  rdfs:label "sequence_variation_affecting_transcript_sequence" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0001230 a rdfs:Class ;
  rdfs:label "inosine" ;
  rdfs:comment "A modified RNA base in which hypoxanthine is bound to the ribose ring." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_1000007 a rdfs:Class .

obo:SO_0001720 a rdfs:Class ;
  rdfs:label "epigenetically_modified_region" ;
  rdfs:comment "A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification." ;
  rdfs:subClassOf obo:SO_0001411 , obo:SO_0005836 .

obo:SO_0001429 a rdfs:Class ;
  rdfs:label "DNA_binding_site" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." ;
  rdfs:subClassOf obo:SO_0001655 .

obo:SO_0001307 a rdfs:Class ;
  rdfs:label "N6_methyl_N6_threonylcarbamoyladenosine" ;
  rdfs:comment "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000944 a rdfs:Class ;
  rdfs:label "attL_site" ;
  rdfs:comment "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0000406 a rdfs:Class ;
  rdfs:label "twintron" ;
  rdfs:comment "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0002103 a rdfs:Class ;
  rdfs:label "TR_V_pseudogene" ;
  rdfs:comment "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002099 .

obo:SO_0001050 a rdfs:Class ;
  rdfs:label "repeat_fragment" ;
  rdfs:comment "A portion of a repeat, interrupted by the insertion of another element." ;
  rdfs:subClassOf obo:SO_0000840 .

obo:BS_00149 a rdfs:Class .

obo:SO_0001502 a rdfs:Class ;
  rdfs:label "high_identity_region" ;
  rdfs:comment "An experimental feature with high sequence identity to another sequence." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0000079 a rdfs:Class ;
  rdfs:label "dicistronic_transcript" ;
  rdfs:comment "A transcript that is dicistronic." ;
  rdfs:subClassOf obo:SO_0000078 , obo:SO_0000673 .

obo:SO_0001782 a rdfs:Class ;
  rdfs:label "TF_binding_site_variant" ;
  rdfs:comment "A sequence variant located within a transcription factor binding site." ;
  rdfs:subClassOf obo:SO_0001566 .

obo:SO_0001434 a rdfs:Class ;
  rdfs:label "cassette_pseudogene" ;
  rdfs:comment "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_1000063 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_terminator_codon_change_in_transcript" ;
  rdfs:comment "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." .

obo:SO_0001069 a rdfs:Class .

obo:SO_0000806 a rdfs:Class ;
  rdfs:label "fusion" ;
  rdfs:comment "When two regions of DNA are joined together that are not normally together." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000520 a rdfs:Class ;
  rdfs:label "V_VDJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_1000036 a rdfs:Class ;
  rdfs:label "inversion" ;
  rdfs:comment "A continuous nucleotide sequence is inverted in the same position." ;
  rdfs:subClassOf obo:SO_0001059 , obo:SO_0001411 .

obo:BS_00220 a rdfs:Class .

obo:SO_0000446 a rdfs:Class ;
  rdfs:label "UTR_intron" ;
  rdfs:comment "Intron located in the untranslated region." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0002294 a rdfs:Class ;
  rdfs:label "mitochondrial_D_loop" ;
  rdfs:comment "Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region." ;
  rdfs:subClassOf obo:SO_0000297 , obo:SO_0002293 .

obo:SO_0000076 a rdfs:Class ;
  rdfs:label "three_prime_five_prime_overlap" ;
  rdfs:comment "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." ;
  rdfs:subClassOf obo:SO_0000068 .

obo:SO_0000691 a rdfs:Class ;
  rdfs:label "cleaved_initiator_methionine" ;
  rdfs:comment "The initiator methionine that has been cleaved from a mature polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0001410 a rdfs:Class ;
  rdfs:label "experimental_feature" ;
  rdfs:comment "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." ;
  rdfs:subClassOf obo:SO_0000001 .

obo:SO_0000016 a rdfs:Class ;
  rdfs:label "BREu_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000986 a rdfs:Class ;
  rdfs:label "topology_attribute" ;
  rdfs:comment "The attribute of whether a nucleotide polymer is linear or circular." ;
  rdfs:subClassOf obo:SO_0000443 .

obo:SO_0001725 a rdfs:Class ;
  rdfs:label "H3K4_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001734 .

obo:SO_0000637 a rdfs:Class ;
  rdfs:label "engineered_plasmid" ;
  rdfs:comment "A plasmid that is engineered." ;
  rdfs:subClassOf obo:SO_0000155 , obo:SO_0000804 .

obo:SO_0001042 a rdfs:Class ;
  rdfs:label "phage_sequence" ;
  rdfs:comment "The nucleotide sequence of a virus that infects bacteria." ;
  rdfs:subClassOf obo:SO_0001041 .

obo:SO_0001465 a rdfs:Class ;
  rdfs:label "three_prime_UST" ;
  rdfs:comment "A UST located in the 3'UTR of a protein-coding transcript." ;
  rdfs:subClassOf obo:SO_0001464 .

obo:SO_0000384 a rdfs:Class ;
  rdfs:label "OxyS_RNA" ;
  rdfs:comment "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0000235 a rdfs:Class ;
  rdfs:label "TF_binding_site" ;
  rdfs:comment "A DNA site where a transcription factor binds." ;
  rdfs:subClassOf obo:SO_0001055 , obo:SO_0001654 .

obo:SO_0000198 a rdfs:Class ;
  rdfs:label "noncoding_exon" ;
  rdfs:comment "An exon that does not contain any codons." ;
  rdfs:subClassOf obo:SO_0000147 .

obo:SO_0001872 a rdfs:Class ;
  rdfs:label "rearrangement_region" ;
  rdfs:comment "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." ;
  rdfs:subClassOf obo:SO_0001411 , obo:SO_0001785 .

obo:SO_0002277 a rdfs:Class ;
  rdfs:label "Crypton_YR_transposon" ;
  rdfs:comment "Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules." ;
  rdfs:subClassOf obo:SO_0000182 .

obo:SO_0002110 a rdfs:Class ;
  rdfs:label "polymorphic_pseudogene_with_retained_intron" ;
  rdfs:comment "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." ;
  rdfs:subClassOf obo:SO_0001841 .

obo:SO_0000435 a rdfs:Class ;
  rdfs:label "RR_tract" ;
  rdfs:comment "A polypurine tract within an LTR_retrotransposon." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_1000034 a rdfs:Class .

obo:SO_0000424 a rdfs:Class ;
  rdfs:label "U3_LTR_region" ;
  rdfs:comment "The U3 segment of the long terminal repeats." ;
  rdfs:subClassOf obo:SO_0000848 .

obo:SO_1000025 a rdfs:Class ;
  rdfs:label "A_to_T_transversion" ;
  rdfs:comment "A transversion from adenine to thymine." ;
  rdfs:subClassOf obo:SO_1000023 .

obo:SO_0000334 a rdfs:Class ;
  rdfs:label "nc_conserved_region" ;
  rdfs:comment "Non-coding region of sequence similarity by descent from a common ancestor." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0002334 a rdfs:Class ;
  rdfs:label "ochre_stop_codon" ;
  rdfs:comment "A stop codon with the DNA sequence TAA." ;
  rdfs:subClassOf obo:SO_0000319 .

obo:SO_0000008 a rdfs:Class ;
  rdfs:label "gene_sensu_your_favorite_organism" .

obo:SO_0002081 a rdfs:Class ;
  rdfs:label "incomplete_transcript_CDS" ;
  rdfs:comment "A sequence variant that intersects the coding regions of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_0000116 a rdfs:Class ;
  rdfs:label "edited" ;
  rdfs:comment "An attribute describing a sequence that is modified by editing." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0002263 a rdfs:Class ;
  rdfs:label "Crick_strand" ;
  rdfs:comment "An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0001456 a rdfs:Class ;
  rdfs:label "pyrrolysine" ;
  rdfs:comment "A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001612 a rdfs:Class ;
  rdfs:label "elongated_in_frame_polypeptide_C_terminal" ;
  rdfs:comment "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." ;
  rdfs:subClassOf obo:SO_0001610 .

obo:SO_0001905 a rdfs:Class ;
  rdfs:label "regional_centromere_outer_repeat_transcript" ;
  rdfs:comment "A transcript that is transcribed from the outer repeat region of a regional centromere." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000767 a rdfs:Class ;
  rdfs:label "clone_insert_start" .

obo:SO_0001837 a rdfs:Class ;
  rdfs:label "mobile_element_insertion" ;
  rdfs:comment "A kind of insertion where the inserted sequence is a mobile element." ;
  rdfs:subClassOf obo:SO_0000667 .

obo:SO_0001154 a rdfs:Class ;
  rdfs:label "beta_turn_type_six_b" ;
  rdfs:comment "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." ;
  rdfs:subClassOf obo:SO_0001150 .

obo:SO_0000705 a rdfs:Class ;
  rdfs:label "tandem_repeat" ;
  rdfs:comment "Two or more adjacent copies of a region (of length greater than 1)." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0000731 a rdfs:Class ;
  rdfs:label "fragmentary" ;
  rdfs:comment "An attribute to describe a feature that is incomplete." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0000786 a rdfs:Class ;
  rdfs:label "reagent_attribute" ;
  rdfs:comment "Added jan 2006 by KE." .

obo:SO_0000960 a rdfs:Class ;
  rdfs:label "circular_single_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." ;
  rdfs:subClassOf obo:SO_0000956 .

obo:BS_00246 a rdfs:Class .

obo:SO_0001890 a rdfs:Class ;
  rdfs:label "transcript_regulatory_region_fusion" ;
  rdfs:comment "A feature fusion where the deletion brings together a regulatory region and a transcript region." ;
  rdfs:subClassOf obo:SO_0001882 .

obo:SO_0002295 a rdfs:Class ;
  rdfs:label "transcription_factor_regulatory_site" ;
  rdfs:comment "A TF_binding_site that is involved in regulation of expression." ;
  rdfs:subClassOf obo:SO_0000235 .

obo:SO_0001920 a rdfs:Class ;
  rdfs:label "N6_methyladenine" ;
  rdfs:comment "An adenine methylated at the 6 nitrogen." ;
  rdfs:subClassOf obo:SO_0000161 .

obo:BS_00137 a rdfs:Class .

obo:SO_1000018 a rdfs:Class ;
  rdfs:label "pyrimidine_to_purine_transversion" ;
  rdfs:comment "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." ;
  rdfs:subClassOf obo:SO_1000017 .

obo:SO_0001358 a rdfs:Class ;
  rdfs:label "five_carboxyhydroxymethyl_uridine" ;
  rdfs:comment "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001144 a rdfs:Class ;
  rdfs:label "st_turn_right_handed_type_one" ;
  rdfs:comment "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0001141 .

obo:SO_0001607 a rdfs:Class ;
  rdfs:label "conservative_amino_acid_substitution" ;
  rdfs:comment "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001606 .

obo:SO_0001063 a rdfs:Class ;
  rdfs:label "immature_peptide_region" ;
  rdfs:comment "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0000496 a rdfs:Class ;
  rdfs:label "five_prime_D_heptamer" ;
  rdfs:comment "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000561 .

obo:SO_1000002 a rdfs:Class ;
  rdfs:label "substitution" ;
  rdfs:comment "A sequence alteration where the length of the change in the variant is the same as that of the reference." ;
  rdfs:subClassOf obo:SO_0001059 , obo:SO_0001411 .

obo:SO_0000684 a rdfs:Class ;
  rdfs:label "nuclease_sensitive_site" ;
  rdfs:comment "A region of nucleotide sequence targeted by a nuclease enzyme." ;
  rdfs:subClassOf obo:SO_0000059 .

obo:SO_0001080 a rdfs:Class ;
  rdfs:label "coiled_coil" ;
  rdfs:comment "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." ;
  rdfs:subClassOf obo:SO_0001079 .

obo:SO_0001001 a rdfs:Class ;
  rdfs:label "cytosolic_23S_rRNA" ;
  rdfs:comment "Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_0001744 a rdfs:Class ;
  rdfs:label "UPD" ;
  rdfs:comment "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." ;
  rdfs:subClassOf obo:SO_0001059 .

obo:SO_0001843 a rdfs:Class ;
  rdfs:label "CRE" ;
  rdfs:comment """MERGED DEFINITION:
TARGET DEFINITION: A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.
--------------------
SOURCE DEFINITION: A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.""" ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_1001284 a rdfs:Class ;
  rdfs:label "regulon" ;
  rdfs:comment "A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0001758 a rdfs:Class ;
  rdfs:label "duplicated_pseudogene" ;
  rdfs:comment "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." ;
  rdfs:subClassOf obo:SO_0001760 .

obo:SO_0000781 a rdfs:Class ;
  rdfs:label "transgenic" ;
  rdfs:comment "Attribute describing sequence that has been integrated with foreign sequence." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000702 a rdfs:Class ;
  rdfs:label "possible_assembly_error" ;
  rdfs:comment "A region of sequence where there may have been an error in the assembly." ;
  rdfs:subClassOf obo:SO_0000413 .

obo:SO_0002282 a rdfs:Class ;
  rdfs:label "Transib_TIR_transposon" ;
  rdfs:comment "Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0001970 a rdfs:Class ;
  rdfs:label "non_coding_transcript_intron_variant" ;
  rdfs:comment "A transcript variant occurring within an intron of a non coding transcript." ;
  rdfs:subClassOf obo:SO_0001619 , obo:SO_0001627 .

obo:SO_0000011 a rdfs:Class ;
  rdfs:label "non_protein_coding" ;
  rdfs:comment "A gene which can be transcribed, but will not be translated into a protein." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0000087 a rdfs:Class ;
  rdfs:label "nuclear_gene" ;
  rdfs:comment "A gene from nuclear sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000222 a rdfs:Class ;
  rdfs:label "lysine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding lysyl tRNA (SO:0000265)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000327 a rdfs:Class ;
  rdfs:label "coding_end" ;
  rdfs:comment "The last base to be translated into protein. It does not include the stop codon." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0000695 a rdfs:Class ;
  rdfs:label "reagent" ;
  rdfs:comment "A sequence used in experiment." ;
  rdfs:subClassOf obo:SO_0001409 .

obo:SO_0000832 a rdfs:Class ;
  rdfs:label "promoter_region" ;
  rdfs:comment "A region of sequence which is part of a promoter." .

obo:SO_0000998 a rdfs:Class ;
  rdfs:label "recursive_splice_site" ;
  rdfs:comment "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." ;
  rdfs:subClassOf obo:SO_0001419 .

obo:SO_0001472 a rdfs:Class ;
  rdfs:label "primer_match" ;
  rdfs:comment "A nucleotide match to a primer sequence." ;
  rdfs:subClassOf obo:SO_0000347 .

obo:SO_0001091 a rdfs:Class ;
  rdfs:label "non_covalent_binding_site" ;
  rdfs:comment "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." .

obo:SO_0001568 a rdfs:Class ;
  rdfs:label "splicing_variant" ;
  rdfs:comment "A sequence variant that changes the process of splicing." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0002136 a rdfs:Class ;
  rdfs:label "TR_J_Gene" ;
  rdfs:comment "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain." ;
  rdfs:subClassOf obo:SO_0002133 .

obo:SO_0000358 a rdfs:Class .

obo:SO_0001832 a rdfs:Class ;
  rdfs:label "immunoglobulin_region" ;
  rdfs:comment "A region of immunoglobulin sequence, either constant or variable." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0002313 a rdfs:Class ;
  rdfs:label "core_viral_promoter_element" ;
  rdfs:comment "An element that always exists within the promoter region of a viral gene." ;
  rdfs:subClassOf obo:SO_0002309 .

obo:SO_0000022 a rdfs:Class ;
  rdfs:label "A_minor_RNA_motif" ;
  rdfs:comment "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." ;
  rdfs:subClassOf obo:SO_0000715 .

obo:SO_1000044 a rdfs:Class ;
  rdfs:label "chromosomal_translocation" ;
  rdfs:comment "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." ;
  rdfs:subClassOf obo:SO_0000199 , obo:SO_1000031 .

obo:SO_0002056 a rdfs:Class ;
  rdfs:label "intronic_splicing_silencer" ;
  rdfs:comment "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." ;
  rdfs:subClassOf obo:SO_0000625 .

obo:SO_1000074 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_cryptic_splice_activation" ;
  rdfs:comment "A sequence variant causing a new (functional) splice site." .

obo:SO_0001913 a rdfs:Class ;
  rdfs:label "bacterial_RNApol_promoter_sigma_ecf_element" ;
  rdfs:comment "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." ;
  rdfs:subClassOf obo:SO_0000613 .

obo:SO_0002013 a rdfs:Class ;
  rdfs:label "5_prime_UTR_truncation" ;
  rdfs:comment "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001623 .

obo:SO_0002287 a rdfs:Class ;
  rdfs:label "DIRS_YR_retrotransposon" ;
  rdfs:comment "Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase." ;
  rdfs:subClassOf obo:SO_0002286 .

obo:SO_0000744 a rdfs:Class ;
  rdfs:label "chromoplast_sequence" ;
  rdfs:comment "DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_0000409 a rdfs:Class ;
  rdfs:label "binding_site" ;
  rdfs:comment "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000182 a rdfs:Class ;
  rdfs:label "DNA_transposon" ;
  rdfs:comment "A transposon where the mechanism of transposition is via a DNA intermediate." ;
  rdfs:subClassOf obo:SO_0000101 .

obo:BS_00155 a rdfs:Class .

obo:SO_0002302 a rdfs:Class ;
  rdfs:label "simple_regulon" ;
  rdfs:comment "A regulon defined by considering one regulatory gene product." ;
  rdfs:subClassOf obo:SO_1001284 .

obo:SO_1000114 a rdfs:Class .

obo:SO_1000148 a rdfs:Class ;
  rdfs:label "inversion_cum_translocation" ;
  rdfs:comment "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." ;
  rdfs:subClassOf obo:SO_1000030 , obo:SO_1000044 .

obo:SO_0001946 a rdfs:Class ;
  rdfs:label "H2BK15_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002143 .

obo:SO_0001494 a rdfs:Class ;
  rdfs:label "centromere_DNA_Element_II" ;
  rdfs:comment "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:BS_00336 a rdfs:Class .

obo:SO_0001714 a rdfs:Class ;
  rdfs:label "H2BK5_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0000525 a rdfs:Class ;
  rdfs:label "V_VJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000863 a rdfs:Class ;
  rdfs:label "mRNA_attribute" ;
  rdfs:comment "An attribute describing an mRNA feature." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0000576 a rdfs:Class ;
  rdfs:label "VJ_gene_segment" ;
  rdfs:comment "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." ;
  rdfs:subClassOf obo:SO_0000936 .

obo:SO_0001386 a rdfs:Class ;
  rdfs:label "modified_glycine" ;
  rdfs:comment "A post translationally modified glycine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001146 a rdfs:Class ;
  rdfs:label "polypeptide_variation_site" ;
  rdfs:comment "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0000417 a rdfs:Class ;
  rdfs:label "polypeptide_domain" ;
  rdfs:comment "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." ;
  rdfs:subClassOf obo:SO_0001070 , obo:SO_0100021 .

obo:SO_1001217 a rdfs:Class ;
  rdfs:label "member_of_regulon" ;
  rdfs:comment "A gene that is a member of a group of genes that are either regulated or transcribed together." ;
  rdfs:subClassOf obo:SO_0000081 .

obo:SO_0000720 a rdfs:Class ;
  rdfs:label "foreign_transposable_element" ;
  rdfs:comment "A transposable element that is foreign." ;
  rdfs:subClassOf obo:SO_0000101 .

obo:SO_0000914 a rdfs:Class ;
  rdfs:label "cloned_genomic_insert" ;
  rdfs:comment "A clone insert made from genomic DNA." ;
  rdfs:subClassOf obo:SO_0000753 .

obo:SO_0001339 a rdfs:Class ;
  rdfs:label "N2_N2_7_trimethylguanosine" ;
  rdfs:comment "N2_N2_7_trimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_1000108 a rdfs:Class ;
  rdfs:label "mutaton_causing_inframe_polypeptide_C_terminal_elongation" .

obo:SO_0001109 a rdfs:Class ;
  rdfs:label "beta_bulge_loop_five" ;
  rdfs:comment "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." ;
  rdfs:subClassOf obo:SO_0001108 .

obo:BS_00070 a rdfs:Class .

obo:SO_0001149 a rdfs:Class ;
  rdfs:label "alternate_sequence_site" ;
  rdfs:comment "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." ;
  rdfs:subClassOf obo:SO_0001146 .

obo:SO_0000142 a rdfs:Class ;
  rdfs:label "DNA_sequence_secondary_structure" ;
  rdfs:comment "A folded DNA sequence." ;
  rdfs:subClassOf obo:SO_0000002 .

obo:SO_0000369 a rdfs:Class ;
  rdfs:label "integrase_coding_region" .

obo:SO_0001859 a rdfs:Class ;
  rdfs:label "STREP_motif" ;
  rdfs:comment "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001675 a rdfs:Class ;
  rdfs:label "A_box_type_1" ;
  rdfs:comment "An A box within an RNA polymerase III type 1 promoter." ;
  rdfs:subClassOf obo:SO_0000619 .

obo:SO_0000673 a rdfs:Class ;
  rdfs:label "transcript" ;
  rdfs:comment "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ;
  rdfs:subClassOf obo:SO_0000831 .

obo:SO_0001989 a rdfs:Class ;
  rdfs:label "5_prime_UTR_premature_start_codon_loss_variant" ;
  rdfs:comment "A 5' UTR variant where a premature start codon is lost." ;
  rdfs:subClassOf obo:SO_0001983 .

obo:SO_0002158 a rdfs:Class ;
  rdfs:label "Mat3M" ;
  rdfs:comment "A gene cassette array containing H- mating type specific information." ;
  rdfs:subClassOf obo:SO_0001984 .

obo:SO_1001192 a rdfs:Class ;
  rdfs:label "encodes_disjoint_polypeptides" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." ;
  rdfs:subClassOf obo:SO_1001189 .

obo:SO_0001935 a rdfs:Class ;
  rdfs:label "H3K20_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0002320 a rdfs:Class ;
  rdfs:label "NMD_escaping_variant" ;
  rdfs:comment "A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0001267 a rdfs:Class ;
  rdfs:label "snoRNA_gene" ;
  rdfs:comment "A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs." ;
  rdfs:subClassOf obo:SO_0002342 .

obo:SO_0002078 a rdfs:Class ;
  rdfs:label "incomplete_transcript_intronic_variant" ;
  rdfs:comment "A sequence variant that intersects the intron of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_1000096 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_amino_acid_insertion" ;
  rdfs:comment "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." .

obo:SO_0002182 a rdfs:Class ;
  rdfs:label "antisense_lncRNA_gene" ;
  rdfs:comment "A gene that encodes an antisense long, non-coding RNA." ;
  rdfs:subClassOf obo:SO_0002127 .

obo:SO_0000947 a rdfs:Class ;
  rdfs:label "resolution_site" ;
  rdfs:comment "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." ;
  rdfs:subClassOf obo:SO_0000342 .

obo:SO_0000457 a rdfs:Class ;
  rdfs:label "interchromosomal_duplication" ;
  rdfs:comment "A chromosome duplication involving an insertion from another chromosome." ;
  rdfs:subClassOf obo:SO_1000037 .

obo:SO_0001557 a rdfs:Class ;
  rdfs:label "polypeptide_gain_of_function_variant" ;
  rdfs:comment "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0001165 a rdfs:Class ;
  rdfs:label "DMv1_motif" ;
  rdfs:comment "A promoter motif with consensus sequence CARCCCT." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002024 a rdfs:Class ;
  rdfs:label "W_region" ;
  rdfs:comment "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." ;
  rdfs:subClassOf obo:SO_0001999 .

obo:SO_0000316 a rdfs:Class ;
  rdfs:label "CDS" ;
  rdfs:comment "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0002274 a rdfs:Class ;
  rdfs:label "tRNA_SINE_retrotransposon" ;
  rdfs:comment "Short interspersed elements that originated from tRNAs." ;
  rdfs:subClassOf obo:SO_0000206 .

obo:SO_0001483 a rdfs:Class ;
  rdfs:label "SNV" ;
  rdfs:comment "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." ;
  rdfs:subClassOf obo:SO_1000002 .

obo:SO_0002366 a rdfs:Class ;
  rdfs:label "plastid_rRNA_gene" ;
  rdfs:comment "A gene that codes for plastid rRNA." ;
  rdfs:subClassOf obo:SO_0000090 , obo:SO_0001637 .

obo:SO_0002147 a rdfs:Class ;
  rdfs:label "H2AZK11_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002144 .

obo:SO_0001369 a rdfs:Class ;
  rdfs:label "five_carboxymethylaminomethyluridine" ;
  rdfs:comment "5_carboxymethylaminomethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000246 a rdfs:Class ;
  rdfs:label "polyadenylated" ;
  rdfs:comment "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." ;
  rdfs:subClassOf obo:SO_0000863 .

obo:SO_0002201 a rdfs:Class ;
  rdfs:label "terminal_repeat" ;
  rdfs:comment "A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0000861 a rdfs:Class ;
  rdfs:label "capped_primary_transcript" ;
  rdfs:comment "A primary transcript that is capped." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000980 a rdfs:Class ;
  rdfs:label "minicircle" ;
  rdfs:comment "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." ;
  rdfs:subClassOf obo:SO_0001235 .

obo:SO_0000195 a rdfs:Class ;
  rdfs:label "coding_exon" ;
  rdfs:comment "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." ;
  rdfs:subClassOf obo:SO_0000147 .

obo:SO_0002290 a rdfs:Class ;
  rdfs:label "Penelope_retrotransposon" ;
  rdfs:comment "Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease." ;
  rdfs:subClassOf obo:SO_0000189 .

obo:SO_0001894 a rdfs:Class ;
  rdfs:label "regulatory_region_ablation" ;
  rdfs:comment "A feature ablation whereby the deleted region includes a regulatory region." ;
  rdfs:subClassOf obo:SO_0001879 .

obo:BS_00182 a rdfs:Class .

obo:SO_0002303 a rdfs:Class ;
  rdfs:label "complex_regulon" ;
  rdfs:comment "A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products." ;
  rdfs:subClassOf obo:SO_1001284 .

obo:SO_0001769 a rdfs:Class ;
  rdfs:label "variant_phenotype" ;
  rdfs:comment "A quality inhering in a variant by virtue of its phenotype." ;
  rdfs:subClassOf obo:SO_0001761 .

obo:SO_0001883 a rdfs:Class ;
  rdfs:label "transcript_translocation" ;
  rdfs:comment "A feature translocation where the region contains a transcript." ;
  rdfs:subClassOf obo:SO_0001881 .

obo:SO_0000756 a rdfs:Class ;
  rdfs:label "cDNA" ;
  rdfs:comment "DNA synthesized by reverse transcriptase using RNA as a template." ;
  rdfs:subClassOf obo:SO_0000352 .

obo:SO_0000502 a rdfs:Class ;
  rdfs:label "transcribed_region" ;
  rdfs:comment "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." .

obo:SO_0000474 a rdfs:Class ;
  rdfs:label "tiling_path_fragment" ;
  rdfs:comment "A piece of sequence that makes up a tiling_path (SO:0000472)." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_0005850 a rdfs:Class ;
  rdfs:label "primer_binding_site" ;
  rdfs:comment "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." ;
  rdfs:subClassOf obo:SO_0001655 .

obo:SO_0001031 a rdfs:Class ;
  rdfs:label "reverse" ;
  rdfs:comment "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." ;
  rdfs:subClassOf obo:SO_0001029 .

obo:SO_0001228 a rdfs:Class ;
  rdfs:label "dihydrouridine" ;
  rdfs:comment "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000531 a rdfs:Class ;
  rdfs:label "V_D_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_1000159 a rdfs:Class ;
  rdfs:label "uninverted_intrachromosomal_transposition" ;
  rdfs:comment "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." ;
  rdfs:subClassOf obo:SO_1000041 .

obo:SO_0000991 a rdfs:Class ;
  rdfs:label "genomic_DNA" ;
  rdfs:comment "DNA located in the genome and able to be transmitted to the offspring." ;
  rdfs:subClassOf obo:SO_0000352 .

obo:SO_0100042 a rdfs:Class .

obo:SO_0001328 a rdfs:Class ;
  rdfs:label "N2_N2_dimethylguanosine" ;
  rdfs:comment "N2_N2_dimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001848 a rdfs:Class ;
  rdfs:label "homol_D_box" ;
  rdfs:comment "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000922 a rdfs:Class ;
  rdfs:label "substitute_C_to_U" ;
  rdfs:comment "An edit to substitute an U for a C." .

obo:SO_0000872 a rdfs:Class ;
  rdfs:label "trans_spliced_mRNA" ;
  rdfs:comment "An mRNA that is trans-spliced." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_0000479 .

obo:SO_0001787 a rdfs:Class ;
  rdfs:label "splice_donor_5th_base_variant" ;
  rdfs:comment "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." ;
  rdfs:subClassOf obo:SO_0001629 .

obo:SO_0002252 a rdfs:Class ;
  rdfs:label "transit_peptide_region_of_CDS" ;
  rdfs:comment "CDS region corresponding to a transit peptide region of a polypeptide." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0000751 a rdfs:Class ;
  rdfs:label "proviral_location" ;
  rdfs:comment "The location of DNA that has come from a viral origin." ;
  rdfs:subClassOf obo:SO_0000735 .

obo:SO_0001461 a rdfs:Class ;
  rdfs:label "enhancer_binding_site" ;
  rdfs:comment "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." ;
  rdfs:subClassOf obo:SO_0001654 .

obo:SO_0000519 a rdfs:Class ;
  rdfs:label "V_DJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001252 a rdfs:Class ;
  rdfs:label "RH_map" ;
  rdfs:comment "A radiation hybrid map is a physical map." ;
  rdfs:subClassOf obo:SO_0001249 .

obo:SO_0001347 a rdfs:Class ;
  rdfs:label "one_methylpseudouridine" ;
  rdfs:comment "1_methylpseudouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000261 a rdfs:Class ;
  rdfs:label "glycyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_1000085 a rdfs:Class ;
  rdfs:label "sequence_variation_affecting_level_of_transcript" ;
  rdfs:comment "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." .

obo:SO_0001579 a rdfs:Class ;
  rdfs:label "transcript_sequence_variant" .

obo:SO_0002325 a rdfs:Class ;
  rdfs:label "splice_donor_variant_NMD_triggering" ;
  rdfs:comment "A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001575 , obo:SO_0002319 .

obo:SO_0001524 a rdfs:Class ;
  rdfs:label "chromosomally_aberrant_genome" ;
  rdfs:comment "When a genome contains an abnormal amount of chromosomes." ;
  rdfs:subClassOf obo:SO_0001506 .

obo:SO_0001731 a rdfs:Class ;
  rdfs:label "H4K8_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001972 .

obo:BS_00041 a rdfs:Class .

obo:SO_0000828 a rdfs:Class ;
  rdfs:label "nuclear_chromosome" ;
  rdfs:comment "A chromosome originating in a nucleus." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001292 a rdfs:Class ;
  rdfs:label "five_hydroxymethylcytidine" ;
  rdfs:comment "5-hydroxymethylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0001794 a rdfs:Class ;
  rdfs:label "point_centromere" ;
  rdfs:comment "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." ;
  rdfs:subClassOf obo:SO_0000577 .

obo:SO_0001949 a rdfs:Class ;
  rdfs:label "H4R3_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:BS_00202 a rdfs:Class .

obo:SO_0001924 a rdfs:Class ;
  rdfs:label "ARRET" ;
  rdfs:comment "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." ;
  rdfs:subClassOf obo:SO_0001927 .

obo:SO_0001580 a rdfs:Class ;
  rdfs:label "coding_sequence_variant" ;
  rdfs:comment "A sequence variant that changes the coding sequence." ;
  rdfs:subClassOf obo:SO_0001791 , obo:SO_0001968 .

obo:SO_0002206 a rdfs:Class ;
  rdfs:label "sequence_source" ;
  rdfs:comment "Identifies the biological source of the specified span of the sequence" ;
  rdfs:subClassOf obo:SO_0000400 .

obo:SO_0001736 a rdfs:Class ;
  rdfs:label "H3K9_methylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0000843 a rdfs:Class ;
  rdfs:label "bacterial_RNApol_promoter_region" ;
  rdfs:comment "A region which is part of a bacterial RNA polymerase promoter." .

obo:SO_0000735 a rdfs:Class ;
  rdfs:label "sequence_location" ;
  rdfs:comment "The location of a sequence." ;
  rdfs:subClassOf obo:SO_0000400 .

obo:SO_0000159 a rdfs:Class ;
  rdfs:label "deletion" ;
  rdfs:comment "The point at which one or more contiguous nucleotides were excised." ;
  rdfs:subClassOf obo:SO_0001059 , obo:SO_0001411 .

obo:SO_0000616 a rdfs:Class ;
  rdfs:label "transcription_end_site" ;
  rdfs:comment "The base where transcription ends." ;
  rdfs:subClassOf obo:SO_0000835 .

obo:SO_0000778 a rdfs:Class ;
  rdfs:label "pseudogenic_tRNA" ;
  rdfs:comment "A non functional descendent of a tRNA." ;
  rdfs:subClassOf obo:SO_0000516 .

obo:SO_0000311 a rdfs:Class ;
  rdfs:label "computed_feature_by_similarity" ;
  rdfs:comment "." .

obo:SO_0001186 a rdfs:Class ;
  rdfs:label "ribozymic" ;
  rdfs:comment "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." ;
  rdfs:subClassOf obo:SO_0001185 .

obo:SO_0001668 a rdfs:Class ;
  rdfs:label "proximal_promoter_element" ;
  rdfs:comment "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." ;
  rdfs:subClassOf obo:SO_0001678 .

obo:SO_0000131 a rdfs:Class ;
  rdfs:label "translationally_regulated" ;
  rdfs:comment "An attribute describing a gene that is regulated as it is translated." ;
  rdfs:subClassOf obo:SO_0000119 .

obo:SO_0000338 a rdfs:Class ;
  rdfs:label "MITE" ;
  rdfs:comment "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0000098 a rdfs:Class ;
  rdfs:label "plasmid_gene" ;
  rdfs:comment "A gene from plasmid sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000659 a rdfs:Class ;
  rdfs:label "tmRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a transfer-messenger RNA (tmRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:BS_00142 a rdfs:Class .

obo:SO_0000590 a rdfs:Class ;
  rdfs:label "SRP_RNA" ;
  rdfs:comment "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000485 a rdfs:Class ;
  rdfs:label "DJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000650 a rdfs:Class ;
  rdfs:label "cytosolic_SSU_rRNA" ;
  rdfs:comment "Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes." ;
  rdfs:subClassOf obo:SO_0002343 .

obo:SO_0000439 a rdfs:Class ;
  rdfs:label "inverted_ring_chromosome" ;
  rdfs:comment "A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome." ;
  rdfs:subClassOf obo:SO_1000030 , obo:SO_1000045 .

obo:SO_0001574 a rdfs:Class ;
  rdfs:label "splice_acceptor_variant" ;
  rdfs:comment "A splice variant that changes the 2 base region at the 3' end of an intron." ;
  rdfs:subClassOf obo:SO_0001629 .

obo:SO_0002114 a rdfs:Class ;
  rdfs:label "NMD_transcript" ;
  rdfs:comment "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay." ;
  rdfs:subClassOf obo:SO_0000120 .

obo:SO_0001084 a rdfs:Class ;
  rdfs:label "non_terminal_residue" ;
  rdfs:comment "The residue at an extremity of the sequence is not the terminal residue." ;
  rdfs:subClassOf obo:SO_0001082 .

obo:SO_0000323 a rdfs:Class ;
  rdfs:label "coding_start" ;
  rdfs:comment "The first base to be translated into protein." ;
  rdfs:subClassOf obo:SO_0000851 .

obo:SO_0000688 a rdfs:Class ;
  rdfs:label "golden_path" ;
  rdfs:comment "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." ;
  rdfs:subClassOf obo:SO_0000353 .

obo:SO_0001124 a rdfs:Class ;
  rdfs:label "schellmann_loop_seven" ;
  rdfs:comment "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." ;
  rdfs:subClassOf obo:SO_0001123 .

obo:SO_0000005 a rdfs:Class ;
  rdfs:label "satellite_DNA" ;
  rdfs:comment "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." ;
  rdfs:subClassOf obo:SO_0000705 .

obo:SO_0000120 a rdfs:Class ;
  rdfs:label "protein_coding_primary_transcript" ;
  rdfs:comment "A primary transcript that, at least in part, encodes one or more proteins." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000936 a rdfs:Class ;
  rdfs:label "vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0002350 a rdfs:Class ;
  rdfs:label "common_fragile_site" ;
  rdfs:comment "A fragile site considered part of the normal chromosomal structure." ;
  rdfs:subClassOf obo:SO_0002349 .

obo:SO_0000276 a rdfs:Class ;
  rdfs:label "miRNA" ;
  rdfs:comment "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes). Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." ;
  rdfs:subClassOf obo:SO_0000370 .

obo:SO_0002099 a rdfs:Class ;
  rdfs:label "T_cell_receptor_pseudogene" ;
  rdfs:comment "A pseudogene derived from a T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0002097 .

obo:SO_0001652 a rdfs:Class .

obo:SO_0000547 a rdfs:Class ;
  rdfs:label "inversion_derived_bipartite_duplication" ;
  rdfs:comment "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." ;
  rdfs:subClassOf obo:SO_1000038 .

obo:SO_0001317 a rdfs:Class ;
  rdfs:label "queuosine" ;
  rdfs:comment "Queuosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0001095 a rdfs:Class ;
  rdfs:label "polypeptide_cobalt_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0000879 a rdfs:Class ;
  rdfs:label "dicistronic" ;
  rdfs:comment "An attribute describing a sequence that contains the code for two gene products." ;
  rdfs:subClassOf obo:SO_0000880 .

obo:SO_0000210 a rdfs:Class ;
  rdfs:label "tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a transfer RNA (SO:0000253)." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000925 a rdfs:Class ;
  rdfs:label "insert_GU" ;
  rdfs:comment "An edit to insert a GU dinucleotide." .

obo:SO_0000836 a rdfs:Class ;
  rdfs:label "mRNA_region" ;
  rdfs:comment "A region of an mRNA." ;
  rdfs:subClassOf obo:SO_0000834 .

obo:SO_0001241 a rdfs:Class ;
  rdfs:label "encodes_alternate_transcription_start_sites" ;
  rdfs:comment "A gene that has multiple possible transcription start sites." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_1001195 a rdfs:Class ;
  rdfs:label "encodes_overlapping_peptides" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." ;
  rdfs:subClassOf obo:SO_1001189 .

obo:SO_0001288 a rdfs:Class ;
  rdfs:label "N4_acetyl_2_prime_O_methylcytidine" ;
  rdfs:comment "N4-acetyl-2'-O-methylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0001709 a rdfs:Class ;
  rdfs:label "H3K27_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001732 .

obo:SO_0000351 a rdfs:Class ;
  rdfs:label "synthetic_sequence" ;
  rdfs:comment "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." ;
  rdfs:subClassOf obo:SO_0000443 .

obo:SO_1000119 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_inactive_ligand_binding_site" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:BS_00032 a rdfs:Class .

obo:SO_0002164 a rdfs:Class ;
  rdfs:label "H2BK5_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002143 .

obo:SO_0000514 a rdfs:Class ;
  rdfs:label "J_nonamer" ;
  rdfs:comment "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000562 .

obo:SO_0001445 a rdfs:Class ;
  rdfs:label "threonine" ;
  rdfs:comment "A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000621 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter_type_3" ;
  rdfs:comment "This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. " ;
  rdfs:subClassOf obo:SO_0000171 .

obo:SO_0001755 a rdfs:Class ;
  rdfs:label "SL10_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0001136 a rdfs:Class ;
  rdfs:label "beta_turn_right_handed_type_one" ;
  rdfs:comment "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:BS_00225 a rdfs:Class .

obo:SO_0000063 a rdfs:Class ;
  rdfs:label "deficient_interchromosomal_transposition" ;
  rdfs:comment "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." ;
  rdfs:subClassOf obo:SO_1000155 .

obo:SO_0000697 a rdfs:Class ;
  rdfs:label "gene_with_stop_codon_read_through" ;
  rdfs:comment "A gene that encodes a transcript with stop codon readthrough." ;
  rdfs:subClassOf obo:SO_0000693 .

obo:SO_0001426 a rdfs:Class ;
  rdfs:label "polymerase_synthesis_read" ;
  rdfs:comment "A read produced by the polymerase based sequence by synthesis method." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0000313 a rdfs:Class ;
  rdfs:label "stem_loop" ;
  rdfs:comment "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." ;
  rdfs:subClassOf obo:SO_0000122 .

obo:SO_0002060 a rdfs:Class ;
  rdfs:label "interchromosomal_translocation" ;
  rdfs:comment "A translocation where the regions involved are from different chromosomes." ;
  rdfs:subClassOf obo:SO_1000044 .

obo:SO_0002239 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_28S_gene" ;
  rdfs:comment "A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0002054 a rdfs:Class ;
  rdfs:label "loss_of_function_variant" ;
  rdfs:comment "A sequence variant whereby the gene product has diminished or abolished function." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0001885 a rdfs:Class ;
  rdfs:label "TFBS_translocation" ;
  rdfs:comment "A feature translocation where the region contains a transcription factor binding site." ;
  rdfs:subClassOf obo:SO_0001884 .

obo:SO_0000560 a rdfs:Class ;
  rdfs:label "D_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0002358 a rdfs:Class ;
  rdfs:label "vault_RNA_gene" ;
  rdfs:comment "A gene that encodes a vault RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0001166 a rdfs:Class ;
  rdfs:label "GAGA_motif" ;
  rdfs:comment "A non directional promoter motif with consensus sequence GAGAGCG." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:BS_00214 a rdfs:Class .

obo:SO_0000403 a rdfs:Class ;
  rdfs:label "U14_snoRNA" ;
  rdfs:comment "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." ;
  rdfs:subClassOf obo:SO_0000593 .

obo:SO_0001816 a rdfs:Class ;
  rdfs:label "non_synonymous" ;
  rdfs:comment "A variant that leads to the change of an amino acid within the protein." ;
  rdfs:subClassOf obo:SO_0001814 .

obo:SO_0002177 a rdfs:Class ;
  rdfs:label "duplication_artifact" ;
  rdfs:comment "A duplication that is the result of base-calling or assembly error." ;
  rdfs:subClassOf obo:SO_0002175 .

obo:SO_0001018 a rdfs:Class ;
  rdfs:label "epitope" ;
  rdfs:comment "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." ;
  rdfs:subClassOf obo:SO_0000409 .

obo:BS_00228 a rdfs:Class .

obo:SO_0001450 a rdfs:Class ;
  rdfs:label "lysine" ;
  rdfs:comment "A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001826 a rdfs:Class ;
  rdfs:label "disruptive_inframe_deletion" ;
  rdfs:comment "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." ;
  rdfs:subClassOf obo:SO_0001822 .

obo:SO_0001626 a rdfs:Class ;
  rdfs:label "incomplete_terminal_codon_variant" ;
  rdfs:comment "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." ;
  rdfs:subClassOf obo:SO_0001590 , obo:SO_0001650 .

obo:SO_0000324 a rdfs:Class ;
  rdfs:label "tag" ;
  rdfs:comment "A nucleotide sequence that may be used to identify a larger sequence." ;
  rdfs:subClassOf obo:SO_0000696 .

obo:SO_0000121 a rdfs:Class ;
  rdfs:label "forward_primer" ;
  rdfs:comment "A single stranded oligo used for polymerase chain reaction." ;
  rdfs:subClassOf obo:SO_0000112 .

obo:SO_0000290 a rdfs:Class ;
  rdfs:label "dinucleotide_repeat_microsatellite_feature" ;
  rdfs:comment "A region of a repeating dinucleotide sequence (two bases)." ;
  rdfs:subClassOf obo:SO_0000289 .

obo:SO_0000903 a rdfs:Class ;
  rdfs:label "endogenous_retroviral_sequence" ;
  rdfs:comment "Endogenous DNA sequence that are likely to have arisen from retroviruses." ;
  rdfs:subClassOf obo:SO_0000751 .

obo:SO_0000240 a rdfs:Class ;
  rdfs:label "chromosome_variation" ;
  rdfs:comment "A deviation in chromosome structure or number." ;
  rdfs:subClassOf obo:SO_0001507 .

obo:SO_0001785 a rdfs:Class ;
  rdfs:label "structural_alteration" ;
  rdfs:comment "An alteration of the genome that leads to a change in the structure of one or more chromosomes." ;
  rdfs:subClassOf obo:SO_0001059 .

obo:SO_0001278 a rdfs:Class ;
  rdfs:label "one_methylinosine" ;
  rdfs:comment "1-methylinosine is a modified inosine." ;
  rdfs:subClassOf obo:SO_0001274 .

obo:SO_0001939 a rdfs:Class ;
  rdfs:label "H4K12_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001972 .

obo:SO_0001045 a rdfs:Class ;
  rdfs:label "cointegrated_plasmid" ;
  rdfs:comment "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." ;
  rdfs:subClassOf obo:SO_0001039 .

obo:SO_0000110 a rdfs:Class ;
  rdfs:label "sequence_feature" ;
  rdfs:comment "Any extent of continuous biological sequence." .

obo:SO_1001271 a rdfs:Class ;
  rdfs:label "archaeal_intron" ;
  rdfs:comment "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." ;
  rdfs:subClassOf obo:SO_0001216 .

obo:SO_0000150 a rdfs:Class ;
  rdfs:label "read" ;
  rdfs:comment "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_1001189 a rdfs:Class ;
  rdfs:label "encodes_greater_than_1_polypeptide" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide." ;
  rdfs:subClassOf obo:SO_0000463 .

obo:SO_0001505 a rdfs:Class ;
  rdfs:label "reference_genome" ;
  rdfs:comment "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." ;
  rdfs:subClassOf obo:SO_0001026 .

obo:SO_0000189 a rdfs:Class ;
  rdfs:label "non_LTR_retrotransposon" ;
  rdfs:comment "A retrotransposon without long terminal repeat sequences." ;
  rdfs:subClassOf obo:SO_0000180 .

obo:SO_0005841 a rdfs:Class ;
  rdfs:label "methylation_guide_snoRNA" ;
  rdfs:comment "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." ;
  rdfs:subClassOf obo:SO_0000593 .

obo:SO_0000667 a rdfs:Class ;
  rdfs:label "insertion" ;
  rdfs:comment "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." ;
  rdfs:subClassOf obo:SO_0001059 , obo:SO_0001411 .

obo:SO_1000123 a rdfs:Class ;
  rdfs:label "polypeptide_post_translational_processing_affected" .

obo:SO_0000161 a rdfs:Class ;
  rdfs:label "methylated_adenine" ;
  rdfs:comment "A modified base in which adenine has been methylated." ;
  rdfs:subClassOf obo:SO_0000306 , obo:SO_0001962 .

obo:SO_0001874 a rdfs:Class ;
  rdfs:label "intrachromosomal_breakpoint" ;
  rdfs:comment "A rearrangement breakpoint within the same chromosome." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0001126 a rdfs:Class ;
  rdfs:label "serine_threonine_motif" ;
  rdfs:comment "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0000753 a rdfs:Class ;
  rdfs:label "clone_insert" ;
  rdfs:comment "The region of sequence that has been inserted and is being propagated by the clone." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0002138 a rdfs:Class ;
  rdfs:label "predicted_transcript" ;
  rdfs:comment "A transcript feature that has been predicted but is not yet validated." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000910 a rdfs:Class ;
  rdfs:label "orphan" ;
  rdfs:comment "A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." ;
  rdfs:subClassOf obo:SO_0000732 .

obo:SO_0000690 a rdfs:Class ;
  rdfs:label "gene_with_polycistronic_transcript" ;
  rdfs:comment "A gene that encodes a polycistronic transcript." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000989 a rdfs:Class ;
  rdfs:label "class_II_RNA" ;
  rdfs:comment "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002288 a rdfs:Class ;
  rdfs:label "Ngaro_YR_retrotransposon" ;
  rdfs:comment "Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs." ;
  rdfs:subClassOf obo:SO_0002286 .

obo:SO_0002008 a rdfs:Class ;
  rdfs:label "rare_amino_acid_variant" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." ;
  rdfs:subClassOf obo:SO_0001586 .

obo:SO_0000881 a rdfs:Class ;
  rdfs:label "recoded" ;
  rdfs:comment "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." ;
  rdfs:subClassOf obo:SO_0000863 .

obo:SO_0001621 a rdfs:Class ;
  rdfs:label "NMD_transcript_variant" ;
  rdfs:comment "A variant in a transcript that is the target of nonsense-mediated mRNA decay." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0001325 a rdfs:Class ;
  rdfs:label "N2_methylguanosine" ;
  rdfs:comment "N2_methylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0002151 a rdfs:Class ;
  rdfs:label "non_AUG_initiated_uORF" ;
  rdfs:comment "A uORF beginning with a codon other than AUG." ;
  rdfs:subClassOf obo:SO_0002027 .

obo:SO_0001535 a rdfs:Class ;
  rdfs:label "P_TIR_transposon" ;
  rdfs:comment "A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0000287 a rdfs:Class ;
  rdfs:label "fusion_gene" ;
  rdfs:comment "A gene that is a fusion." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001376 a rdfs:Class ;
  rdfs:label "five_methyldihydrouridine" ;
  rdfs:comment "5_methyldihydrouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002319 a rdfs:Class ;
  rdfs:label "NMD_triggering_variant" ;
  rdfs:comment "A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0002270 a rdfs:Class ;
  rdfs:label "RTE_LINE_retrotransposon" ;
  rdfs:comment "RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain." ;
  rdfs:subClassOf obo:SO_0000194 .

obo:SO_1001282 a rdfs:Class ;
  rdfs:label "UAG_stop_codon_signal" ;
  rdfs:comment "A stop codon signal for a UAG stop codon redefinition." ;
  rdfs:subClassOf obo:SO_1001288 .

obo:SO_0001147 a rdfs:Class ;
  rdfs:label "natural_variant_site" ;
  rdfs:comment "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." ;
  rdfs:subClassOf obo:SO_0001146 .

obo:SO_0001034 a rdfs:Class ;
  rdfs:label "miRtron" ;
  rdfs:comment "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." ;
  rdfs:subClassOf obo:SO_0001014 .

obo:SO_0002347 a rdfs:Class ;
  rdfs:label "plastid_SSU_rRNA" ;
  rdfs:comment "Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes." ;
  rdfs:subClassOf obo:SO_0002346 .

obo:SO_0001206 a rdfs:Class ;
  rdfs:label "T3_RNA_Polymerase_Promoter" ;
  rdfs:comment "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0001204 .

obo:SO_0100010 a rdfs:Class ;
  rdfs:label "no_output" ;
  rdfs:comment "An experimental region wherean analysis has been run and not produced any annotation." ;
  rdfs:subClassOf obo:SO_0000703 .

obo:SO_0001670 a rdfs:Class ;
  rdfs:label "distal_promoter_element" ;
  rdfs:comment "A regulatory promoter element that is distal from the TSS." ;
  rdfs:subClassOf obo:SO_0001678 .

obo:SO_0001499 a rdfs:Class ;
  rdfs:label "whole_genome_sequence_status" ;
  rdfs:comment "The status of whole genome sequence." ;
  rdfs:subClassOf obo:SO_0000905 .

obo:SO_0001669 a rdfs:Class ;
  rdfs:label "RNApol_II_core_promoter" ;
  rdfs:comment "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." ;
  rdfs:subClassOf obo:SO_0000170 .

obo:SO_0001217 a rdfs:Class ;
  rdfs:label "protein_coding_gene" ;
  rdfs:comment "A gene that codes for an RNA that can be translated into a protein." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000717 a rdfs:Class ;
  rdfs:label "reading_frame" ;
  rdfs:comment "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0000817 a rdfs:Class ;
  rdfs:label "wild_type" ;
  rdfs:comment "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001835 a rdfs:Class ;
  rdfs:label "N_region" ;
  rdfs:comment "Extra nucleotides inserted between rearranged immunoglobulin segments." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0002331 a rdfs:Class ;
  rdfs:label "accessible_DNA_region" ;
  rdfs:comment "A region of DNA that is depleted of nucleosomes and accessible to DNA-binding proteins including transcription factors and nucleases." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_1001265 a rdfs:Class ;
  rdfs:label "mRNA_recoded_by_codon_redefinition" ;
  rdfs:comment "A recoded_mRNA that was modified by an alteration of codon meaning." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_1001261 .

obo:SO_0000493 a rdfs:Class ;
  rdfs:label "three_prime_D_heptamer" ;
  rdfs:comment "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000561 .

obo:SO_0001151 a rdfs:Class ;
  rdfs:label "beta_turn_type_six_a" ;
  rdfs:comment "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." ;
  rdfs:subClassOf obo:SO_0001150 .

obo:SO_0002194 a rdfs:Class ;
  rdfs:label "unprocessed_pseudogenic_rRNA" ;
  rdfs:comment "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions." ;
  rdfs:subClassOf obo:SO_0000777 .

obo:SO_0000381 a rdfs:Class ;
  rdfs:label "group_IIA_intron" ;
  rdfs:comment "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon." ;
  rdfs:subClassOf obo:SO_0000603 .

obo:SO_1000138 a rdfs:Class ;
  rdfs:label "homo_compound_chromosome" ;
  rdfs:comment "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." ;
  rdfs:subClassOf obo:SO_1000042 .

obo:SO_0002100 a rdfs:Class ;
  rdfs:label "IG_C_pseudogene" ;
  rdfs:comment "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon." ;
  rdfs:subClassOf obo:SO_0002098 .

obo:SO_0000191 a rdfs:Class ;
  rdfs:label "interior_intron" ;
  rdfs:comment "An intron that is not the most 3-prime or the most 5-prime in a given transcript." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0002378 a rdfs:Class ;
  rdfs:label "U3_snoRNA_gene" ;
  rdfs:comment "A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." ;
  rdfs:subClassOf obo:SO_0002375 .

obo:SO_0001336 a rdfs:Class ;
  rdfs:label "wyosine" ;
  rdfs:comment "Wyosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_1001247 a rdfs:Class ;
  rdfs:label "orphan_CDS" ;
  rdfs:comment "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." ;
  rdfs:subClassOf obo:SO_1001254 .

obo:SO_0000846 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter_type_2_region" ;
  rdfs:comment "A region of sequence which is a promoter for RNA polymerase III type 2." .

obo:SO_0000764 a rdfs:Class ;
  rdfs:label "BAC_clone" .

obo:SO_0002255 a rdfs:Class ;
  rdfs:label "stem" ;
  rdfs:comment "The portion of a stem loop where the RNA is folded back upon itself. " ;
  rdfs:subClassOf obo:SO_0002253 .

obo:SO_0001976 a rdfs:Class ;
  rdfs:label "three_prime_sticky_end_restriction_enzyme_cleavage_site" ;
  rdfs:comment "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." ;
  rdfs:subClassOf obo:SO_0001692 .

obo:SO_0001238 a rdfs:Class ;
  rdfs:label "major_TSS" ;
  rdfs:comment "The tanscription start site that is most frequently used for transcription of a gene." ;
  rdfs:subClassOf obo:SO_0000315 .

obo:SO_0001969 a rdfs:Class ;
  rdfs:label "coding_transcript_intron_variant" ;
  rdfs:comment "A transcript variant occurring within an intron of a coding transcript." ;
  rdfs:subClassOf obo:SO_0001627 , obo:SO_0001968 .

obo:SO_0000589 a rdfs:Class ;
  rdfs:label "SRP_RNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a signal recognition particle RNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0002041 a rdfs:Class ;
  rdfs:label "miR_encoding_vaultRNA_primary_transcript" ;
  rdfs:comment "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0002040 .

obo:SO_0000533 a rdfs:Class ;
  rdfs:label "V_heptamer" ;
  rdfs:comment "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000561 .

obo:SO_0000634 a rdfs:Class ;
  rdfs:label "polycistronic_mRNA" ;
  rdfs:comment "An mRNA that encodes multiple proteins from at least two non-overlapping regions." ;
  rdfs:subClassOf obo:SO_0000078 , obo:SO_0000234 .

obo:SO_0000824 a rdfs:Class ;
  rdfs:label "macronuclear_chromosome" ;
  rdfs:comment "A chromosome originating in a macronucleus." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0100017 a rdfs:Class ;
  rdfs:label "polypeptide_conserved_motif" ;
  rdfs:comment "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." ;
  rdfs:subClassOf obo:SO_0001067 .

obo:SO_0000526 a rdfs:Class ;
  rdfs:label "V_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0001928 a rdfs:Class ;
  rdfs:label "distal_duplication" ;
  rdfs:comment "A duplication of the distal region of a chromosome." ;
  rdfs:subClassOf obo:SO_1000035 .

obo:SO_0002266 a rdfs:Class ;
  rdfs:label "Bel_Pao_LTR_retrotransposon" ;
  rdfs:comment "LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001763 a rdfs:Class ;
  rdfs:label "variant_frequency" ;
  rdfs:comment "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." ;
  rdfs:subClassOf obo:SO_0001761 .

obo:SO_0001296 a rdfs:Class ;
  rdfs:label "two_methyladenosine" ;
  rdfs:comment "2_methyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000018 a rdfs:Class ;
  rdfs:label "linkage_group" ;
  rdfs:comment "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001659 a rdfs:Class ;
  rdfs:label "promoter_element" ;
  rdfs:comment "An element that can exist within the promoter region of a gene." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000515 a rdfs:Class ;
  rdfs:label "J_heptamer" ;
  rdfs:comment "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000561 .

obo:SO_0001543 a rdfs:Class ;
  rdfs:label "transcript_processing_variant" ;
  rdfs:comment "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001538 .

obo:SO_0000739 a rdfs:Class ;
  rdfs:label "nucleomorphic_sequence" ;
  rdfs:comment "DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic." ;
  rdfs:subClassOf obo:SO_0000736 .

obo:SO_0001983 a rdfs:Class ;
  rdfs:label "5_prime_UTR_premature_start_codon_variant" ;
  rdfs:comment "A 5' UTR variant where a premature start codon is introduced, moved or lost." ;
  rdfs:subClassOf obo:SO_0001623 .

obo:SO_0002169 a rdfs:Class ;
  rdfs:label "splice_polypyrimidine_tract_variant" ;
  rdfs:comment "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0002144 a rdfs:Class ;
  rdfs:label "histone_2AZ_acetylation_site" ;
  rdfs:comment "A histone 2AZ modification where the modification is the acetylation of the residue." ;
  rdfs:subClassOf obo:SO_0002142 .

obo:SO_0002360 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_gene" ;
  rdfs:comment "A gene that codes for cytosolic rRNA." ;
  rdfs:subClassOf obo:SO_0001637 .

obo:SO_0001304 a rdfs:Class ;
  rdfs:label "N6_glycinylcarbamoyladenosine" ;
  rdfs:comment "N6_glycinylcarbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_1000081 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_rate_of_transcription" ;
  rdfs:comment "A mutation that alters the rate a which transcription of the sequence occurs." .

obo:SO_0005852 a rdfs:Class ;
  rdfs:label "gene_subarray" ;
  rdfs:comment "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." ;
  rdfs:subClassOf obo:SO_0005855 .

obo:SO_0001591 a rdfs:Class ;
  rdfs:label "frame_restoring_variant" ;
  rdfs:comment "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." ;
  rdfs:subClassOf obo:SO_0001589 .

obo:SO_0001419 a rdfs:Class ;
  rdfs:label "cis_splice_site" ;
  rdfs:comment "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." ;
  rdfs:subClassOf obo:SO_0000162 .

obo:SO_0000056 a rdfs:Class ;
  rdfs:label "hypoploid" ;
  rdfs:comment "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." ;
  rdfs:subClassOf obo:SO_0000054 .

obo:SO_0002121 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_gene" ;
  rdfs:comment "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci)." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0000205 a rdfs:Class ;
  rdfs:label "three_prime_UTR" ;
  rdfs:comment "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." ;
  rdfs:subClassOf obo:SO_0000203 .

obo:SO_0001643 a rdfs:Class ;
  rdfs:label "telomerase_RNA_gene" ;
  rdfs:comment "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0001182 a rdfs:Class ;
  rdfs:label "iron_responsive_element" ;
  rdfs:comment "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." ;
  rdfs:subClassOf obo:SO_0000837 .

obo:SO_0000019 a rdfs:Class .

obo:SO_0001365 a rdfs:Class ;
  rdfs:label "five_methylaminomethyl_two_thiouridine" ;
  rdfs:comment "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001168 a rdfs:Class ;
  rdfs:label "NDM3_motif" ;
  rdfs:comment "A non directional promoter motif with consensus sequence GAAAGCT." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002212 a rdfs:Class ;
  rdfs:label "linear_plasmid" ;
  rdfs:comment "A self replicating linear nucleic acid molecule that is distinct from a chromosome in the organism. They are capped by terminal proteins covalently bound to the 5' ends of the DNA." ;
  rdfs:subClassOf obo:SO_0000155 .

obo:SO_0001805 a rdfs:Class ;
  rdfs:label "destruction_box" ;
  rdfs:comment "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." ;
  rdfs:subClassOf obo:SO_0100017 .

obo:SO_0001639 a rdfs:Class ;
  rdfs:label "RNase_P_RNA_gene" ;
  rdfs:comment "A gene that encodes an RNase P RNA." ;
  rdfs:subClassOf obo:SO_0002180 .

obo:SO_0002304 a rdfs:Class ;
  rdfs:label "topologically_associated_domain" ;
  rdfs:comment "An instance of a self-interacting DNA region flanked by left and right TAD boundaries." ;
  rdfs:subClassOf obo:SO_0001412 .

obo:SO_0000899 a rdfs:Class ;
  rdfs:label "nuclear_mitochondrial" ;
  rdfs:comment "An attribute describing a nuclear pseudogene of a mitochndrial gene." .

obo:SO_0001007 a rdfs:Class ;
  rdfs:label "cryptic_prophage" ;
  rdfs:comment "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_0001488 a rdfs:Class ;
  rdfs:label "improved_high_quality_draft" ;
  rdfs:comment "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0001103 a rdfs:Class ;
  rdfs:label "polypeptide_zinc_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001056 a rdfs:Class ;
  rdfs:label "splicing_regulatory_region" ;
  rdfs:comment "A regulatory_region that modulates splicing." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0000892 a rdfs:Class ;
  rdfs:label "positively_autoregulated_gene" ;
  rdfs:comment "A gene that is positively autoregulated." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001997 a rdfs:Class ;
  rdfs:label "subtelomere" ;
  rdfs:comment "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." ;
  rdfs:subClassOf obo:SO_0000628 .

obo:BS_00158 a rdfs:Class .

obo:SO_1001254 a rdfs:Class ;
  rdfs:label "CDS_predicted" ;
  rdfs:comment "A CDS that is predicted." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:SO_0001527 a rdfs:Class ;
  rdfs:label "peptide_localization_signal" ;
  rdfs:comment "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0002095 a rdfs:Class ;
  rdfs:label "scaRNA" ;
  rdfs:comment "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs)." ;
  rdfs:subClassOf obo:SO_0000275 .

obo:SO_0000898 a rdfs:Class ;
  rdfs:label "epigenetically_modified_gene" ;
  rdfs:comment "A gene that is epigenetically modified." ;
  rdfs:subClassOf obo:SO_0000704 , obo:SO_0001720 .

obo:SO_0001157 a rdfs:Class ;
  rdfs:label "DMv4_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000798 a rdfs:Class ;
  rdfs:label "engineered_transposable_element" ;
  rdfs:comment "TE that has been modified by manipulations in vitro." ;
  rdfs:subClassOf obo:SO_0000101 , obo:SO_0000804 .

obo:SO_0000959 a rdfs:Class ;
  rdfs:label "linear_single_stranded_DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." ;
  rdfs:subClassOf obo:SO_0000956 .

obo:SO_0001323 a rdfs:Class ;
  rdfs:label "archaeosine" ;
  rdfs:comment "Archaeosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_1000092 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_complex_change_of_translational_product" ;
  rdfs:comment "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." .

obo:SO_0001804 a rdfs:Class ;
  rdfs:label "DDB_box" ;
  rdfs:comment "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." ;
  rdfs:subClassOf obo:SO_0001093 .

obo:SO_0000094 a rdfs:Class ;
  rdfs:label "cyanelle_gene" ;
  rdfs:comment "A gene from cyanelle sequence." ;
  rdfs:subClassOf obo:SO_0000090 .

obo:SO_0000440 a rdfs:Class ;
  rdfs:label "vector_replicon" ;
  rdfs:comment "A replicon that has been modified to act as a vector for foreign sequence." ;
  rdfs:subClassOf obo:SO_0001235 .

obo:BS_00206 a rdfs:Class .

obo:SO_0000295 a rdfs:Class ;
  rdfs:label "U12_intron" ;
  rdfs:comment "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." ;
  rdfs:subClassOf obo:SO_0000662 .

obo:SO_0001585 a rdfs:Class ;
  rdfs:label "conservative_missense_variant" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." ;
  rdfs:subClassOf obo:SO_0001583 .

obo:SO_0000675 a rdfs:Class ;
  rdfs:label "canonical_splice_site" ;
  rdfs:comment "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." .

obo:SO_0002076 a rdfs:Class ;
  rdfs:label "incomplete_transcript_3UTR_variant" ;
  rdfs:comment "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002075 .

obo:SO_0001173 a rdfs:Class ;
  rdfs:label "anticodon_loop" ;
  rdfs:comment "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." ;
  rdfs:subClassOf obo:SO_0001172 .

obo:SO_0002082 a rdfs:Class ;
  rdfs:label "incomplete_transcript_coding_splice_variant" ;
  rdfs:comment "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript." ;
  rdfs:subClassOf obo:SO_0002079 .

obo:SO_0000921 a rdfs:Class ;
  rdfs:label "insert_dinucleotide" ;
  rdfs:comment "An edit to insert a dinucleotide." .

obo:SO_0000645 a rdfs:Class ;
  rdfs:label "antisense_primary_transcript" ;
  rdfs:comment "The reverse complement of the primary transcript." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0001088 a rdfs:Class ;
  rdfs:label "disulfide_bond" ;
  rdfs:comment "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." .

obo:BS_00232 a rdfs:Class .

obo:SO_0000001 a rdfs:Class ;
  rdfs:label "region" ;
  rdfs:comment "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." ;
  rdfs:subClassOf obo:SO_0000110 .

obo:SO_0002105 a rdfs:Class ;
  rdfs:label "translated_processed_pseudogene" ;
  rdfs:comment "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." ;
  rdfs:subClassOf obo:SO_0000043 .

obo:SO_0002361 a rdfs:Class ;
  rdfs:label "cytosolic_LSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for cytosolic LSU rRNA." ;
  rdfs:subClassOf obo:SO_0002360 .

obo:SO_0001432 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_polyadenylation" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000306 a rdfs:Class ;
  rdfs:label "methylated_DNA_base_feature" ;
  rdfs:comment "A nucleotide modified by methylation." ;
  rdfs:subClassOf obo:SO_0000305 .

obo:SO_0000143 a rdfs:Class ;
  rdfs:label "assembly_component" ;
  rdfs:comment "A region of known length which may be used to manufacture a longer region." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0001264 a rdfs:Class ;
  rdfs:label "gRNA_gene" ;
  rdfs:comment "A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0000418 a rdfs:Class ;
  rdfs:label "signal_peptide" ;
  rdfs:comment "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." ;
  rdfs:subClassOf obo:SO_0001527 .

obo:SO_0001538 a rdfs:Class ;
  rdfs:label "transcript_function_variant" ;
  rdfs:comment "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0000762 a rdfs:Class ;
  rdfs:label "PAC_clone" .

obo:SO_0000611 a rdfs:Class ;
  rdfs:label "branch_site" ;
  rdfs:comment "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." ;
  rdfs:subClassOf obo:SO_0000841 .

obo:SO_0002336 a rdfs:Class ;
  rdfs:label "cytosolic_rRNA_2S_gene" ;
  rdfs:comment "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera." ;
  rdfs:subClassOf obo:SO_0002361 .

obo:SO_0000310 a rdfs:Class ;
  rdfs:label "predicted_ab_initio_computation" .

obo:SO_0000458 a rdfs:Class ;
  rdfs:label "D_gene_segment" ;
  rdfs:comment "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." ;
  rdfs:subClassOf obo:SO_0000460 .

obo:SO_0000255 a rdfs:Class ;
  rdfs:label "rRNA_small_subunit_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a small ribosomal subunit RNA." ;
  rdfs:subClassOf obo:SO_0000209 .

obo:SO_0002342 a rdfs:Class ;
  rdfs:label "sncRNA_gene" ;
  rdfs:comment "A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0001408 a rdfs:Class ;
  rdfs:label "cleaved_for_gpi_anchor_region" ;
  rdfs:comment "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_0001099 a rdfs:Class ;
  rdfs:label "polypeptide_manganese_ion_contact_site" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." ;
  rdfs:subClassOf obo:SO_0001092 .

obo:SO_0001896 a rdfs:Class ;
  rdfs:label "transposable_element_CDS" ;
  rdfs:comment "A CDS that is part of a transposable element." ;
  rdfs:subClassOf obo:SO_0000316 .

obo:SO_0002389 a rdfs:Class ;
  rdfs:label "5_prime_UTR_uORF_stop_codon_loss_variant" ;
  rdfs:comment "A 5' UTR variant where the stop codon of an upstream open reading frame is lost." ;
  rdfs:subClassOf obo:SO_0002386 .

obo:SO_0000629 a rdfs:Class ;
  rdfs:label "five_prime_open_reading_frame" ;
  rdfs:comment "An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001766 a rdfs:Class ;
  rdfs:label "polymorphic_variant" ;
  rdfs:comment "A variant that affects one of several possible alleles at that location, such as the major histocompatibility complex (MHC) genes." ;
  rdfs:subClassOf obo:SO_0001763 .

obo:SO_0001162 a rdfs:Class ;
  rdfs:label "MTE" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000436 a rdfs:Class ;
  rdfs:label "ARS" ;
  rdfs:comment "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001619 a rdfs:Class ;
  rdfs:label "non_coding_transcript_variant" ;
  rdfs:comment "A transcript variant of a non coding RNA gene." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0001781 a rdfs:Class ;
  rdfs:label "de_novo_variant" ;
  rdfs:comment "A variant arising in the offspring that is not found in either of the parents." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0000954 a rdfs:Class ;
  rdfs:label "DNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, DNA molecule." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0000244 a rdfs:Class ;
  rdfs:label "four_cutter_restriction_site" .

obo:SO_0000407 a rdfs:Class ;
  rdfs:label "cytosolic_18S_rRNA" ;
  rdfs:comment "Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes." ;
  rdfs:subClassOf obo:SO_0000650 .

obo:SO_0002111 a rdfs:Class ;
  rdfs:label "pseudogene_processed_transcript" ;
  rdfs:comment "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus)." ;
  rdfs:subClassOf obo:SO_0001503 .

obo:SO_0001081 a rdfs:Class ;
  rdfs:label "helix_turn_helix" ;
  rdfs:comment "A motif comprising two helices separated by a turn." ;
  rdfs:subClassOf obo:SO_0001079 .

obo:SO_0001703 a rdfs:Class ;
  rdfs:label "H3K9_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0001749 a rdfs:Class ;
  rdfs:label "SL4_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0001662 a rdfs:Class ;
  rdfs:label "RNA_polymerase_III_TATA_box" ;
  rdfs:comment "A TATA box core promoter of a gene transcribed by RNA polymerase III." ;
  rdfs:subClassOf obo:SO_0000174 .

obo:SO_0001401 a rdfs:Class ;
  rdfs:label "modified_L_leucine" ;
  rdfs:comment "A post translationally modified leucine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001596 a rdfs:Class ;
  rdfs:label "transcript_secondary_structure_variant" ;
  rdfs:comment "A sequence variant within a transcript that changes the secondary structure of the RNA product." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0000233 a rdfs:Class ;
  rdfs:label "mature_transcript" ;
  rdfs:comment "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0000332 a rdfs:Class ;
  rdfs:label "coding_conserved_region" ;
  rdfs:comment "Coding region of sequence similarity by descent from a common ancestor." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0001516 a rdfs:Class ;
  rdfs:label "free" ;
  rdfs:comment "The quality of a duplication where the new region exists independently of the original." ;
  rdfs:subClassOf obo:SO_0001523 .

obo:SO_0001155 a rdfs:Class ;
  rdfs:label "beta_turn_type_eight" ;
  rdfs:comment "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:SO_0000962 a rdfs:Class ;
  rdfs:label "single_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, single-stranded RNA molecule." ;
  rdfs:subClassOf obo:SO_0000961 .

obo:SO_0000023 a rdfs:Class ;
  rdfs:label "K_turn_RNA_motif" ;
  rdfs:comment "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." ;
  rdfs:subClassOf obo:SO_0000021 .

obo:SO_0000136 a rdfs:Class ;
  rdfs:label "paternally_imprinted" ;
  rdfs:comment "The paternal copy of the gene is modified, rendering it transcriptionally silent." ;
  rdfs:subClassOf obo:SO_0000134 .

obo:SO_1000162 a rdfs:Class ;
  rdfs:label "unoriented_intrachromosomal_transposition" ;
  rdfs:comment "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." ;
  rdfs:subClassOf obo:SO_1000041 .

obo:SO_0002189 a rdfs:Class ;
  rdfs:label "allelic_pseudogene" ;
  rdfs:comment "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." ;
  rdfs:subClassOf obo:SO_0001759 .

obo:SO_0000728 a rdfs:Class ;
  rdfs:label "intein" ;
  rdfs:comment "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." ;
  rdfs:subClassOf obo:SO_0100011 .

obo:SO_1000083 a rdfs:Class ;
  rdfs:label "sequence_variant_increasing_transcript_stability" ;
  rdfs:comment "Sequence variant increases the stability (half-life) of the transcript." .

obo:SO_0000273 a rdfs:Class ;
  rdfs:label "valyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0000447 a rdfs:Class ;
  rdfs:label "five_prime_UTR_intron" ;
  rdfs:comment "An intron located in the 5' UTR." ;
  rdfs:subClassOf obo:SO_0000446 .

obo:SO_1000011 a rdfs:Class ;
  rdfs:label "C_to_T_transition" ;
  rdfs:comment "A transition of a cytidine to a thymine." ;
  rdfs:subClassOf obo:SO_1000010 .

obo:SO_0000544 a rdfs:Class ;
  rdfs:label "helitron" ;
  rdfs:comment "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." ;
  rdfs:subClassOf obo:SO_0000182 .

obo:SO_0002394 a rdfs:Class ;
  rdfs:label "decreased_enzyme_activity_variant" ;
  rdfs:comment "A decrease in the activity of an enzyme, as a result of a variant in the gene that encodes the enzyme or a regulatory region." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0001196 a rdfs:Class ;
  rdfs:label "S_GNA" ;
  rdfs:comment "An attribute describing a GNA sequence in the (S)-GNA enantiomer." ;
  rdfs:subClassOf obo:SO_0001192 .

obo:SO_0000066 a rdfs:Class ;
  rdfs:label "gene_by_polyadenylation_attribute" .

obo:SO_0001454 a rdfs:Class ;
  rdfs:label "glutamic_acid" ;
  rdfs:comment "A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000784 a rdfs:Class ;
  rdfs:label "foreign" ;
  rdfs:comment "An attribute to describe a region from another species." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001893 a rdfs:Class ;
  rdfs:label "transcript_ablation" ;
  rdfs:comment "A feature ablation whereby the deleted region includes a transcript feature." ;
  rdfs:subClassOf obo:SO_0001879 .

obo:SO_0002010 a rdfs:Class ;
  rdfs:label "pyrrolysine_loss" ;
  rdfs:comment "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." ;
  rdfs:subClassOf obo:SO_0002008 .

obo:SO_0000505 a rdfs:Class ;
  rdfs:label "D_DJ_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000624 a rdfs:Class ;
  rdfs:label "telomere" ;
  rdfs:comment "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." ;
  rdfs:subClassOf obo:SO_0000628 .

obo:SO_0001179 a rdfs:Class ;
  rdfs:label "U3_snoRNA" ;
  rdfs:comment "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." ;
  rdfs:subClassOf obo:SO_0000593 .

obo:SO_0001285 a rdfs:Class ;
  rdfs:label "N4_acetylcytidine" ;
  rdfs:comment "N4-acetylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_0000876 a rdfs:Class ;
  rdfs:label "bound_by_nucleic_acid" ;
  rdfs:comment "An attribute describing a sequence that is bound by a nucleic acid." ;
  rdfs:subClassOf obo:SO_0000277 .

obo:SO_0001478 a rdfs:Class ;
  rdfs:label "promoter_trap_construct" ;
  rdfs:comment "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." ;
  rdfs:subClassOf obo:SO_0000637 .

obo:SO_0001077 a rdfs:Class ;
  rdfs:label "transmembrane_polypeptide_region" ;
  rdfs:comment "Polypeptide region traversing the lipid bilayer." ;
  rdfs:subClassOf obo:SO_0001075 .

obo:SO_0000284 a rdfs:Class ;
  rdfs:label "type_I_enzyme_restriction_site" ;
  rdfs:comment "The recognition site is bipartite and interrupted." .

obo:SO_0000773 a rdfs:Class ;
  rdfs:label "pathogenic_island" ;
  rdfs:comment "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_0000542 a rdfs:Class ;
  rdfs:label "V_DJ_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_1000050 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_no_change_in_transcript" ;
  rdfs:comment "No effect on the state of the RNA." .

obo:SO_0000656 a rdfs:Class ;
  rdfs:label "stRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0001601 a rdfs:Class ;
  rdfs:label "conformational_change_variant" ;
  rdfs:comment "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." ;
  rdfs:subClassOf obo:SO_0001599 .

obo:SO_0001807 a rdfs:Class ;
  rdfs:label "KEN_box" ;
  rdfs:comment "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." ;
  rdfs:subClassOf obo:SO_0100017 .

obo:SO_0002315 a rdfs:Class ;
  rdfs:label "increased_gene_product_level" ;
  rdfs:comment "A variant that increases the level or amount of gene product produced." ;
  rdfs:subClassOf obo:SO_0002314 .

obo:SO_0001383 a rdfs:Class ;
  rdfs:label "histone_binding_site" ;
  rdfs:comment "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." ;
  rdfs:subClassOf obo:SO_0001654 .

obo:SO_1000173 a rdfs:Class ;
  rdfs:label "tandem_duplication" ;
  rdfs:comment "A duplication consisting of 2 identical adjacent regions." ;
  rdfs:subClassOf obo:SO_1000035 .

obo:SO_0001115 a rdfs:Class ;
  rdfs:label "left_handed_peptide_helix" ;
  rdfs:comment "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." ;
  rdfs:subClassOf obo:SO_0001114 .

obo:SO_0000216 a rdfs:Class ;
  rdfs:label "glutamic_acid_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding glutaminyl tRNA (SO:0000260)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000321 a rdfs:Class ;
  rdfs:label "mRNA_with_plus_1_frameshift" ;
  rdfs:comment "An mRNA with a plus 1 frameshift." ;
  rdfs:subClassOf obo:SO_0000108 .

obo:SO_1000134 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_polypeptide_fusion" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000034 a rdfs:Class ;
  rdfs:label "morpholino_oligo" ;
  rdfs:comment "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." ;
  rdfs:subClassOf obo:SO_0001247 .

obo:SO_0000007 a rdfs:Class ;
  rdfs:label "read_pair" ;
  rdfs:comment "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0001443 a rdfs:Class ;
  rdfs:label "glycine" ;
  rdfs:comment "A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000686 a rdfs:Class ;
  rdfs:label "translocation_element" ;
  rdfs:comment "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." ;
  rdfs:subClassOf obo:SO_1000044 .

obo:SO_0002126 a rdfs:Class ;
  rdfs:label "IG_V_gene" ;
  rdfs:comment "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002122 .

obo:SO_0000802 a rdfs:Class ;
  rdfs:label "assortment_derived_deficiency" ;
  rdfs:comment "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." ;
  rdfs:subClassOf obo:SO_0001504 .

obo:SO_0002228 a rdfs:Class ;
  rdfs:label "CDS_five_prime_extension" ;
  rdfs:comment "A sequence variant extending the CDS at the 5' end, that causes elongation of the resulting polypeptide sequence at the N terminus." ;
  rdfs:subClassOf obo:SO_0002227 .

obo:SO_0001312 a rdfs:Class ;
  rdfs:label "N6_2_prime_O_dimethyladenosine" ;
  rdfs:comment "N6_2prime_O_dimethyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000887 a rdfs:Class ;
  rdfs:label "translationally_frameshifted" ;
  rdfs:comment "Recoding by frameshifting a particular site." ;
  rdfs:subClassOf obo:SO_0000881 .

obo:SO_0000813 a rdfs:Class ;
  rdfs:label "partially_processed_cDNA_clone" ;
  rdfs:comment "A cDNA invalidated clone by partial processing." ;
  rdfs:subClassOf obo:SO_0000809 .

obo:SO_0000157 a rdfs:Class ;
  rdfs:label "phagemid" ;
  rdfs:comment "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0000105 a rdfs:Class ;
  rdfs:label "chromosome_arm" ;
  rdfs:comment "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0002155 a rdfs:Class ;
  rdfs:label "meiotic_recombination_region" ;
  rdfs:comment "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:SO_0001343 a rdfs:Class ;
  rdfs:label "N2_7_2prirme_O_trimethylguanosine" ;
  rdfs:comment "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001274 a rdfs:Class ;
  rdfs:label "modified_inosine" ;
  rdfs:comment "A modified inosine is an inosine base feature that has been altered." ;
  rdfs:subClassOf obo:SO_0001230 .

obo:SO_0000370 a rdfs:Class ;
  rdfs:label "small_regulatory_ncRNA" ;
  rdfs:comment "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others)." ;
  rdfs:subClassOf obo:SO_0002247 .

obo:BS_00063 a rdfs:Class .

obo:SO_0001752 a rdfs:Class ;
  rdfs:label "SL7_acceptor_site" ;
  rdfs:comment "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000709 .

obo:SO_0000012 a rdfs:Class ;
  rdfs:label "scRNA_primary_transcript" ;
  rdfs:comment "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000385 a rdfs:Class ;
  rdfs:label "RNase_MRP_RNA" ;
  rdfs:comment "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." ;
  rdfs:subClassOf obo:SO_0000372 .

obo:SO_0001822 a rdfs:Class ;
  rdfs:label "inframe_deletion" ;
  rdfs:comment "An inframe non synonymous variant that deletes bases from the coding sequence." ;
  rdfs:subClassOf obo:SO_0001820 , obo:SO_0001906 .

obo:SO_0000224 a rdfs:Class ;
  rdfs:label "phenylalanine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000780 a rdfs:Class ;
  rdfs:label "transposable_element_attribute" ;
  rdfs:comment "Added by KE Jan 2006 to capture the kinds of attributes of TEs" .

obo:SO_0000537 a rdfs:Class ;
  rdfs:label "V_spacer" ;
  rdfs:comment "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000563 .

obo:SO_0001654 a rdfs:Class ;
  rdfs:label "nucleotide_to_protein_binding_site" ;
  rdfs:comment "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." ;
  rdfs:subClassOf obo:SO_0000410 .

obo:SO_0000072 a rdfs:Class ;
  rdfs:label "end_overlapping_gene" .

obo:SO_0002323 a rdfs:Class ;
  rdfs:label "frameshift_variant_NMD_triggering" ;
  rdfs:comment "A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001589 , obo:SO_0002319 .

obo:SO_0001934 a rdfs:Class ;
  rdfs:label "monomeric_repeat" ;
  rdfs:comment "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." ;
  rdfs:subClassOf obo:SO_0000705 .

obo:SO_0001391 a rdfs:Class ;
  rdfs:label "modified_L_glutamic_acid" ;
  rdfs:comment "A post translationally modified glutamic acid." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:BS_00068 a rdfs:Class .

obo:SO_0001314 a rdfs:Class ;
  rdfs:label "one_two_prime_O_dimethyladenosine" ;
  rdfs:comment "1,2'-O-dimethyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_0000866 a rdfs:Class ;
  rdfs:label "minus_1_frameshift" ;
  rdfs:comment "A frameshift caused by deleting one base." ;
  rdfs:subClassOf obo:SO_0000865 .

obo:SO_0001879 a rdfs:Class ;
  rdfs:label "feature_ablation" ;
  rdfs:comment "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_1001260 a rdfs:Class ;
  rdfs:label "internal_Shine_Dalgarno_sequence" ;
  rdfs:comment "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." ;
  rdfs:subClassOf obo:SO_0000243 , obo:SO_1001268 .

obo:SO_0000638 a rdfs:Class ;
  rdfs:label "transcribed_spacer_region" ;
  rdfs:comment "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." ;
  rdfs:subClassOf obo:SO_0000838 .

obo:SO_0001420 a rdfs:Class ;
  rdfs:label "trans_splice_site" ;
  rdfs:comment "Primary transcript region bordering trans-splice junction." ;
  rdfs:subClassOf obo:SO_0000162 .

obo:SO_0001901 a rdfs:Class ;
  rdfs:label "AACCCT_box" ;
  rdfs:comment "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000712 a rdfs:Class ;
  rdfs:label "gene_with_transcript_with_translational_frameshift" ;
  rdfs:comment "A gene encoding a transcript that has a translational frameshift." ;
  rdfs:subClassOf obo:SO_0000693 .

obo:SO_0000511 a rdfs:Class ;
  rdfs:label "J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0002046 a rdfs:Class ;
  rdfs:label "FRE" ;
  rdfs:comment "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." ;
  rdfs:subClassOf obo:SO_0001461 .

obo:SO_0000482 a rdfs:Class ;
  rdfs:label "vertebrate_immunoglobulin_T_cell_receptor_gene_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration." ;
  rdfs:subClassOf obo:SO_0000301 .

obo:SO_0002183 a rdfs:Class ;
  rdfs:label "sense_overlap_lncRNA_gene" ;
  rdfs:comment "A gene that encodes a sense overlap long non-coding RNA." ;
  rdfs:subClassOf obo:SO_0002127 .

obo:SO_0001860 a rdfs:Class ;
  rdfs:label "rDNA_intergenic_spacer_element" ;
  rdfs:comment "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). The S. pombe telomeric repeat consensus is TTAC(0-1)A(0-1)G(1-8)." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0002116 a rdfs:Class ;
  rdfs:label "polymorphic_pseudogene_processed_transcript" ;
  rdfs:comment "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding." ;
  rdfs:subClassOf obo:SO_0002111 .

obo:SO_1001287 a rdfs:Class ;
  rdfs:label "distant_three_prime_recoding_signal" ;
  rdfs:comment "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." ;
  rdfs:subClassOf obo:SO_1001277 .

obo:SO_1000170 a rdfs:Class ;
  rdfs:label "uncharacterized_chromosomal_mutation" ;
  rdfs:comment "A chromosome structure variant that has not been characterized." ;
  rdfs:subClassOf obo:SO_1000183 .

obo:SO_0001354 a rdfs:Class ;
  rdfs:label "five_hydroxyuridine" ;
  rdfs:comment "5_hydroxyuridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000701 a rdfs:Class ;
  rdfs:label "possible_base_call_error" ;
  rdfs:comment "A region of sequence where the validity of the base calling is questionable." ;
  rdfs:subClassOf obo:SO_0000413 .

obo:SO_0002140 a rdfs:Class ;
  rdfs:label "early_origin_of_replication" ;
  rdfs:comment "An origin of replication that initiates early in S phase." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0001371 a rdfs:Class ;
  rdfs:label "five_carboxymethylaminomethyl_two_thiouridine" ;
  rdfs:comment "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0000179 a rdfs:Class ;
  rdfs:label "clone_insert_start" ;
  rdfs:comment "The start of the clone insert." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0002308 a rdfs:Class ;
  rdfs:label "DNA_loop_anchor" ;
  rdfs:comment "The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites." ;
  rdfs:subClassOf obo:SO_0000727 .

obo:SO_0000147 a rdfs:Class ;
  rdfs:label "exon" ;
  rdfs:comment "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0001958 a rdfs:Class ;
  rdfs:label "lariat_intron" ;
  rdfs:comment "A kind of intron whereby the excision is driven by lariat formation." ;
  rdfs:subClassOf obo:SO_0000188 .

obo:SO_0000559 a rdfs:Class ;
  rdfs:label "D_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." ;
  rdfs:subClassOf obo:SO_0000482 .

obo:SO_0001692 a rdfs:Class ;
  rdfs:label "sticky_end_restriction_enzyme_cleavage_site" ;
  rdfs:comment "A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'." ;
  rdfs:subClassOf obo:SO_0001687 .

obo:SO_0002059 a rdfs:Class ;
  rdfs:label "recombination_enhancer" ;
  rdfs:comment "A regulatory_region that promotes or induces the process of recombination." ;
  rdfs:subClassOf obo:SO_0001681 .

obo:SO_0002172 a rdfs:Class ;
  rdfs:label "sequence_alteration_artifact" ;
  rdfs:comment "A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process." ;
  rdfs:subClassOf obo:SO_0000413 .

obo:SO_0000471 a rdfs:Class ;
  rdfs:label "autoregulated" ;
  rdfs:comment "The gene product is involved in its own transcriptional regulation." ;
  rdfs:subClassOf obo:SO_0000123 .

obo:SO_0001818 a rdfs:Class ;
  rdfs:label "protein_altering_variant" ;
  rdfs:comment "A sequence_variant which is predicted to change the protein encoded in the coding sequence." ;
  rdfs:subClassOf obo:SO_0001580 .

obo:SO_0000649 a rdfs:Class .

obo:SO_0002291 a rdfs:Class ;
  rdfs:label "circular_ncRNA" ;
  rdfs:comment "A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0001092 a rdfs:Class ;
  rdfs:label "polypeptide_metal_contact" ;
  rdfs:comment "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." ;
  rdfs:subClassOf obo:SO_0001656 , obo:SO_0100002 .

obo:SO_0001628 a rdfs:Class ;
  rdfs:label "intergenic_variant" ;
  rdfs:comment "A sequence variant located in the intergenic region, between genes." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0001688 a rdfs:Class ;
  rdfs:label "restriction_enzyme_cleavage_junction" ;
  rdfs:comment "The boundary at which a restriction enzyme breaks the nucleotide sequence." ;
  rdfs:subClassOf obo:SO_0002204 .

obo:SO_0001632 a rdfs:Class ;
  rdfs:label "downstream_gene_variant" ;
  rdfs:comment "A sequence variant located 3' of a gene." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:SO_0001513 a rdfs:Class ;
  rdfs:label "tandem" ;
  rdfs:comment "An insertion of extension of a tandem repeat." ;
  rdfs:subClassOf obo:SO_0001512 .

obo:SO_0000661 a rdfs:Class ;
  rdfs:label "intron_attribute" .

obo:SO_0000997 a rdfs:Class ;
  rdfs:label "gene_fragment" ;
  rdfs:comment "A portion of a gene that is not the complete gene." ;
  rdfs:subClassOf obo:SO_0000842 .

obo:SO_0000747 a rdfs:Class ;
  rdfs:label "leucoplast_sequence" ;
  rdfs:comment "DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_0000820 a rdfs:Class ;
  rdfs:label "chloroplast_chromosome" ;
  rdfs:comment "A chromosome originating in a chloroplast." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0000950 a rdfs:Class ;
  rdfs:label "attC_site" ;
  rdfs:comment "An attC site is a sequence required for the integration of a DNA of an integron." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0000335 a rdfs:Class ;
  rdfs:label "mRNA_with_minus_2_frameshift" ;
  rdfs:comment "A mRNA with a minus 2 frameshift." ;
  rdfs:subClassOf obo:SO_0000108 .

obo:SO_0000168 a rdfs:Class ;
  rdfs:label "restriction_enzyme_cut_site" ;
  rdfs:comment "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." .

obo:SO_0000229 a rdfs:Class ;
  rdfs:label "tyrosine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding tyrosyl tRNA (SO:000272)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000090 a rdfs:Class ;
  rdfs:label "plastid_gene" ;
  rdfs:comment "A gene from plastid sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001412 a rdfs:Class ;
  rdfs:label "topologically_defined_region" ;
  rdfs:comment "A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping." ;
  rdfs:subClassOf obo:SO_0000001 .

obo:SO_0000172 a rdfs:Class ;
  rdfs:label "CAAT_signal" ;
  rdfs:comment "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0002199 a rdfs:Class ;
  rdfs:label "unitary_pseudogenic_tRNA" ;
  rdfs:comment "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain." ;
  rdfs:subClassOf obo:SO_0000778 .

obo:SO_0000775 a rdfs:Class ;
  rdfs:label "adaptive_island" ;
  rdfs:comment "An adaptive island is a genomic island that provides an adaptive advantage to the host." ;
  rdfs:subClassOf obo:SO_0000772 .

obo:SO_1000094 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_conservative_amino_acid_substitution" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000571 a rdfs:Class ;
  rdfs:label "miRNA_encoding" ;
  rdfs:comment "A region that can be transcribed into a microRNA (miRNA)." ;
  rdfs:subClassOf obo:SO_0000011 .

obo:SO_0000399 a rdfs:Class ;
  rdfs:label "U12_snRNA" ;
  rdfs:comment "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0000248 a rdfs:Class ;
  rdfs:label "sequence_length_alteration" ;
  rdfs:comment "A kind of kind of sequence alteration where the copies of a region present varies across a population." ;
  rdfs:subClassOf obo:SO_0001059 .

obo:SO_0001640 a rdfs:Class ;
  rdfs:label "RNase_MRP_RNA_gene" ;
  rdfs:comment "A gene that encodes a RNase_MRP_RNA." ;
  rdfs:subClassOf obo:SO_0002180 .

obo:BS_00052 a rdfs:Class .

obo:SO_0001467 a rdfs:Class ;
  rdfs:label "RST" ;
  rdfs:comment "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." ;
  rdfs:subClassOf obo:SO_0000345 .

obo:SO_0000414 a rdfs:Class ;
  rdfs:label "invalidated_by_genomic_contamination" ;
  rdfs:comment "An attribute to describe a feature that is invalidated due to genomic contamination." ;
  rdfs:subClassOf obo:SO_0000790 .

obo:SO_0100002 a rdfs:Class ;
  rdfs:label "molecular_contact_region" ;
  rdfs:comment "A region that is involved a contact with another molecule." ;
  rdfs:subClassOf obo:SO_0100001 .

obo:SO_0000976 a rdfs:Class ;
  rdfs:label "cryptic" ;
  rdfs:comment "A feature_attribute describing a feature that is not manifest under normal conditions." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0002217 a rdfs:Class ;
  rdfs:label "unspecified_indel" ;
  rdfs:comment "A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category." ;
  rdfs:subClassOf obo:SO_0001059 .

obo:SO_0001200 a rdfs:Class ;
  rdfs:label "negative_sense_ssRNA_viral_sequence" ;
  rdfs:comment "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." ;
  rdfs:subClassOf obo:SO_0001199 .

obo:SO_0000600 a rdfs:Class ;
  rdfs:label "edited_by_A_to_I_substitution" .

obo:SO_0000083 a rdfs:Class ;
  rdfs:label "macronuclear_sequence" ;
  rdfs:comment "DNA belonging to the macronuclei of ciliates." ;
  rdfs:subClassOf obo:SO_0000736 .

obo:SO_0001381 a rdfs:Class ;
  rdfs:label "five_isopentenylaminomethyl_two_thiouridine" ;
  rdfs:comment "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001917 a rdfs:Class ;
  rdfs:label "CAGE_cluster" ;
  rdfs:comment "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." ;
  rdfs:subClassOf obo:SO_0001915 .

obo:SO_0002003 a rdfs:Class ;
  rdfs:label "Z2_region" ;
  rdfs:comment "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." ;
  rdfs:subClassOf obo:SO_0001999 .

obo:SO_0000522 a rdfs:Class ;
  rdfs:label "V_VDJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:BS_00134 a rdfs:Class .

obo:SO_0000197 a rdfs:Class ;
  rdfs:label "three_prime_coding_exon_coding_region" ;
  rdfs:comment "The sequence of the three_prime_coding_exon that codes for protein." ;
  rdfs:subClassOf obo:SO_0001215 .

obo:BS_00203 a rdfs:Class .

obo:SO_0000965 a rdfs:Class ;
  rdfs:label "double_stranded_RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, double-stranded RNA molecule." ;
  rdfs:subClassOf obo:SO_0000961 .

obo:SO_0001141 a rdfs:Class ;
  rdfs:label "serine_threonine_turn" ;
  rdfs:comment "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." ;
  rdfs:subClassOf obo:SO_0001128 .

obo:SO_0000429 a rdfs:Class ;
  rdfs:label "U3_five_prime_LTR_region" ;
  rdfs:comment "The U3 segment of the three-prime long terminal repeat." ;
  rdfs:subClassOf obo:SO_0000424 , obo:SO_0000850 .

obo:SO_0000266 a rdfs:Class ;
  rdfs:label "methionyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0002071 a rdfs:Class ;
  rdfs:label "CDS_supported_by_peptide_spectrum_match" ;
  rdfs:comment "A CDS that is supported by proteomics data." ;
  rdfs:subClassOf obo:SO_1001251 .

obo:SO_0000251 a rdfs:Class ;
  rdfs:label "eight_cutter_restriction_site" .

obo:SO_0002188 a rdfs:Class ;
  rdfs:label "functional_gene_region" ;
  rdfs:comment "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product." ;
  rdfs:subClassOf obo:SO_0000831 .

obo:SO_0001941 a rdfs:Class ;
  rdfs:label "H4K91_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001972 .

obo:SO_0000347 a rdfs:Class ;
  rdfs:label "nucleotide_match" ;
  rdfs:comment "A match against a nucleotide sequence." ;
  rdfs:subClassOf obo:SO_0000343 .

obo:SO_0001681 a rdfs:Class ;
  rdfs:label "recombination_regulatory_region" ;
  rdfs:comment "A regulatory region that is involved in the control of the process of recombination." ;
  rdfs:subClassOf obo:SO_0005836 .

obo:SO_0001777 a rdfs:Class ;
  rdfs:label "somatic_variant" ;
  rdfs:comment "A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body." ;
  rdfs:subClassOf obo:SO_0001762 .

obo:SO_0000132 a rdfs:Class ;
  rdfs:label "reverse_primer" ;
  rdfs:comment "A single stranded oligo used for polymerase chain reaction." ;
  rdfs:subClassOf obo:SO_0000112 .

obo:SO_0002065 a rdfs:Class ;
  rdfs:label "SVA_insertion" ;
  rdfs:comment "An insertion of sequence from the SVA family of mobile elements." ;
  rdfs:subClassOf obo:SO_0001837 .

obo:SO_0000973 a rdfs:Class ;
  rdfs:label "insertion_sequence" ;
  rdfs:comment "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0001360 a rdfs:Class ;
  rdfs:label "five_methoxycarbonylmethyluridine" ;
  rdfs:comment "Five_methoxycarbonylmethyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0001193 a rdfs:Class ;
  rdfs:label "GNA_oligo" ;
  rdfs:comment "An oligo composed of GNA residues." ;
  rdfs:subClassOf obo:SO_0001247 .

obo:SO_0000045 a rdfs:Class ;
  rdfs:label "delete" ;
  rdfs:comment "To remove a subsection of sequence." .

obo:SO_0000186 a rdfs:Class ;
  rdfs:label "LTR_retrotransposon" ;
  rdfs:comment "A retrotransposon flanked by long terminal repeat sequences." ;
  rdfs:subClassOf obo:SO_0000180 .

obo:SO_0000466 a rdfs:Class ;
  rdfs:label "V_gene_segment" ;
  rdfs:comment "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." ;
  rdfs:subClassOf obo:SO_0000460 .

obo:SO_0001846 a rdfs:Class ;
  rdfs:label "FLEX_element" ;
  rdfs:comment "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0001508 a rdfs:Class ;
  rdfs:label "alteration_attribute" ;
  rdfs:comment "An attribute of alteration of one or more chromosomes." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001002 a rdfs:Class ;
  rdfs:label "cytosolic_25S_rRNA" ;
  rdfs:comment "Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes." ;
  rdfs:subClassOf obo:SO_0000651 .

obo:SO_0002200 a rdfs:Class ;
  rdfs:label "allelic_pseudogenic_tRNA" ;
  rdfs:comment "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." ;
  rdfs:subClassOf obo:SO_0000778 .

obo:SO_0002382 a rdfs:Class ;
  rdfs:label "range_extender_element" ;
  rdfs:comment "A conserved cis-acting element that confers extreme-distance regulatory activity to an enhancer." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0002154 a rdfs:Class ;
  rdfs:label "mitotic_recombination_region" ;
  rdfs:comment "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:SO_0000238 a rdfs:Class ;
  rdfs:label "foldback_element" ;
  rdfs:comment "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." ;
  rdfs:subClassOf obo:SO_0000182 .

obo:SO_0001029 a rdfs:Class ;
  rdfs:label "direction_attribute" ;
  rdfs:comment "The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse)." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000895 a rdfs:Class ;
  rdfs:label "silenced_by_DNA_methylation" ;
  rdfs:comment "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." ;
  rdfs:subClassOf obo:SO_0000894 .

obo:SO_0001519 a rdfs:Class ;
  rdfs:label "paracentric" ;
  rdfs:comment "An inversion event that does not include the centromere." ;
  rdfs:subClassOf obo:SO_0001517 .

obo:SO_0000374 a rdfs:Class ;
  rdfs:label "ribozyme" ;
  rdfs:comment "An RNA with catalytic activity." ;
  rdfs:subClassOf obo:SO_0000372 .

obo:SO_0001745 a rdfs:Class ;
  rdfs:label "maternal_uniparental_disomy" ;
  rdfs:comment "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." ;
  rdfs:subClassOf obo:SO_0001744 .

obo:SO_0001435 a rdfs:Class ;
  rdfs:label "alanine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_1000047 a rdfs:Class ;
  rdfs:label "paracentric_inversion" ;
  rdfs:comment "A chromosomal inversion that does not include the centromere." ;
  rdfs:subClassOf obo:SO_1000030 .

obo:SO_0001289 a rdfs:Class ;
  rdfs:label "lysidine" ;
  rdfs:comment "Lysidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_1000076 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_transcription" ;
  rdfs:comment "Mutation affects the process of transcription, its initiation, progression or termination." .

obo:SO_0000943 a rdfs:Class ;
  rdfs:label "attB_site" ;
  rdfs:comment "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0000146 a rdfs:Class ;
  rdfs:label "capped" ;
  rdfs:comment "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." ;
  rdfs:subClassOf obo:SO_0000237 .

obo:SO_0001249 a rdfs:Class ;
  rdfs:label "fragment_assembly" ;
  rdfs:comment "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." ;
  rdfs:subClassOf obo:SO_0001248 .

obo:SO_0000791 a rdfs:Class ;
  rdfs:label "cloned_genomic" .

obo:SO_0002367 a rdfs:Class ;
  rdfs:label "plastid_LSU_rRNA_gene" ;
  rdfs:comment "A gene that codes for plastid LSU rRNA." ;
  rdfs:subClassOf obo:SO_0002366 .

obo:SO_1000070 a rdfs:Class ;
  rdfs:label "sequence_variant_affecting_transcript_processing" ;
  rdfs:comment "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." .

obo:SO_0001382 a rdfs:Class ;
  rdfs:label "five_isopentenylaminomethyl_two_prime_O_methyluridine" ;
  rdfs:comment "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_0002162 a rdfs:Class ;
  rdfs:label "short_tandem_repeat_expansion" ;
  rdfs:comment "A short tandem repeat variant containing more repeat units than the reference sequence." ;
  rdfs:subClassOf obo:SO_0002161 .

obo:SO_0001231 a rdfs:Class ;
  rdfs:label "seven_methylguanine" ;
  rdfs:comment "A modified RNA base in which guanine is methylated at the 7- position." ;
  rdfs:subClassOf obo:SO_0000250 .

obo:SO_0000765 a rdfs:Class ;
  rdfs:label "cosmid_clone" .

obo:SO_0000277 a rdfs:Class ;
  rdfs:label "bound_by_factor" ;
  rdfs:comment "An attribute describing a sequence that is bound by another molecule." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000586 a rdfs:Class ;
  rdfs:label "tmRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a tmRNA (SO:0000584)." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0001342 a rdfs:Class ;
  rdfs:label "isowyosine" ;
  rdfs:comment "Isowyosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0002405 a rdfs:Class ;
  rdfs:label "three_prime_gene_fusion" ;
  rdfs:comment "A sequence variant whereby two genomic features have become joined with one breakend within the 3' end of a gene." ;
  rdfs:subClassOf obo:SO_0001564 , obo:SO_0001882 .

obo:SO_0002351 a rdfs:Class ;
  rdfs:label "rare_fragile_site" ;
  rdfs:comment "A fragile site found in the chromosomes of less than five percent of the human population." ;
  rdfs:subClassOf obo:SO_0002349 .

obo:SO_1000104 a rdfs:Class ;
  rdfs:label "sequence_variant_increasing_level_of_translation_product" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000548 a rdfs:Class ;
  rdfs:label "gene_with_edited_transcript" ;
  rdfs:comment "A gene that encodes a transcript that is edited." ;
  rdfs:subClassOf obo:SO_0001217 .

obo:SO_0000086 a rdfs:Class ;
  rdfs:label "gene_by_organelle_of_genome" .

obo:SO_0002014 a rdfs:Class ;
  rdfs:label "5_prime_UTR_elongation" ;
  rdfs:comment "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001623 .

obo:SO_1000087 a rdfs:Class ;
  rdfs:label "sequence_variation_increasing_level_of_transcript" ;
  rdfs:comment "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." .

obo:SO_0000918 a rdfs:Class ;
  rdfs:label "delete_U" ;
  rdfs:comment "An edit to delete a uridine." .

obo:SO_0000288 a rdfs:Class ;
  rdfs:label "engineered_fusion_gene" ;
  rdfs:comment "A fusion gene that is engineered." ;
  rdfs:subClassOf obo:SO_0000280 , obo:SO_0000287 .

obo:SO_0000181 a rdfs:Class ;
  rdfs:label "translated_nucleotide_match" ;
  rdfs:comment "A match against a translated sequence." ;
  rdfs:subClassOf obo:SO_0000347 .

obo:SO_0000501 a rdfs:Class ;
  rdfs:label "reverse_Hoogsteen_base_pair" ;
  rdfs:comment "A type of non-canonical base-pairing." ;
  rdfs:subClassOf obo:SO_0000028 .

obo:SO_0000227 a rdfs:Class ;
  rdfs:label "threonine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding threonyl tRNA (SO:000270)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_1001196 a rdfs:Class ;
  rdfs:label "cryptogene" ;
  rdfs:comment "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." ;
  rdfs:subClassOf obo:SO_0000654 , obo:SO_0001431 .

obo:SO_0001459 a rdfs:Class ;
  rdfs:label "CRISPR" ;
  rdfs:comment "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." ;
  rdfs:subClassOf obo:SO_0000314 .

obo:SO_0001930 a rdfs:Class ;
  rdfs:label "chloroplast_DNA_read" ;
  rdfs:comment "A sequencer read of a chloroplast DNA sample." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0000030 a rdfs:Class ;
  rdfs:label "sugar_edge_base_pair" ;
  rdfs:comment "A type of non-canonical base-pairing." ;
  rdfs:subClassOf obo:SO_0000028 .

obo:SO_0002020 a rdfs:Class ;
  rdfs:label "boundary_element" ;
  rdfs:comment "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." ;
  rdfs:subClassOf obo:SO_0000627 .

obo:SO_0000857 a rdfs:Class ;
  rdfs:label "homologous" ;
  rdfs:comment "Similarity due to common ancestry." ;
  rdfs:subClassOf obo:SO_0000856 .

obo:SO_0000106 a rdfs:Class ;
  rdfs:label "non_capped_primary_transcript" .

obo:SO_0002369 a rdfs:Class ;
  rdfs:label "C_D_box_scaRNA" ;
  rdfs:comment "A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002095 .

obo:SO_0001882 a rdfs:Class ;
  rdfs:label "feature_fusion" ;
  rdfs:comment "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." ;
  rdfs:subClassOf obo:SO_0001537 .

obo:SO_0001605 a rdfs:Class ;
  rdfs:label "amino_acid_insertion" ;
  rdfs:comment "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_0000169 a rdfs:Class ;
  rdfs:label "RNApol_I_promoter" ;
  rdfs:comment "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0002221 .

obo:SO_0001466 a rdfs:Class ;
  rdfs:label "five_prime_UST" ;
  rdfs:comment "An UST located in the 5'UTR of a protein-coding transcript." ;
  rdfs:subClassOf obo:SO_0001464 .

obo:SO_0001521 a rdfs:Class ;
  rdfs:label "reciprocal" ;
  rdfs:comment "When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials." ;
  rdfs:subClassOf obo:SO_0001520 .

obo:SO_1000054 a rdfs:Class ;
  rdfs:label "sequence_variation_affecting_coding_sequence" ;
  rdfs:comment "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." .

obo:SO_0000961 a rdfs:Class ;
  rdfs:label "RNA_chromosome" ;
  rdfs:comment "Structural unit composed of a self-replicating, RNA molecule." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001923 a rdfs:Class ;
  rdfs:label "TERRA" ;
  rdfs:comment "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." ;
  rdfs:subClassOf obo:SO_0001927 .

obo:SO_0002326 a rdfs:Class ;
  rdfs:label "splice_donor_variant_NMD_escaping" ;
  rdfs:comment "A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD)." ;
  rdfs:subClassOf obo:SO_0001575 , obo:SO_0002320 .

obo:SO_0000723 a rdfs:Class ;
  rdfs:label "iDNA" ;
  rdfs:comment "Genomic sequence removed from the genome, as a normal event, by a process of recombination." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:SO_0000553 a rdfs:Class ;
  rdfs:label "polyA_site" ;
  rdfs:comment "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." ;
  rdfs:subClassOf obo:SO_0000699 .

obo:SO_0001402 a rdfs:Class ;
  rdfs:label "modified_L_selenocysteine" ;
  rdfs:comment "A post translationally modified selenocysteine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001699 a rdfs:Class ;
  rdfs:label "dCAPS_primer" ;
  rdfs:comment "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." ;
  rdfs:subClassOf obo:SO_0000112 .

obo:SO_0001185 a rdfs:Class ;
  rdfs:label "enzymatic" ;
  rdfs:comment "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0000228 a rdfs:Class ;
  rdfs:label "tryptophan_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding tryptophanyl tRNA (SO:000271)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0002115 a rdfs:Class ;
  rdfs:label "pseudogenic_transcript_with_retained_intron" ;
  rdfs:comment "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence." ;
  rdfs:subClassOf obo:SO_0000185 .

obo:SO_0000730 a rdfs:Class ;
  rdfs:label "gap" ;
  rdfs:comment "A gap in the sequence of known length. The unknown bases are filled in with N's." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_1000183 a rdfs:Class ;
  rdfs:label "chromosome_structure_variation" ;
  rdfs:comment "An alteration of the genome that leads to a change in the structure or number of one or more chromosomes." ;
  rdfs:subClassOf obo:SO_0000240 .

obo:SO_0002234 a rdfs:Class ;
  rdfs:label "pumilio_response_element" ;
  rdfs:comment "A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA)." ;
  rdfs:subClassOf obo:SO_0000837 .

obo:SO_0000529 a rdfs:Class ;
  rdfs:label "V_D_DJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000089 a rdfs:Class ;
  rdfs:label "kinetoplast_gene" ;
  rdfs:comment "A gene located in kinetoplast sequence." ;
  rdfs:subClassOf obo:SO_0000088 .

obo:SO_0002281 a rdfs:Class ;
  rdfs:label "Merlin_TIR_transposon" ;
  rdfs:comment "Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD)." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_0001119 a rdfs:Class ;
  rdfs:label "three_ten_helix" ;
  rdfs:comment "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." ;
  rdfs:subClassOf obo:SO_0001116 .

obo:SO_0100021 a rdfs:Class ;
  rdfs:label "polypeptide_conserved_region" ;
  rdfs:comment "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001387 a rdfs:Class ;
  rdfs:label "modified_L_alanine" ;
  rdfs:comment "A post translationally modified alanine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0001161 a rdfs:Class ;
  rdfs:label "DMv2_motif" ;
  rdfs:comment "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002159 a rdfs:Class ;
  rdfs:label "SHP_box" ;
  rdfs:comment "A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG." ;
  rdfs:subClassOf obo:SO_0100017 .

obo:SO_0000750 a rdfs:Class ;
  rdfs:label "amplification_origin" ;
  rdfs:comment "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." ;
  rdfs:subClassOf obo:SO_0000296 .

obo:SO_0002278 a rdfs:Class ;
  rdfs:label "Tc1_Mariner_TIR_transposon" ;
  rdfs:comment "Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp." ;
  rdfs:subClassOf obo:SO_0000208 .

obo:SO_1000112 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_no_3D_structural_change" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term." .

obo:SO_0000530 a rdfs:Class ;
  rdfs:label "V_D_DJ_J_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000396 a rdfs:Class ;
  rdfs:label "U6_snRNA" ;
  rdfs:comment "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0001370 a rdfs:Class ;
  rdfs:label "five_carboxymethylaminomethyl_two_prime_O_methyluridine" ;
  rdfs:comment "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." ;
  rdfs:subClassOf obo:SO_0001277 .

obo:SO_1000141 a rdfs:Class ;
  rdfs:label "chromosome_fission" ;
  rdfs:comment "A chromosome that occurred by the division of a larger chromosome." ;
  rdfs:subClassOf obo:SO_1000028 .

obo:SO_1001279 a rdfs:Class ;
  rdfs:label "three_prime_stem_loop_structure" ;
  rdfs:comment "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." ;
  rdfs:subClassOf obo:SO_1001277 .

obo:BS_00146 a rdfs:Class .

obo:SO_0001842 a rdfs:Class ;
  rdfs:label "AP_1_binding_site" ;
  rdfs:comment "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0005849 a rdfs:Class ;
  rdfs:label "gene_subarray_member" ;
  rdfs:comment "A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together." ;
  rdfs:subClassOf obo:SO_0000081 .

obo:SO_0001636 a rdfs:Class ;
  rdfs:label "2KB_upstream_variant" ;
  rdfs:comment "A sequence variant located within 2KB 5' of a gene." ;
  rdfs:subClassOf obo:SO_0001631 .

obo:SO_1000152 a rdfs:Class ;
  rdfs:label "uninverted_insertional_duplication" ;
  rdfs:comment "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." ;
  rdfs:subClassOf obo:SO_1000154 .

obo:SO_0000566 a rdfs:Class ;
  rdfs:label "V_VJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0000379 a rdfs:Class ;
  rdfs:label "GcvB_RNA" ;
  rdfs:comment "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." ;
  rdfs:subClassOf obo:SO_0000378 .

obo:SO_0001503 a rdfs:Class ;
  rdfs:label "processed_transcript" ;
  rdfs:comment "A transcript for which no open reading frame has been identified and for which no other function has been determined." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:BS_00027 a rdfs:Class .

obo:SO_0000078 a rdfs:Class ;
  rdfs:label "polycistronic_transcript" ;
  rdfs:comment "A transcript that is polycistronic." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0001448 a rdfs:Class ;
  rdfs:label "glutamine" ;
  rdfs:comment "A polar, hydorophilic amino acid encoded by the codons CAA and CAG. " ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0000175 a rdfs:Class ;
  rdfs:label "minus_10_signal" ;
  rdfs:comment "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000795 a rdfs:Class ;
  rdfs:label "rescue_mini_gene" ;
  rdfs:comment "A mini_gene that rescues." ;
  rdfs:subClassOf obo:SO_0000815 .

obo:SO_0000344 a rdfs:Class ;
  rdfs:label "splice_enhancer" ;
  rdfs:comment "Region of a transcript that regulates splicing." ;
  rdfs:subClassOf obo:SO_0001056 .

obo:SO_1001244 a rdfs:Class ;
  rdfs:label "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping" .

obo:SO_1000101 a rdfs:Class ;
  rdfs:label "mutation_causing_polypeptide_C_terminal_elongation" ;
  rdfs:comment "." .

obo:SO_0002353 a rdfs:Class ;
  rdfs:label "sbRNA_gene" ;
  rdfs:comment "A gene encoding a stem-bulge RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0000486 a rdfs:Class ;
  rdfs:label "five_prime_coding_exon_noncoding_region" ;
  rdfs:comment "The sequence of the 5' exon preceding the start codon." ;
  rdfs:subClassOf obo:SO_0001214 .

obo:SO_0000425 a rdfs:Class ;
  rdfs:label "five_prime_LTR" ;
  rdfs:comment "The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome." ;
  rdfs:subClassOf obo:SO_0000286 .

obo:SO_0000411 a rdfs:Class ;
  rdfs:label "rescue_region" ;
  rdfs:comment "A region that rescues." ;
  rdfs:subClassOf obo:SO_0000695 .

obo:SO_0001959 a rdfs:Class ;
  rdfs:label "TCT_motif" ;
  rdfs:comment "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0001032 a rdfs:Class ;
  rdfs:label "mitochondrial_DNA" ;
  rdfs:comment "DNA belonging to the genome of a mitochondria." ;
  rdfs:subClassOf obo:SO_0000737 .

obo:SO_0000981 a rdfs:Class ;
  rdfs:label "rho_dependent_bacterial_terminator" ;
  rdfs:comment "A transcription terminator that is dependent upon Rho." ;
  rdfs:subClassOf obo:SO_0000614 .

obo:SO_1000058 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_non_synonymous_codon_change_in_transcript" ;
  rdfs:comment "A DNA point mutation that causes a substitution of an amino acid by an other." .

obo:SO_0001651 a rdfs:Class .

obo:SO_0002137 a rdfs:Class ;
  rdfs:label "TR_V_Gene" ;
  rdfs:comment "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain." ;
  rdfs:subClassOf obo:SO_0002133 .

obo:SO_0000807 a rdfs:Class ;
  rdfs:label "engineered_tag" ;
  rdfs:comment "A tag that is engineered." ;
  rdfs:subClassOf obo:SO_0000324 , obo:SO_0000804 .

obo:SO_0001696 a rdfs:Class ;
  rdfs:label "experimentally_defined_binding_region" ;
  rdfs:comment "A region that has been implicated in binding although the exact coordinates of binding may be unknown." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0001569 a rdfs:Class ;
  rdfs:label "cryptic_splice_site_variant" ;
  rdfs:comment "A sequence variant causing a new (functional) splice site." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0001013 a rdfs:Class ;
  rdfs:label "MNP" ;
  rdfs:comment "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." ;
  rdfs:subClassOf obo:SO_0002007 .

obo:SO_0001954 a rdfs:Class ;
  rdfs:label "restriction_enzyme_region" ;
  rdfs:comment "A region related to restriction enzyme function." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001477 a rdfs:Class ;
  rdfs:label "gene_trap_construct" ;
  rdfs:comment "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." ;
  rdfs:subClassOf obo:SO_0000637 .

obo:SO_0001318 a rdfs:Class ;
  rdfs:label "epoxyqueuosine" ;
  rdfs:comment "Epoxyqueuosine is a modified 7-deazoguanosine." ;
  rdfs:subClassOf obo:SO_0001316 .

obo:SO_0002062 a rdfs:Class ;
  rdfs:label "complex_chromosomal_rearrangement" ;
  rdfs:comment "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." ;
  rdfs:subClassOf obo:SO_0001784 .

obo:SO_0002055 a rdfs:Class ;
  rdfs:label "null_mutation" ;
  rdfs:comment "A variant whereby the gene product is not functional or the gene product is not produced." ;
  rdfs:subClassOf obo:SO_0002218 .

obo:SO_0000135 a rdfs:Class ;
  rdfs:label "maternally_imprinted" ;
  rdfs:comment "The maternal copy of the gene is modified, rendering it transcriptionally silent." ;
  rdfs:subClassOf obo:SO_0000134 .

obo:SO_0001770 a rdfs:Class ;
  rdfs:label "benign_variant" ;
  rdfs:comment "A variant that does not affect the function of the gene or cause disease." ;
  rdfs:subClassOf obo:SO_0001769 .

obo:SO_0000555 a rdfs:Class ;
  rdfs:label "five_prime_clip" ;
  rdfs:comment "5' most region of a precursor transcript that is clipped off during processing." ;
  rdfs:subClassOf obo:SO_0000303 .

obo:SO_0000831 a rdfs:Class ;
  rdfs:label "gene_member_region" ;
  rdfs:comment "A region of a gene." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0000926 a rdfs:Class ;
  rdfs:label "insert_CU" ;
  rdfs:comment "An edit to insert a CU dinucleotide." .

obo:SO_0002042 a rdfs:Class ;
  rdfs:label "Y_RNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding a Y-RNA." ;
  rdfs:subClassOf obo:SO_0000483 .

obo:SO_0000743 a rdfs:Class ;
  rdfs:label "apicoplast_sequence" ;
  rdfs:comment "DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid." ;
  rdfs:subClassOf obo:SO_0000740 .

obo:SO_0000475 a rdfs:Class ;
  rdfs:label "positively_autoregulated" ;
  rdfs:comment "The gene product is involved in its own transcriptional regulation, where it increases transcription." ;
  rdfs:subClassOf obo:SO_0000125 , obo:SO_0000471 .

obo:SO_0001330 a rdfs:Class ;
  rdfs:label "N2_N2_2_prime_O_trimethylguanosine" ;
  rdfs:comment "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0001130 a rdfs:Class ;
  rdfs:label "asx_turn_left_handed_type_two" ;
  rdfs:comment "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0000912 .

obo:SO_1000026 a rdfs:Class ;
  rdfs:label "G_to_C_transversion" ;
  rdfs:comment "A transversion from guanine to cytidine." ;
  rdfs:subClassOf obo:SO_1000023 .

obo:SO_0000518 a rdfs:Class ;
  rdfs:label "V_DJ_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001024 a rdfs:Class ;
  rdfs:label "haplotype" ;
  rdfs:comment "A haplotype is one of a set of coexisting sequence variants of a haplotype block." ;
  rdfs:subClassOf obo:SO_0001507 .

obo:SO_0001449 a rdfs:Class ;
  rdfs:label "asparagine" ;
  rdfs:comment "A polar, hydorophilic amino acid encoded by the codons AAT and AAC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_1000115 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_complex_3D_structural_change" ;
  rdfs:comment "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." .

obo:SO_0000619 a rdfs:Class ;
  rdfs:label "A_box" ;
  rdfs:comment "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0001685 a rdfs:Class ;
  rdfs:label "score" ;
  rdfs:comment "The score of an experimentally derived feature such as a p-value." ;
  rdfs:subClassOf obo:SO_0001684 .

obo:SO_0002047 a rdfs:Class ;
  rdfs:label "transcription_pause_site" ;
  rdfs:comment "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." ;
  rdfs:subClassOf obo:SO_0001055 .

obo:SO_0000929 a rdfs:Class ;
  rdfs:label "edited_mRNA" ;
  rdfs:comment "An mRNA that is edited." ;
  rdfs:subClassOf obo:SO_0000234 , obo:SO_0000873 .

obo:SO_0000176 a rdfs:Class ;
  rdfs:label "minus_35_signal" ;
  rdfs:comment "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001253 a rdfs:Class ;
  rdfs:label "sonicate_fragment" ;
  rdfs:comment "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." ;
  rdfs:subClassOf obo:SO_0000143 .

obo:SO_1000098 a rdfs:Class ;
  rdfs:label "sequence_variant_causing_polypeptide_truncation" ;
  rdfs:comment "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." .

obo:SO_0000604 a rdfs:Class ;
  rdfs:label "editing_block" ;
  rdfs:comment "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." ;
  rdfs:subClassOf obo:SO_0000579 .

obo:SO_0000694 a rdfs:Class ;
  rdfs:label "SNP" ;
  rdfs:comment "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." ;
  rdfs:subClassOf obo:SO_0001483 .

obo:SO_0002301 a rdfs:Class ;
  rdfs:label "transcription_unit" ;
  rdfs:comment "DNA regions delimited by different nonspurious TSS-TTS pairs." ;
  rdfs:subClassOf obo:SO_0002300 .

obo:SO_0000262 a rdfs:Class ;
  rdfs:label "histidyl_tRNA" ;
  rdfs:comment "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." ;
  rdfs:subClassOf obo:SO_0000253 .

obo:SO_0001104 a rdfs:Class ;
  rdfs:label "catalytic_residue" ;
  rdfs:comment "Amino acid involved in the activity of an enzyme." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0002036 a rdfs:Class ;
  rdfs:label "miR_encoding_lncRNA_primary_transcript" ;
  rdfs:comment "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." ;
  rdfs:subClassOf obo:SO_0002035 .

obo:SO_0001291 a rdfs:Class ;
  rdfs:label "N4_2_prime_O_dimethylcytidine" ;
  rdfs:comment "N4,2'-O-dimethylcytidine is a modified cytidine." ;
  rdfs:subClassOf obo:SO_0001275 .

obo:SO_1000082 a rdfs:Class ;
  rdfs:label "sequence variant_affecting_transcript_stability" ;
  rdfs:comment "Sequence variant affects the stability of the transcript." .

obo:SO_0001945 a rdfs:Class ;
  rdfs:label "H3K56_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0001973 .

obo:SO_0001114 a rdfs:Class ;
  rdfs:label "peptide_helix" ;
  rdfs:comment "A helix is a secondary_structure conformation where the peptide backbone forms a coil." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001735 a rdfs:Class ;
  rdfs:label "H3K79_methylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0001608 a rdfs:Class ;
  rdfs:label "non_conservative_amino_acid_substitution" ;
  rdfs:comment "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." ;
  rdfs:subClassOf obo:SO_0001606 .

obo:SO_0001423 a rdfs:Class ;
  rdfs:label "dye_terminator_read" ;
  rdfs:comment "A read produced by the dye terminator method of sequencing." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0000368 a rdfs:Class ;
  rdfs:label "transposable_element_insertion_site" ;
  rdfs:comment "The junction in a genome where a transposable_element has inserted." ;
  rdfs:subClassOf obo:SO_0000366 .

obo:SO_0000158 a rdfs:Class ;
  rdfs:label "fosmid" ;
  rdfs:comment "A cloning vector that utilizes the E. coli F factor." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_1000065 a rdfs:Class ;
  rdfs:label "frameshift_sequence_variation" ;
  rdfs:comment "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." .

obo:SO_0000672 a rdfs:Class ;
  rdfs:label "macronucleus_destined_segment" ;
  rdfs:comment "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." ;
  rdfs:subClassOf obo:SO_0000669 .

obo:SO_0000932 a rdfs:Class ;
  rdfs:label "pre_edited_mRNA" ;
  rdfs:comment "A primary transcript that, at least in part, encodes one or more proteins that has not been edited." ;
  rdfs:subClassOf obo:SO_0000120 .

obo:SO_1000033 a rdfs:Class .

obo:SO_0001551 a rdfs:Class ;
  rdfs:label "increased_transcription_rate_variant" ;
  rdfs:comment "A sequence variant that increases the rate of transcription with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001550 .

obo:SO_0001863 a rdfs:Class ;
  rdfs:label "GTT_trinucleotide_repeat" ;
  rdfs:comment "A trinucleotide repeat region composed of GTT repeating elements." ;
  rdfs:subClassOf obo:SO_0000291 .

obo:SO_0000041 a rdfs:Class ;
  rdfs:label "sequence_operation" ;
  rdfs:comment "An operation that can be applied to a sequence, that results in a change." .

obo:SO_0000339 a rdfs:Class ;
  rdfs:label "recombination_hotspot" ;
  rdfs:comment "A region in a genome which promotes recombination." ;
  rdfs:subClassOf obo:SO_0000298 .

obo:SO_1001191 a rdfs:Class ;
  rdfs:label "encodes_overlapping_peptides_different_start" ;
  rdfs:comment "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." ;
  rdfs:subClassOf obo:SO_1001195 .

obo:SO_0001723 a rdfs:Class ;
  rdfs:label "H3K36_dimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." ;
  rdfs:subClassOf obo:SO_0001733 .

obo:SO_0001994 a rdfs:Class ;
  rdfs:label "intron_base_5" ;
  rdfs:comment "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." ;
  rdfs:subClassOf obo:SO_0001014 .

obo:SO_0002069 a rdfs:Class ;
  rdfs:label "LINE1_deletion" ;
  rdfs:comment "A deletion of a LINE1 mobile element with respect to a reference." ;
  rdfs:subClassOf obo:SO_0002066 .

obo:SO_0000664 a rdfs:Class ;
  rdfs:label "introgressed_chromosome_region" ;
  rdfs:comment "A region of a chromosome that has been introduced by backcrossing with a separate species." ;
  rdfs:subClassOf obo:SO_0000830 .

obo:SO_0001514 a rdfs:Class ;
  rdfs:label "direct" ;
  rdfs:comment "A quality of an insertion where the insert is not in a cytologically inverted orientation." ;
  rdfs:subClassOf obo:SO_0001512 .

obo:SO_0000992 a rdfs:Class ;
  rdfs:label "BAC_cloned_genomic_insert" ;
  rdfs:comment "A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome." ;
  rdfs:subClassOf obo:SO_0000914 .

obo:SO_0000564 a rdfs:Class ;
  rdfs:label "V_DJ_J_C_cluster" ;
  rdfs:comment "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." ;
  rdfs:subClassOf obo:SO_0000938 .

obo:SO_0001811 a rdfs:Class ;
  rdfs:label "phosphorylation_site" ;
  rdfs:comment "A post-translationally modified region in which residues of the protein are modified by phosphorylation." ;
  rdfs:subClassOf obo:SO_0001089 .

obo:SO_0000779 a rdfs:Class ;
  rdfs:label "engineered_episome" ;
  rdfs:comment "An episome that is engineered." ;
  rdfs:subClassOf obo:SO_0000637 , obo:SO_0000768 .

obo:SO_0000757 a rdfs:Class ;
  rdfs:label "single_stranded_cDNA" ;
  rdfs:comment "DNA synthesized from RNA by reverse transcriptase, single stranded." ;
  rdfs:subClassOf obo:SO_0000756 .

obo:SO_0000594 a rdfs:Class ;
  rdfs:label "H_ACA_box_snoRNA" ;
  rdfs:comment "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." ;
  rdfs:subClassOf obo:SO_0000275 .

obo:SO_0001706 a rdfs:Class ;
  rdfs:label "H3K4_trimethylation" ;
  rdfs:comment "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001734 .

obo:SO_0001622 a rdfs:Class ;
  rdfs:label "UTR_variant" ;
  rdfs:comment "A transcript variant that is located within the UTR." ;
  rdfs:subClassOf obo:SO_0001791 , obo:SO_0001968 .

obo:SO_0001759 a rdfs:Class ;
  rdfs:label "unitary_pseudogene" ;
  rdfs:comment "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional." ;
  rdfs:subClassOf obo:SO_0001760 .

<https://w3id.org/linkml/Any> a rdfs:Class ;
  rdfs:comment "An unconstrained type or object" .

obo:SO_0000165 a rdfs:Class ;
  rdfs:label "enhancer" ;
  rdfs:comment "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." ;
  rdfs:subClassOf obo:SO_0000727 .

obo:SO_0000884 a rdfs:Class ;
  rdfs:label "stop_codon_redefined_as_pyrrolysine" ;
  rdfs:comment "A stop codon redefined to be the new amino acid, pyrrolysine." ;
  rdfs:subClassOf obo:SO_0000883 .

obo:SO_1000008 a rdfs:Class ;
  rdfs:label "point_mutation" ;
  rdfs:comment "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." ;
  rdfs:subClassOf obo:SO_0001483 .

obo:SO_0002371 a rdfs:Class ;
  rdfs:label "C-D_H_ACA_box_scaRNA" ;
  rdfs:comment "A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002095 .

obo:SO_0001871 a rdfs:Class ;
  rdfs:label "PCB" ;
  rdfs:comment "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000317 a rdfs:Class ;
  rdfs:label "cDNA_clone" ;
  rdfs:comment "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." ;
  rdfs:subClassOf obo:SO_0000151 .

obo:SO_0001741 a rdfs:Class ;
  rdfs:label "pseudogenic_gene_segment" ;
  rdfs:comment "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." ;
  rdfs:subClassOf obo:SO_3000000 .

obo:SO_0002244 a rdfs:Class ;
  rdfs:label "partially_duplicated_transcript" ;
  rdfs:comment "A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional." ;
  rdfs:subClassOf obo:SO_0001576 .

obo:SO_0000818 a rdfs:Class ;
  rdfs:label "wild_type_rescue_gene" ;
  rdfs:comment "A gene that rescues." ;
  rdfs:subClassOf obo:SO_0000704 , obo:SO_0000816 .

obo:SO_0002340 a rdfs:Class ;
  rdfs:label "RNA_7SK" ;
  rdfs:comment "An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0002098 a rdfs:Class ;
  rdfs:label "immunoglobulin_pseudogene" ;
  rdfs:comment "A pseudogene derived from an immunoglobulin gene." ;
  rdfs:subClassOf obo:SO_0002097 .

obo:SO_0001889 a rdfs:Class ;
  rdfs:label "transcript_amplification" ;
  rdfs:comment "A feature amplification of a region containing a transcript." ;
  rdfs:subClassOf obo:SO_0001880 .

obo:SO_0001965 a rdfs:Class ;
  rdfs:label "8_oxoguanine" ;
  rdfs:comment "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." ;
  rdfs:subClassOf obo:SO_0001964 .

obo:SO_0002025 a rdfs:Class ;
  rdfs:label "cis_acting_homologous_chromosome_pairing_region" ;
  rdfs:comment "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001573 a rdfs:Class ;
  rdfs:label "intron_gain_variant" ;
  rdfs:comment "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." ;
  rdfs:subClassOf obo:SO_0001568 .

obo:SO_0001792 a rdfs:Class ;
  rdfs:label "non_coding_transcript_exon_variant" ;
  rdfs:comment "A sequence variant that changes non-coding exon sequence in a non-coding transcript." ;
  rdfs:subClassOf obo:SO_0001619 , obo:SO_0001791 .

obo:SO_0002383 a rdfs:Class ;
  rdfs:label "oncogenic_variant" ;
  rdfs:comment "A variant that has been found to be pathogenic in the context of a neoplastic disease." ;
  rdfs:subClassOf obo:SO_0001771 .

obo:SO_0000102 a rdfs:Class ;
  rdfs:label "expressed_sequence_match" ;
  rdfs:comment "A match to an EST or cDNA sequence." ;
  rdfs:subClassOf obo:SO_0000347 .

obo:SO_0000328 a rdfs:Class ;
  rdfs:label "microarray_oligo" ;
  rdfs:comment "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." ;
  rdfs:subClassOf obo:SO_0000051 .

obo:SO_0001068 a rdfs:Class ;
  rdfs:label "polypeptide_repeat" ;
  rdfs:comment "A polypeptide_repeat is a single copy of an internal sequence repetition." ;
  rdfs:subClassOf obo:SO_0100021 .

obo:SO_0001713 a rdfs:Class ;
  rdfs:label "H4K20_monomethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." ;
  rdfs:subClassOf obo:SO_0001701 .

obo:SO_0000937 a rdfs:Class ;
  rdfs:label "vertebrate_immune_system_feature" .

obo:SO_0001489 a rdfs:Class ;
  rdfs:label "annotation_directed_improved_draft" ;
  rdfs:comment "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." ;
  rdfs:subClassOf obo:SO_0001499 .

obo:SO_0002190 a rdfs:Class ;
  rdfs:label "enhancer_blocking_element" ;
  rdfs:comment "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator." ;
  rdfs:subClassOf obo:SO_0000627 .

obo:SO_0001242 a rdfs:Class .

obo:SO_0000463 a rdfs:Class ;
  rdfs:label "encodes_alternately_spliced_transcripts" ;
  rdfs:comment "A gene that encodes more than one transcript." ;
  rdfs:subClassOf obo:SO_0000401 .

obo:SO_0000154 a rdfs:Class ;
  rdfs:label "PAC" ;
  rdfs:comment "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." ;
  rdfs:subClassOf obo:SO_0000440 .

obo:SO_0001712 a rdfs:Class ;
  rdfs:label "H3K79_trimethylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." ;
  rdfs:subClassOf obo:SO_0001735 .

obo:SO_0002093 a rdfs:Class ;
  rdfs:label "structural_interaction_variant" ;
  rdfs:comment "A variant that impacts the internal interactions of the resulting polypeptide structure." ;
  rdfs:subClassOf obo:SO_0001599 .

obo:SO_0001438 a rdfs:Class ;
  rdfs:label "isoleucine" ;
  rdfs:comment "A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA)." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001990 a rdfs:Class ;
  rdfs:label "five_prime_UTR_premature_start_codon_location_variant" ;
  rdfs:comment "A 5' UTR variant where a premature start codon is moved." ;
  rdfs:subClassOf obo:SO_0001983 .

obo:SO_0001831 a rdfs:Class ;
  rdfs:label "protein_hmm_match" ;
  rdfs:comment "A match to a protein HMM such as pfam." ;
  rdfs:subClassOf obo:SO_0000349 .

obo:SO_0002031 a rdfs:Class ;
  rdfs:label "shRNA" ;
  rdfs:comment "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:BS_00221 a rdfs:Class .

obo:SO_0000357 a rdfs:Class ;
  rdfs:label "flanked" ;
  rdfs:comment "An attribute describing a region that is bounded either side by a particular kind of region." ;
  rdfs:subClassOf obo:SO_0000733 .

obo:SO_0001549 a rdfs:Class ;
  rdfs:label "transcription_variant" ;
  rdfs:comment "A variant that changes alters the transcription of a transcript with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001538 .

obo:SO_0002087 a rdfs:Class ;
  rdfs:label "pseudogenic_CDS" ;
  rdfs:comment "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." ;
  rdfs:subClassOf obo:SO_0000462 .

obo:SO_0001446 a rdfs:Class ;
  rdfs:label "tyrosine" ;
  rdfs:comment "A polar, hydorophilic amino acid encoded by the codons TAT and TAC." ;
  rdfs:subClassOf obo:SO_0001237 .

obo:SO_0001532 a rdfs:Class ;
  rdfs:label "recombination_signal_sequence" ;
  rdfs:comment "A region recognized by a recombinase." ;
  rdfs:subClassOf obo:SO_0000299 .

obo:SO_0001562 a rdfs:Class ;
  rdfs:label "polypeptide_post_translational_processing_variant" ;
  rdfs:comment "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0001329 a rdfs:Class ;
  rdfs:label "N2_2_prime_O_dimethylguanosine" ;
  rdfs:comment "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." ;
  rdfs:subClassOf obo:SO_0001276 .

obo:SO_0000734 a rdfs:Class ;
  rdfs:label "exemplar_mRNA" ;
  rdfs:comment "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." ;
  rdfs:subClassOf obo:SO_0000234 .

obo:SO_0001462 a rdfs:Class ;
  rdfs:label "contig_collection" ;
  rdfs:comment "A collection of contigs." ;
  rdfs:subClassOf obo:SO_0001085 , obo:SO_0001260 .

obo:SO_0000853 a rdfs:Class ;
  rdfs:label "homologous_region" ;
  rdfs:comment "A region that is homologous to another region." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0000842 a rdfs:Class ;
  rdfs:label "gene_component_region" ;
  rdfs:comment "A region of a gene that has a specific function." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0001906 a rdfs:Class ;
  rdfs:label "feature_truncation" ;
  rdfs:comment "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001878 .

obo:SO_0000582 a rdfs:Class ;
  rdfs:label "rRNA_cleavage_snoRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding an rRNA cleavage snoRNA." ;
  rdfs:subClassOf obo:SO_0000232 .

obo:SO_0001674 a rdfs:Class ;
  rdfs:label "minus_24_signal" ;
  rdfs:comment "A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0001525 a rdfs:Class ;
  rdfs:label "assembly_error_correction" ;
  rdfs:comment "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." ;
  rdfs:subClassOf obo:SO_0000413 .

obo:BS_00131 a rdfs:Class .

obo:SO_0001793 a rdfs:Class ;
  rdfs:label "clone_end" ;
  rdfs:comment "A read from an end of the clone sequence." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0002335 a rdfs:Class ;
  rdfs:label "opal_stop_codon" ;
  rdfs:comment "A stop codon with the DNA sequence TGA." ;
  rdfs:subClassOf obo:SO_0000319 .

obo:SO_0001960 a rdfs:Class ;
  rdfs:label "5_hydroxymethylcytosine" ;
  rdfs:comment "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." ;
  rdfs:subClassOf obo:SO_0000114 .

obo:SO_0001054 a rdfs:Class ;
  rdfs:label "transposon_fragment" ;
  rdfs:comment "A portion of a transposon, interrupted by the insertion of another element." ;
  rdfs:subClassOf obo:SO_0000840 .

obo:SO_0001495 a rdfs:Class ;
  rdfs:label "centromere_DNA_Element_III" ;
  rdfs:comment "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_0001070 a rdfs:Class ;
  rdfs:label "polypeptide_structural_region" ;
  rdfs:comment "Region of polypeptide with a given structural property." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0000768 a rdfs:Class ;
  rdfs:label "episome" ;
  rdfs:comment "A plasmid that may integrate with a chromosome." ;
  rdfs:subClassOf obo:SO_0000155 .

obo:SO_0000829 a rdfs:Class ;
  rdfs:label "nucleomorphic_chromosome" ;
  rdfs:comment "A chromosome originating in a nucleomorph." ;
  rdfs:subClassOf obo:SO_0000340 .

obo:SO_0001827 a rdfs:Class ;
  rdfs:label "mRNA_read" ;
  rdfs:comment "A sequencer read of an mRNA substrate." ;
  rdfs:subClassOf obo:SO_0000150 .

obo:SO_0001546 a rdfs:Class ;
  rdfs:label "transcript_stability_variant" ;
  rdfs:comment "A variant that changes the stability of a transcript with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001538 .

obo:SO_1000019 a rdfs:Class ;
  rdfs:label "C_to_A_transversion" ;
  rdfs:comment "A transversion from cytidine to adenine." ;
  rdfs:subClassOf obo:SO_1000018 .

obo:SO_0001611 a rdfs:Class ;
  rdfs:label "elongated_polypeptide_N_terminal" ;
  rdfs:comment "An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS." ;
  rdfs:subClassOf obo:SO_0001609 .

obo:SO_0000497 a rdfs:Class ;
  rdfs:label "five_prime_D_nonamer" ;
  rdfs:comment "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." ;
  rdfs:subClassOf obo:SO_0000562 .

obo:SO_0001172 a rdfs:Class ;
  rdfs:label "tRNA_region" ;
  rdfs:comment "A region of a tRNA." ;
  rdfs:subClassOf obo:SO_0000834 .

obo:SO_1000156 a rdfs:Class ;
  rdfs:label "inverted_interchromosomal_transposition" ;
  rdfs:comment "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." ;
  rdfs:subClassOf obo:SO_1000155 .

obo:SO_0001986 a rdfs:Class ;
  rdfs:label "upstream_transcript_variant" ;
  rdfs:comment "A feature variant, where the alteration occurs upstream of the transcript TSS." ;
  rdfs:subClassOf obo:SO_0001628 .

obo:BS_00210 a rdfs:Class .

obo:SO_0002084 a rdfs:Class ;
  rdfs:label "exonic_splice_region_variant" ;
  rdfs:comment "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary." ;
  rdfs:subClassOf obo:SO_0001630 .

obo:SO_0001189 a rdfs:Class ;
  rdfs:label "LNA_oligo" ;
  rdfs:comment "An oligo composed of LNA residues." ;
  rdfs:subClassOf obo:SO_0001247 .

obo:SO_0002104 a rdfs:Class ;
  rdfs:label "TR_J_pseudogene" ;
  rdfs:comment "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." ;
  rdfs:subClassOf obo:SO_0002099 .

obo:SO_0001665 a rdfs:Class ;
  rdfs:label "DCE_SI" ;
  rdfs:comment "A sub element of the DCE core promoter element, with consensus sequence CTTC." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0002073 a rdfs:Class ;
  rdfs:label "no_sequence_alteration" ;
  rdfs:comment "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence." ;
  rdfs:subClassOf obo:SO_0002072 .

obo:SO_0000948 a rdfs:Class ;
  rdfs:label "inversion_site" ;
  rdfs:comment "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." ;
  rdfs:subClassOf obo:SO_0000342 .

obo:SO_0000683 a rdfs:Class ;
  rdfs:label "exonic_splice_enhancer" ;
  rdfs:comment "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." ;
  rdfs:subClassOf obo:SO_0000344 .

obo:SO_0000577 a rdfs:Class ;
  rdfs:label "centromere" ;
  rdfs:comment "A region of chromosome where the spindle fibers attach during mitosis and meiosis." ;
  rdfs:subClassOf obo:SO_0000628 .

obo:SO_0000900 a rdfs:Class ;
  rdfs:label "processed" ;
  rdfs:comment "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." .

obo:SO_0000545 a rdfs:Class ;
  rdfs:label "recoding_pseudoknot" ;
  rdfs:comment "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." ;
  rdfs:subClassOf obo:SO_0000591 .

obo:SO_0000392 a rdfs:Class ;
  rdfs:label "U2_snRNA" ;
  rdfs:comment "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0002357 a rdfs:Class ;
  rdfs:label "biosynthetic_gene_cluster" ;
  rdfs:comment "A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants)." ;
  rdfs:subClassOf obo:SO_0001411 .

obo:SO_0002230 a rdfs:Class ;
  rdfs:label "CAAX_box" ;
  rdfs:comment "A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E." ;
  rdfs:subClassOf obo:SO_0100017 .

obo:SO_0001473 a rdfs:Class ;
  rdfs:label "miRNA_antiguide" ;
  rdfs:comment "A region of the pri miRNA that base pairs with the guide to form the hairpin." ;
  rdfs:subClassOf obo:SO_0001243 .

obo:SO_0001908 a rdfs:Class ;
  rdfs:label "internal_feature_elongation" ;
  rdfs:comment "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." ;
  rdfs:subClassOf obo:SO_0001907 .

obo:SO_0001680 a rdfs:Class ;
  rdfs:label "translation_regulatory_region" ;
  rdfs:comment "A regulatory region that is involved in the control of the process of translation." ;
  rdfs:subClassOf obo:SO_0005836 .

obo:SO_0001847 a rdfs:Class ;
  rdfs:label "forkhead_motif" ;
  rdfs:comment "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0000915 a rdfs:Class ;
  rdfs:label "engineered_insert" ;
  rdfs:comment "A clone insert that is engineered." ;
  rdfs:subClassOf obo:SO_0000753 , obo:SO_0000804 .

obo:BS_00154 a rdfs:Class .

obo:SO_0001829 a rdfs:Class ;
  rdfs:label "mRNA_contig" ;
  rdfs:comment "A contig composed of mRNA_reads." ;
  rdfs:subClassOf obo:SO_0000149 .

obo:SO_0001125 a rdfs:Class ;
  rdfs:label "schellmann_loop_six" ;
  rdfs:comment "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." ;
  rdfs:subClassOf obo:SO_0001123 .

obo:SO_0000052 a rdfs:Class ;
  rdfs:label "assortment_derived_deficiency" .

obo:SO_0001677 a rdfs:Class ;
  rdfs:label "intermediate_element" ;
  rdfs:comment "A core promoter region of RNA polymerase III type 1 promoters." ;
  rdfs:subClassOf obo:SO_0001660 .

obo:SO_0000363 a rdfs:Class ;
  rdfs:label "floxed_gene" ;
  rdfs:comment "A transgene that is floxed." ;
  rdfs:subClassOf obo:SO_0000902 .

obo:SO_0001912 a rdfs:Class ;
  rdfs:label "copy_number_decrease" ;
  rdfs:comment "A sequence variant where copies of a feature are decreased relative to the reference." ;
  rdfs:subClassOf obo:SO_0001563 .

obo:SO_0001043 a rdfs:Class ;
  rdfs:label "attCtn_site" ;
  rdfs:comment "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." ;
  rdfs:subClassOf obo:SO_0000946 .

obo:SO_0001308 a rdfs:Class ;
  rdfs:label "N6_hydroxynorvalylcarbamoyladenosine" ;
  rdfs:comment "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." ;
  rdfs:subClassOf obo:SO_0001273 .

obo:SO_1000145 a rdfs:Class ;
  rdfs:label "free_ring_duplication" ;
  rdfs:comment "A ring chromosome which is a copy of another chromosome." ;
  rdfs:subClassOf obo:SO_1000045 , obo:SO_1000144 .

obo:SO_0001484 a rdfs:Class ;
  rdfs:label "X_element_combinatorial_repeat" ;
  rdfs:comment "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." ;
  rdfs:subClassOf obo:SO_0000657 .

obo:SO_0001558 a rdfs:Class ;
  rdfs:label "polypeptide_localization_variant" ;
  rdfs:comment "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." ;
  rdfs:subClassOf obo:SO_0001554 .

obo:SO_0000689 a rdfs:Class ;
  rdfs:label "cDNA_match" ;
  rdfs:comment "A match against cDNA sequence." ;
  rdfs:subClassOf obo:SO_0000102 .

obo:SO_0002267 a rdfs:Class ;
  rdfs:label "Retrovirus_LTR_retrotransposon" ;
  rdfs:comment "LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein." ;
  rdfs:subClassOf obo:SO_0000186 .

obo:SO_0001616 a rdfs:Class ;
  rdfs:label "polypeptide_fusion" ;
  rdfs:comment "A sequence variant that causes a fusion of two polypeptide sequences." ;
  rdfs:subClassOf obo:SO_0001603 .

obo:SO_0000171 a rdfs:Class ;
  rdfs:label "RNApol_III_promoter" ;
  rdfs:comment "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." ;
  rdfs:subClassOf obo:SO_0002221 .

obo:SO_0002148 a rdfs:Class ;
  rdfs:label "H2AZK13_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002144 .

obo:SO_0000302 a rdfs:Class ;
  rdfs:label "J_gene_recombination_feature" ;
  rdfs:comment "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." ;
  rdfs:subClassOf obo:SO_0000939 .

obo:SO_0000221 a rdfs:Class ;
  rdfs:label "leucine_tRNA_primary_transcript" ;
  rdfs:comment "A primary transcript encoding leucyl tRNA (SO:0000264)." ;
  rdfs:subClassOf obo:SO_0000210 .

obo:SO_0000340 a rdfs:Class ;
  rdfs:label "chromosome" ;
  rdfs:comment "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." ;
  rdfs:subClassOf obo:SO_0001235 .

obo:SO_0000194 a rdfs:Class ;
  rdfs:label "LINE_element" ;
  rdfs:comment "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." ;
  rdfs:subClassOf obo:SO_0000189 .

obo:SO_0001774 a rdfs:Class ;
  rdfs:label "quantitative_variant" ;
  rdfs:comment "A variant within a gene that contributes to a quantitative trait such as height or weight." ;
  rdfs:subClassOf obo:SO_0001769 .

obo:SO_0002312 a rdfs:Class ;
  rdfs:label "core_prokaryotic_promoter_element" ;
  rdfs:comment "An element that always exists within the promoter region of a prokaryotic gene." ;
  rdfs:subClassOf obo:SO_0002309 .

obo:SO_0000709 a rdfs:Class ;
  rdfs:label "SL2_acceptor_site" ;
  rdfs:comment "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." ;
  rdfs:subClassOf obo:SO_0000706 .

obo:SO_0000599 a rdfs:Class ;
  rdfs:label "edited_by_C_to_U_substitution" .

obo:SO_0001150 a rdfs:Class ;
  rdfs:label "beta_turn_type_six" ;
  rdfs:comment "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:SO_0001647 a rdfs:Class ;
  rdfs:label "kozak_sequence" ;
  rdfs:comment "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." ;
  rdfs:subClassOf obo:SO_0000139 .

obo:SO_0002019 a rdfs:Class ;
  rdfs:label "start_retained_variant" ;
  rdfs:comment "A sequence variant where at least one base in the start codon is changed, but the start remains." ;
  rdfs:subClassOf obo:SO_0001582 , obo:SO_0001819 .

obo:SO_0001971 a rdfs:Class ;
  rdfs:label "zinc_finger_binding_site" ;
  rdfs:comment "A binding site to which a polypeptide will bind with a zinc finger motif, which is characterized by requiring one or more Zinc 2+ ions for stabilized folding." ;
  rdfs:subClassOf obo:SO_0001429 .

obo:SO_0000380 a rdfs:Class ;
  rdfs:label "hammerhead_ribozyme" ;
  rdfs:comment "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." ;
  rdfs:subClassOf obo:SO_0000715 .

obo:SO_0000678 a rdfs:Class ;
  rdfs:label "non_canonical_three_prime_splice_site" ;
  rdfs:comment "A 3' splice site that does not have the sequence \"AG\"." ;
  rdfs:subClassOf obo:SO_0000164 .

obo:SO_0001137 a rdfs:Class ;
  rdfs:label "beta_turn_right_handed_type_two" ;
  rdfs:comment "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." ;
  rdfs:subClassOf obo:SO_0001133 .

obo:SO_0000835 a rdfs:Class ;
  rdfs:label "primary_transcript_region" ;
  rdfs:comment "A part of a primary transcript." ;
  rdfs:subClassOf obo:SO_0000833 .

obo:SO_0000352 a rdfs:Class ;
  rdfs:label "DNA" ;
  rdfs:comment "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." ;
  rdfs:subClassOf obo:SO_0000348 .

obo:SO_0002165 a rdfs:Class ;
  rdfs:label "trinucleotide_repeat_expansion" ;
  rdfs:comment "A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence." ;
  rdfs:subClassOf obo:SO_0002162 .

obo:SO_0000631 a rdfs:Class ;
  rdfs:label "polycistronic_primary_transcript" ;
  rdfs:comment "A primary transcript encoding for more than one gene product." ;
  rdfs:subClassOf obo:SO_0000078 , obo:SO_0000185 .

obo:SO_0002051 a rdfs:Class ;
  rdfs:label "inducible_promoter" ;
  rdfs:comment "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." ;
  rdfs:subClassOf obo:SO_0000167 .

obo:SO_0002372 a rdfs:Class ;
  rdfs:label "C_D_box_scaRNA_gene" ;
  rdfs:comment "A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs." ;
  rdfs:subClassOf obo:SO_0002339 .

obo:SO_0002127 a rdfs:Class ;
  rdfs:label "lncRNA_gene" ;
  rdfs:comment "A gene that encodes a long non-coding RNA." ;
  rdfs:subClassOf obo:SO_0001263 .

obo:SO_0000615 a rdfs:Class ;
  rdfs:label "terminator_of_type_2_RNApol_III_promoter" ;
  rdfs:comment "A terminator signal for RNA polymerase III transcription." ;
  rdfs:subClassOf obo:SO_0000951 .

obo:SO_0001581 a rdfs:Class .

obo:SO_0001457 a rdfs:Class ;
  rdfs:label "transcribed_cluster" ;
  rdfs:comment "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." ;
  rdfs:subClassOf obo:SO_0001410 .

obo:SO_0001800 a rdfs:Class ;
  rdfs:label "tasiRNA" ;
  rdfs:comment "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." ;
  rdfs:subClassOf obo:SO_0000655 .

obo:SO_0000391 a rdfs:Class ;
  rdfs:label "U1_snRNA" ;
  rdfs:comment "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." ;
  rdfs:subClassOf obo:SO_0000274 .

obo:SO_0001108 a rdfs:Class ;
  rdfs:label "beta_bulge_loop" ;
  rdfs:comment "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0001227 a rdfs:Class ;
  rdfs:label "gene_silenced_by_histone_deacetylation" ;
  rdfs:comment "A gene that is silenced by histone deacetylation." ;
  rdfs:subClassOf obo:SO_0001225 .

obo:SO_0001177 a rdfs:Class ;
  rdfs:label "T_loop" ;
  rdfs:comment "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." ;
  rdfs:subClassOf obo:SO_0001172 .

obo:SO_0001415 a rdfs:Class ;
  rdfs:label "deletion_breakpoint" ;
  rdfs:comment "The point within a chromosome where a deletion begins or ends." ;
  rdfs:subClassOf obo:SO_0001021 .

obo:SO_0001148 a rdfs:Class ;
  rdfs:label "mutated_variant_site" ;
  rdfs:comment "Site which has been experimentally altered." ;
  rdfs:subClassOf obo:SO_0001146 .

obo:SO_1001268 a rdfs:Class ;
  rdfs:label "recoding_stimulatory_region" ;
  rdfs:comment "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." ;
  rdfs:subClassOf obo:SO_0000836 .

obo:SO_0001397 a rdfs:Class ;
  rdfs:label "modified_L_phenylalanine" ;
  rdfs:comment "A post translationally modified phenylalanine amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:BS_00187 a rdfs:Class .

obo:SO_0001867 a rdfs:Class ;
  rdfs:label "candidate_gene" ;
  rdfs:comment "A gene suspected of being involved in the expression of a trait." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:SO_0001853 a rdfs:Class ;
  rdfs:label "androgen_response_element" ;
  rdfs:comment "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." ;
  rdfs:subClassOf obo:SO_0000713 .

obo:SO_0000608 a rdfs:Class ;
  rdfs:label "H_ACA_box_snoRNA_encoding" ;
  rdfs:comment "snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA)." ;
  rdfs:subClassOf obo:SO_0000578 .

obo:SO_0000706 a rdfs:Class ;
  rdfs:label "trans_splice_acceptor_site" ;
  rdfs:comment "The 3' splice site of the acceptor primary transcript." ;
  rdfs:subClassOf obo:SO_0001420 .

obo:SO_0002132 a rdfs:Class ;
  rdfs:label "sense_overlap_lncRNA" ;
  rdfs:comment "A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence." ;
  rdfs:subClassOf obo:SO_0001877 .

obo:SO_0001858 a rdfs:Class ;
  rdfs:label "TR_box" ;
  rdfs:comment "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." ;
  rdfs:subClassOf obo:SO_0001659 .

obo:SO_0002346 a rdfs:Class ;
  rdfs:label "plastid_rRNA" ;
  rdfs:comment "Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes." ;
  rdfs:subClassOf obo:SO_0000252 .

obo:SO_0000679 a rdfs:Class ;
  rdfs:label "non_canonical_five_prime_splice_site" ;
  rdfs:comment "A 5' splice site which does not have the sequence \"GT\"." ;
  rdfs:subClassOf obo:SO_0000163 .

obo:SO_0002149 a rdfs:Class ;
  rdfs:label "H2AZK15_acetylation_site" ;
  rdfs:comment "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated." ;
  rdfs:subClassOf obo:SO_0002144 .

obo:SO_0100007 a rdfs:Class ;
  rdfs:label "catmat_right_handed_four" ;
  rdfs:comment "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." ;
  rdfs:subClassOf obo:SO_0001078 .

obo:SO_0002207 a rdfs:Class ;
  rdfs:label "UNAAAC_motif" ;
  rdfs:comment "A hexameric RNA motif consisting of nucleotides UNAAAC (where N can be any nucleotide) that targets the RNA for degradation." ;
  rdfs:subClassOf obo:SO_0001979 .

obo:SO_0000299 a rdfs:Class ;
  rdfs:label "specific_recombination_site" ;
  rdfs:comment "A location where recombination or occurs during mitosis or meiosis." ;
  rdfs:subClassOf obo:SO_0000669 .

obo:SO_0001212 a rdfs:Class ;
  rdfs:label "plus_2_translational_frameshift" ;
  rdfs:comment "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." ;
  rdfs:subClassOf obo:SO_0001210 .

obo:SO_0002393 a rdfs:Class ;
  rdfs:label "precursor_RNA" ;
  rdfs:comment "Any RNA species that is not yet the mature RNA product; may include ncRNA, rRNA, tRNA, 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR)." ;
  rdfs:subClassOf obo:SO_0000673 .

obo:SO_0002223 a rdfs:Class ;
  rdfs:label "inert_DNA_spacer" ;
  rdfs:comment "Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes." ;
  rdfs:subClassOf obo:SO_0005836 .

obo:SO_0001066 a rdfs:Class ;
  rdfs:label "compositionally_biased_region_of_peptide" ;
  rdfs:comment "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." ;
  rdfs:subClassOf obo:SO_0000839 .

obo:SO_0001788 a rdfs:Class ;
  rdfs:label "U_box" ;
  rdfs:comment "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." ;
  rdfs:subClassOf obo:SO_0000330 .

obo:SO_1000022 a rdfs:Class ;
  rdfs:label "T_to_G_transversion" ;
  rdfs:comment "A transversion from T to G." ;
  rdfs:subClassOf obo:SO_1000018 .

obo:SO_0001590 a rdfs:Class ;
  rdfs:label "terminator_codon_variant" ;
  rdfs:comment "A sequence variant whereby at least one of the bases in the terminator codon is changed." ;
  rdfs:subClassOf obo:SO_0001580 .

obo:SO_0001815 a rdfs:Class ;
  rdfs:label "synonymous" ;
  rdfs:comment "A variant that does not lead to any change in the amino acid sequence." ;
  rdfs:subClassOf obo:SO_0001814 .

obo:SO_0000787 a rdfs:Class ;
  rdfs:label "clone_attribute" .

obo:SO_0001404 a rdfs:Class ;
  rdfs:label "modified_L_proline" ;
  rdfs:comment "A post translationally modified proline amino acid feature." ;
  rdfs:subClassOf obo:SO_0001385 .

obo:SO_0000160 a rdfs:Class ;
  rdfs:label "lambda_clone" ;
  rdfs:comment "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." .

obo:SO_0001510 a rdfs:Class ;
  rdfs:label "intrachromosomal" ;
  rdfs:comment "A change in chromosomes that occurs between two separate chromosomes." ;
  rdfs:subClassOf obo:SO_0001509 .

obo:SO_0000097 a rdfs:Class ;
  rdfs:label "nucleomorph_gene" ;
  rdfs:comment "A gene from nucleomorph sequence." ;
  rdfs:subClassOf obo:SO_0000704 .

obo:IAO_0000115 a rdf:Property ;
  rdfs:label "definition" ;
  rdfs:range xsd:string .

obo:IAO_0100001 a rdf:Property ;
  rdfs:label "term replaced by" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#AAMOD> a rdf:Property ;
  rdfs:label "amino acid modification" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#AGR> a rdf:Property ;
  rdfs:label "Alliance of Genome Resources" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources> a rdf:Property ;
  rdfs:comment "Alliance of Genome Resources Gene Biotype Slim" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#BS> a rdf:Property ;
  rdfs:label "biosapiens" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#DBVAR> a rdf:Property ;
  rdfs:comment "database of genomic structural variation" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#RNAMOD> a rdf:Property ;
  rdfs:label "RNA modification" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#SOFA> a rdf:Property ;
  rdfs:comment "SO feature annotation" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#VAR> a rdf:Property ;
  rdfs:label "variant annotation term" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#aa1> a rdf:Property ;
  rdfs:label "amino acid 1 letter code" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#aa3> a rdf:Property ;
  rdfs:label "amino acid 3 letter code" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#associated_with> a rdf:Property ;
  rdfs:label "associated_with" ;
  rdfs:comment "This relationship is vague and up for discussion." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#biosapiens> a rdf:Property ;
  rdfs:comment "biosapiens protein feature ontology" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#complete_evidence_for_feature> a rdf:Property ;
  rdfs:label "complete_evidence_for_feature" ;
  rdfs:comment "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#evidence_for_feature> .

<http://purl.obolibrary.org/obo/so#connects_on> a rdf:Property ;
  rdfs:label "connects_on" ;
  rdfs:comment "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#contained_by> a rdf:Property ;
  rdfs:label "contained_by" ;
  rdfs:comment "X contained_by Y iff X starts after start of Y and X ends before end of Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#dbsnp> a rdf:Property ;
  rdfs:label "dbsnp variant terms" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#dbvar> a rdf:Property ;
  rdfs:label "DBVAR" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#disconnected_from> a rdf:Property ;
  rdfs:label "disconnected_from" ;
  rdfs:comment "X is disconnected_from Y iff it is not the case that X overlaps Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#ebi_variants> a rdf:Property ;
  rdfs:label "ensembl variant terms" ;
  rdfs:range xsd:string .

<http://purl.obolibrary.org/obo/so#edited_from> a rdf:Property ;
  rdfs:label "edited_from" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#edited_to> a rdf:Property ;
  rdfs:label "edited_to" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#evidence_for_feature> a rdf:Property ;
  rdfs:label "evidence_for_feature" ;
  rdfs:comment "B is evidence_for_feature A, if an instance of B supports the existence of A." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#exemplar_of> a rdf:Property ;
  rdfs:label "exemplar_of" ;
  rdfs:comment "X is exemplar of Y if X is the best evidence for Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#finished_by> a rdf:Property ;
  rdfs:label "finished_by" ;
  rdfs:comment "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#finishes> a rdf:Property ;
  rdfs:label "finishes" ;
  rdfs:comment "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#gained> a rdf:Property ;
  rdfs:label "gained" ;
  rdfs:comment "X gained Y if X is a variant_of X' and Y part of X but not X'." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#genome_of> a rdf:Property ;
  rdfs:label "genome_of" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#guides> a rdf:Property ;
  rdfs:label "guides" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#has_integral_part> a rdf:Property ;
  rdfs:label "has_integral_part" ;
  rdfs:comment "X has_integral_part Y if and only if: X has_part Y and Y part_of X." ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#has_part> .

<http://purl.obolibrary.org/obo/so#homologous_to> a rdf:Property ;
  rdfs:label "homologous_to" ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#similar_to> .

<http://purl.obolibrary.org/obo/so#integral_part_of> a rdf:Property ;
  rdfs:label "integral_part_of" ;
  rdfs:comment "X integral_part_of Y if and only if: X part_of Y and Y has_part X." ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#part_of> .

<http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of> a rdf:Property ;
  rdfs:label "is_consecutive_sequence_of" ;
  rdfs:comment "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#lost> a rdf:Property ;
  rdfs:label "lost" ;
  rdfs:comment "X lost Y if X is a variant_of X' and Y part of X' but not X." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#maximally_overlaps> a rdf:Property ;
  rdfs:label "maximally_overlaps" ;
  rdfs:comment "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#orthologous_to> a rdf:Property ;
  rdfs:label "orthologous_to" ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#homologous_to> .

<http://purl.obolibrary.org/obo/so#paralogous_to> a rdf:Property ;
  rdfs:label "paralogous_to" ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#homologous_to> .

<http://purl.obolibrary.org/obo/so#partial_evidence_for_feature> a rdf:Property ;
  rdfs:label "partial_evidence_for_feature" ;
  rdfs:comment "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." ;
  rdfs:range xsd:string ;
  rdfs:subPropertyOf <http://purl.obolibrary.org/obo/so#evidence_for_feature> .

<http://purl.obolibrary.org/obo/so#position_of> a rdf:Property ;
  rdfs:label "position_of" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#processed_from> a rdf:Property ;
  rdfs:label "processed_from" ;
  rdfs:comment "Inverse of processed_into." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#processed_into> a rdf:Property ;
  rdfs:label "processed_into" ;
  rdfs:comment "X is processed_into Y if a region X is modified to create Y." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#recombined_from> a rdf:Property ;
  rdfs:label "recombined_from" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#recombined_to> a rdf:Property ;
  rdfs:label "recombined_to" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#sequence_of> a rdf:Property ;
  rdfs:label "sequence_of" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#similar_to> a rdf:Property ;
  rdfs:label "similar_to" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#started_by> a rdf:Property ;
  rdfs:label "started_by" ;
  rdfs:comment "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#starts> a rdf:Property ;
  rdfs:label "starts" ;
  rdfs:comment "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#trans_spliced_from> a rdf:Property ;
  rdfs:label "trans_spliced_from" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#trans_spliced_to> a rdf:Property ;
  rdfs:label "trans_spliced_to" ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#translates_to> a rdf:Property ;
  rdfs:label "translates_to" ;
  rdfs:comment "Inverse of translation _of." ;
  rdfs:range <https://w3id.org/linkml/Any> .

<http://purl.obolibrary.org/obo/so#translation_of> a rdf:Property ;
  rdfs:label "translation_of" ;
  rdfs:comment "X is translation of Y if Y is translated by ribosome to create X." ;
  rdfs:range <https://w3id.org/linkml/Any> .