region
type: Class
subclass of: sequence_feature
IAO_0000115: 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.
has exact synonym: sequence
has OBO namespace: sequence
id: SO:0000001
in subset: SOFA

Axiom
annotated source: region
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:ke

protein_coding
type: Class
subclass of: gene_attribute
IAO_0000115: A gene which, when transcribed, can be translated into a protein.
has exact synonym: protein-coding
has OBO namespace: sequence
id: SO:0000010

polypeptide
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: derives from
  some values from: CDS
IAO_0000115: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
has alternative id: SO:0000358
has db xref: http://en.wikipedia.org/wiki/Polypeptide
has exact synonym: protein
has OBO namespace: sequence
id: SO:0000104
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.

Axiom
annotated source: polypeptide
annotated property: IAO_0000115
annotated target: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
has db xref: SO:ma

wiki
type: Axiom
annotated source: polypeptide
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Polypeptide

sequence_feature
type: Class
disjoint with: sequence_attribute
IAO_0000115: Any extent of continuous biological sequence.
has exact synonym: INSDC_feature:misc_feature
has exact synonym: INSDC_note:other
has exact synonym: INSDC_note:sequence_feature
has exact synonym: located_sequence_feature
has exact synonym: sequence feature
has OBO namespace: sequence
has related synonym: located sequence feature
id: SO:0000110
in subset: SOFA

Axiom
annotated source: sequence_feature
annotated property: IAO_0000115
annotated target: Any extent of continuous biological sequence.
has db xref: LAMHDI:mb
has db xref: SO:ke

epigenetically_modified
type: Class
subclass of: gene_attribute
IAO_0000115: 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.
has exact synonym: epigenetically modified
has OBO namespace: sequence
id: SO:0000133

Axiom
annotated source: epigenetically_modified
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:ke

capped
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
has OBO namespace: sequence
id: SO:0000146

Axiom
annotated source: capped
annotated property: IAO_0000115
annotated target: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
has db xref: SO:ke

enhancer
type: Class
subclass of: cis_regulatory_module
IAO_0000115: 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.
has broad synonym: INSDC_feature:regulatory
has db xref: http://en.wikipedia.org/wiki/Enhancer_(genetics)
has exact synonym: INSDC_qualifier:enhancer
has OBO namespace: sequence
id: SO:0000165
in subset: SOFA
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.

Axiom
annotated source: enhancer
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: enhancer
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Enhancer_(genetics)

promoter
type: Class
subclass of: gene_component_region
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: 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.
has broad synonym: INSDC_feature:regulatory
has db xref: http://en.wikipedia.org/wiki/Promoter
has exact synonym: INSDC_qualifier:promoter
has exact synonym: promoter sequence
has OBO namespace: sequence
id: SO:0000167
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.

Axiom
annotated source: promoter
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:regcreative

wiki
type: Axiom
annotated source: promoter
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Promoter

RNApol_II_promoter
type: Class
subclass of: eukaryotic_promoter
IAO_0000115: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
has exact synonym: RNA polymerase B promoter
has exact synonym: RNApol II promoter
has exact synonym: polymerase II promoter
has OBO namespace: sequence
has related synonym: pol II promoter
id: SO:0000170
comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.

Axiom
annotated source: RNApol_II_promoter
annotated property: IAO_0000115
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
has db xref: SO:ke

GC_rich_promoter_region
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part of
  some values from: RNApol_II_promoter
IAO_0000115: 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.
has broad synonym: INSDC_feature:regulatory
has exact synonym: GC rich promoter region
has exact synonym: GC-rich region
has exact synonym: INSDC_qualifier:GC_rich_promoter_region
has OBO namespace: sequence
id: SO:0000173

Axiom
annotated source: GC_rich_promoter_region
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://www.insdc.org/files/feature_table.html

primary_transcript
type: Class
subclass of: transcript
IAO_0000115: A transcript that in its initial state requires modification to be functional.
has db xref: http://en.wikipedia.org/wiki/Primary_transcript
has exact synonym: INSDC_feature:precursor_RNA
has exact synonym: INSDC_feature:prim_transcript
has exact synonym: precursor RNA
has exact synonym: primary transcript
has OBO namespace: sequence
id: SO:0000185
in subset: SOFA

Axiom
annotated source: primary_transcript
annotated property: IAO_0000115
annotated target: A transcript that in its initial state requires modification to be functional.
has db xref: SO:ma

wiki
type: Axiom
annotated source: primary_transcript
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Primary_transcript

intron
type: Class
subclass of: primary_transcript_region
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Intron
has exact synonym: INSDC_feature:intron
has OBO namespace: sequence
id: SO:0000188
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: intron
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: intron
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Intron

UTR
type: Class
subclass of: mRNA_region
IAO_0000115: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
has exact synonym: untranslated region
has OBO namespace: sequence
id: SO:0000203
in subset: SOFA

Axiom
annotated source: UTR
annotated property: IAO_0000115
annotated target: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
has db xref: SO:ke

three_prime_UTR
type: Class
subclass of: UTR
IAO_0000115: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
has db xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region
has exact synonym: INSDC_feature:3'UTR
has exact synonym: three prime UTR
has exact synonym: three prime untranslated region
has OBO namespace: sequence
id: SO:0000205
in subset: SOFA

Axiom
annotated source: three_prime_UTR
annotated property: IAO_0000115
annotated target: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: three_prime_UTR
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Three_prime_untranslated_region

rRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a ribosomal RNA.
has exact synonym: rRNA primary transcript
has exact synonym: ribosomal RNA primary transcript
has OBO namespace: sequence
id: SO:0000209
in subset: SOFA

Axiom
annotated source: rRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a ribosomal RNA.
has db xref: SO:ke

tRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a transfer RNA (SO:0000253).
has exact synonym: tRNA primary transcript
has OBO namespace: sequence
id: SO:0000210

Axiom
annotated source: tRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a transfer RNA (SO:0000253).
has db xref: SO:ke

snRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a small nuclear RNA (SO:0000274).
has exact synonym: snRNA primary transcript
has OBO namespace: sequence
id: SO:0000231

Axiom
annotated source: snRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a small nuclear RNA (SO:0000274).
has db xref: SO:ke

snoRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
has exact synonym: snoRNA primary transcript
has OBO namespace: sequence
id: SO:0000232
comment: This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520).

Axiom
annotated source: snoRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
has db xref: SO:ke

mature_transcript
type: Class
subclass of: transcript
subclass of: Restriction
  on property: derives from
  some values from: primary_transcript
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Mature_transcript
has exact synonym: mature transcript
has OBO namespace: sequence
id: SO:0000233
in subset: SOFA
comment: A processed transcript cannot contain introns.

Axiom
annotated source: mature_transcript
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:ke

wiki
type: Axiom
annotated source: mature_transcript
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Mature_transcript

mRNA
type: Class
subclass of: mature_transcript
IAO_0000115: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
has db xref: http://en.wikipedia.org/wiki/MRNA
has db xref: http://www.gencodegenes.org/gencode_biotypes.html
has exact synonym: INSDC_feature:mRNA
has exact synonym: messenger RNA
has exact synonym: protein_coding_transcript
has OBO namespace: sequence
id: SO:0000234
in subset: SOFA
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: mRNA
annotated property: IAO_0000115
annotated target: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
has db xref: SO:ma

wiki
type: Axiom
annotated source: mRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/MRNA

GENCODE
type: Axiom
annotated source: mRNA
annotated property: hasDbXref
annotated target: http://www.gencodegenes.org/gencode_biotypes.html

TF_binding_site
type: Class
subclass of: transcriptional_cis_regulatory_region
subclass of: nucleotide_to_protein_binding_site
subclass of: Restriction
  on property: part of
  some values from: cis_regulatory_module
IAO_0000115: A DNA site where a transcription factor binds.
has exact synonym: TF binding site
has exact synonym: transcription factor binding site
has OBO namespace: sequence
id: SO:0000235
in subset: SOFA
comment: Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: TF_binding_site
annotated property: IAO_0000115
annotated target: A DNA site where a transcription factor binds.
has db xref: SO:ke

transcript_attribute
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a transcript.
has exact synonym: transcript attribute
has OBO namespace: sequence
id: SO:0000237

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives from
  some values from: rRNA_primary_transcript
IAO_0000115: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
has broad synonym: INSDC_qualifier:unknown
has db xref: http://en.wikipedia.org/wiki/RRNA
has exact synonym: INSDC_feature:rRNA
has exact synonym: ribosomal RNA
has exact synonym: ribosomal ribonucleic acid
has OBO namespace: sequence
id: SO:0000252
in subset: SOFA
comment: Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493

Axiom
annotated source: rRNA
annotated property: IAO_0000115
annotated target: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
has db xref: ISBN:0198506732
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: rRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/RRNA

tRNA
type: Class
subclass of: sncRNA
subclass of: Restriction
  on property: derives from
  some values from: tRNA_primary_transcript
IAO_0000115: 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.
has broad synonym: INSDC_qualifier:unknown
has db xref: http://en.wikipedia.org/wiki/TRNA
has exact synonym: INSDC_feature:tRNA
has OBO namespace: sequence
has related synonym: transfer RNA
has related synonym: transfer ribonucleic acid
id: SO:0000253
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: tRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: ISBN:0198506732
has db xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: tRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/TRNA

snRNA
type: Class
subclass of: sncRNA
subclass of: Restriction
  on property: derives from
  some values from: snRNA_primary_transcript
IAO_0000115: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
has broad synonym: INSDC_feature:ncRNA
has db xref: http://en.wikipedia.org/wiki/SnRNA
has exact synonym: INSDC_qualifier:snRNA
has exact synonym: small nuclear RNA
has OBO namespace: sequence
id: SO:0000274
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: snRNA
annotated property: IAO_0000115
annotated target: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
has db xref: PMID:11733745
has db xref: WB:ems
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: snRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/SnRNA

snoRNA
type: Class
subclass of: sncRNA
subclass of: Restriction
  on property: derives from
  some values from: snoRNA_primary_transcript
IAO_0000115: 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.
has broad synonym: INSDC_feature:ncRNA
has exact synonym: INSDC_qualifier:snoRNA
has exact synonym: small nucleolar RNA
has OBO namespace: sequence
id: SO:0000275
in subset: SOFA
comment: Updated the definition of snoRNA (SO:0000275) from "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "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." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578.

Axiom
annotated source: snoRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: GOC:kgc
has db xref: PMID:31828325

miRNA
type: Class
subclass of: small_regulatory_ncRNA
subclass of: Restriction
  on property: derives from
  some values from: pre_miRNA
IAO_0000115: 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.
has alternative id: SO:0000649
has broad synonym: INSDC_feature:ncRNA
has db xref: http://en.wikipedia.org/wiki/MiRNA
has db xref: http://en.wikipedia.org/wiki/StRNA
has exact synonym: INSDC_qualifier:miRNA
has exact synonym: micro RNA
has exact synonym: microRNA
has exact synonym: small temporal RNA
has exact synonym: stRNA
has OBO namespace: sequence
id: SO:0000276
in subset: SOFA

Axiom
annotated source: miRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: PMID:11081512
has db xref: PMID:12592000

wiki
type: Axiom
annotated source: miRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/MiRNA

wiki
type: Axiom
annotated source: miRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/StRNA

origin_of_replication
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part of
  some values from: replicon
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Origin_of_replication
has exact synonym: INSDC_feature:rep_origin
has exact synonym: ori
has exact synonym: origin of replication
has OBO namespace: sequence
id: SO:0000296
in subset: SOFA

Axiom
annotated source: origin_of_replication
annotated property: IAO_0000115
annotated target: 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.
has db xref: NCBI:cf
has db xref: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: origin_of_replication
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Origin_of_replication

modified_DNA_base
type: Class
subclass of: base
subclass of: epigenetically_modified_region
IAO_0000115: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
has exact synonym: INSDC_feature:modified_base
has exact synonym: modified base site
has OBO namespace: sequence
id: SO:0000305
in subset: SOFA
comment: Modified base:<modified_base>.

Axiom
annotated source: modified_DNA_base
annotated property: IAO_0000115
annotated target: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
has db xref: http://www.insdc.org/files/feature_table.html

TSS
type: Class
subclass of: primary_transcript_region
subclass of: core_promoter_element
IAO_0000115: The first base where RNA polymerase begins to synthesize the RNA transcript.
has broad synonym: INSDC_feature:misc_feature
has exact synonym: INSDC_note:transcription_start_site
has exact synonym: transcription start site
has exact synonym: transcription_start_site
has OBO namespace: sequence
id: SO:0000315
in subset: SOFA
comment: Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant.

Axiom
annotated source: TSS
annotated property: IAO_0000115
annotated target: The first base where RNA polymerase begins to synthesize the RNA transcript.
has db xref: SO:ke

CDS
type: Class
subclass of: mRNA_region
IAO_0000115: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
has exact synonym: INSDC_feature:CDS
has exact synonym: coding sequence
has exact synonym: coding_sequence
has OBO namespace: sequence
id: SO:0000316
in subset: SOFA

Axiom
annotated source: CDS
annotated property: IAO_0000115
annotated target: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
has db xref: SO:ma

rRNA_large_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
IAO_0000115: A primary transcript encoding a large ribosomal subunit RNA.
has exact synonym: 35S rRNA primary transcript
has exact synonym: rRNA large subunit primary transcript
has OBO namespace: sequence
id: SO:0000325
in subset: SOFA

Axiom
annotated source: rRNA_large_subunit_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a large ribosomal subunit RNA.
has db xref: SO:ke

conserved_region
type: Class
subclass of: experimental_feature
IAO_0000115: Region of sequence similarity by descent from a common ancestor.
has broad synonym: INSDC_feature:misc_feature
has db xref: http://en.wikipedia.org/wiki/Conserved_region
has exact synonym: INSDC_note:conserved_region
has exact synonym: conserved region
has OBO namespace: sequence
id: SO:0000330
in subset: SOFA

Axiom
annotated source: conserved_region
annotated property: IAO_0000115
annotated target: Region of sequence similarity by descent from a common ancestor.
has db xref: SO:ke

wiki
type: Axiom
annotated source: conserved_region
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Conserved_region

pseudogene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: non functional homolog of
  some values from: gene
IAO_0000115: 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).
has broad synonym: INSDC_feature:gene
has db xref: http://en.wikipedia.org/wiki/Pseudogene
has exact synonym: INSDC_qualifier:pseudo
has exact synonym: INSDC_qualifier:unknown
has OBO namespace: sequence
id: SO:0000336
in subset: Alliance of Genome Resources
in subset: SOFA

Axiom
annotated source: pseudogene
annotated property: IAO_0000115
annotated target: 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).
has db xref: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

wiki
type: Axiom
annotated source: pseudogene
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Pseudogene

chromosome
type: Class
subclass of: replicon
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Chromosome
has OBO namespace: sequence
id: SO:0000340
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: chromosome
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:ma

wiki
type: Axiom
annotated source: chromosome
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Chromosome

small_regulatory_ncRNA
type: Class
subclass of: sncRNA
IAO_0000115: 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).
has exact synonym: small regulatory ncRNA
has OBO namespace: sequence
id: SO:0000370
in subset: SOFA

Axiom
annotated source: small_regulatory_ncRNA
annotated property: IAO_0000115
annotated target: 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).
has db xref: PMID:28541282
has db xref: PomBase:al
has db xref: SO:ma

cytosolic_5_8S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives from
  some values from: cytosolic_rRNA_5_8S_gene
IAO_0000115: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
has db xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
has exact synonym: cytosolic 5.8S LSU rRNA
has exact synonym: cytosolic 5.8S rRNA
has exact synonym: cytosolic 5.8S ribosomal RNA
has exact synonym: cytosolic rRNA 5 8S
has OBO namespace: sequence
id: SO:0000375
in subset: SOFA
comment: Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_5_8S_rRNA
annotated property: IAO_0000115
annotated target: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
has db xref: https://rfam.xfam.org/family/RF00002

wiki
type: Axiom
annotated source: cytosolic_5_8S_rRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA

sequence_attribute
type: Class
IAO_0000115: An attribute describes a quality of sequence.
has exact synonym: sequence attribute
has OBO namespace: sequence
id: SO:0000400

Axiom
annotated source: sequence_attribute
annotated property: IAO_0000115
annotated target: An attribute describes a quality of sequence.
has db xref: SO:ke

gene_attribute
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a gene.
has exact synonym: gene attribute
has OBO namespace: sequence
id: SO:0000401

binding_site
type: Class
subclass of: biological_region
IAO_0000115: 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.
has alternative id: BS:00033
has db xref: http://en.wikipedia.org/wiki/Binding_site
has exact synonym: INSDC_feature:misc_binding
has exact synonym: binding site
has exact synonym: binding_or_interaction_site
has OBO namespace: sequence
has related synonym: site
id: SO:0000409
in subset: SOFA
in subset: biosapiens
comment: See GO:0005488 : binding.

Axiom
annotated source: binding_site
annotated property: IAO_0000115
annotated target: 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.
has db xref: EBIBS:GAR
has db xref: SO:ke

wiki
type: Axiom
annotated source: binding_site
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Binding_site

protein_binding_site
type: Class
subclass of: binding_site
IAO_0000115: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
has exact synonym: INSDC_feature:protein_bind
has exact synonym: protein binding site
has OBO namespace: sequence
id: SO:0000410
in subset: SOFA
comment: See GO:0042277 : peptide binding.

Axiom
annotated source: protein_binding_site
annotated property: IAO_0000115
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
has db xref: SO:ke

nc_primary_transcript
type: Class
subclass of: primary_transcript
IAO_0000115: A primary transcript that is never translated into a protein.
has exact synonym: nc primary transcript
has exact synonym: noncoding primary transcript
has OBO namespace: sequence
id: SO:0000483
in subset: SOFA

Axiom
annotated source: nc_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript that is never translated into a protein.
has db xref: SO:ke

centromere
type: Class
subclass of: chromosomal_structural_element
IAO_0000115: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
has db xref: http://en.wikipedia.org/wiki/Centromere
has exact synonym: INSDC_feature:centromere
has OBO namespace: sequence
id: SO:0000577
in subset: SOFA

Axiom
annotated source: centromere
annotated property: IAO_0000115
annotated target: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
has db xref: SO:ke

wiki
type: Axiom
annotated source: centromere
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Centromere

cap
type: Class
subclass of: biological_region
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/5%27_cap
has OBO namespace: sequence
id: SO:0000581
in subset: SOFA

Axiom
annotated source: cap
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html

wiki
type: Axiom
annotated source: cap
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/5%27_cap

group_I_intron
type: Class
subclass of: autocatalytically_spliced_intron
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Group_I_intron
has exact synonym: group I intron
has OBO namespace: sequence
id: SO:0000587
in subset: SOFA
comment: GO:0000372.

Axiom
annotated source: group_I_intron
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: group_I_intron
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Group_I_intron

autocatalytically_spliced_intron
type: Class
equivalent class: Class
  intersection of: intron
  intersection of: Restriction
    on property: has quality
    some values from: ribozymic
subclass of: intron
subclass of: Restriction
  on property: has quality
  some values from: ribozymic
IAO_0000115: A self spliced intron.
has broad synonym: INSDC_feature:ncRNA
has exact synonym: INSDC_qualifier:autocatalytically_spliced_intron
has exact synonym: autocatalytically spliced intron
has OBO namespace: sequence
id: SO:0000588
in subset: SOFA

Axiom
annotated source: autocatalytically_spliced_intron
annotated property: IAO_0000115
annotated target: A self spliced intron.
has db xref: SO:ke

C_D_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives from
  some values from: C_D_box_snoRNA_primary_transcript
IAO_0000115: 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'.
has exact synonym: C D box snoRNA
has exact synonym: C/D box snoRNA
has exact synonym: SNORD
has exact synonym: box C/D snoRNA
has OBO namespace: sequence
id: SO:0000593
in subset: SOFA
comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.

Axiom
annotated source: C_D_box_snoRNA
annotated property: IAO_0000115
annotated target: 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'.
has db xref: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

Axiom
annotated source: C_D_box_snoRNA
annotated property: hasExactSynonym
annotated target: SNORD
has db xref: PMID:31828325

H_ACA_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives from
  some values from: H_ACA_box_snoRNA_primary_transcript
IAO_0000115: 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.
has exact synonym: H ACA box snoRNA
has exact synonym: H/ACA box snoRNA
has exact synonym: SNORA
has exact synonym: box H/ACA snoRNA
has OBO namespace: sequence
id: SO:0000594
comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.

Axiom
annotated source: H_ACA_box_snoRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

Axiom
annotated source: H_ACA_box_snoRNA
annotated property: hasExactSynonym
annotated target: SNORA
has db xref: PMID:31828325

C_D_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small nucleolar RNA of the box C/D family.
has exact synonym: C/D box snoRNA primary transcript
has OBO namespace: sequence
id: SO:0000595

Axiom
annotated source: C_D_box_snoRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a small nucleolar RNA of the box C/D family.
has db xref: SO:ke

H_ACA_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
has exact synonym: H ACA box snoRNA primary transcript
has OBO namespace: sequence
id: SO:0000596

Axiom
annotated source: H_ACA_box_snoRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
has db xref: SO:ke

bacterial_RNApol_promoter
type: Class
subclass of: prokaryotic_promoter
IAO_0000115: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
has exact synonym: bacterial RNApol promoter
has OBO namespace: sequence
id: SO:0000613
comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.

Axiom
annotated source: bacterial_RNApol_promoter
annotated property: IAO_0000115
annotated target: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
has db xref: SO:ke

telomere
type: Class
subclass of: chromosomal_structural_element
IAO_0000115: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
has db xref: http://en.wikipedia.org/wiki/Telomere
has exact synonym: INSDC_feature:telomere
has exact synonym: telomeric DNA
has exact synonym: telomeric sequence
has OBO namespace: sequence
id: SO:0000624
in subset: SOFA

Axiom
annotated source: telomere
annotated property: IAO_0000115
annotated target: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
has db xref: SO:ma

wiki
type: Axiom
annotated source: telomere
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Telomere

silencer
type: Class
subclass of: cis_regulatory_module
IAO_0000115: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
has broad synonym: INSDC_feature:regulatory
has db xref: http://en.wikipedia.org/wiki/Silencer_(DNA)
has exact synonym: INSDC_qualifier:silencer
has OBO namespace: sequence
id: SO:0000625
in subset: SOFA

Axiom
annotated source: silencer
annotated property: IAO_0000115
annotated target: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
has db xref: SO:ke

wiki
type: Axiom
annotated source: silencer
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Silencer_(DNA)

insulator
type: Class
subclass of: cis_regulatory_module
IAO_0000115: 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.
has broad synonym: INSDC_feature:regulatory
has db xref: http://en.wikipedia.org/wiki/Insulator_(genetics)
has exact synonym: INSDC_qualifier:insulator
has exact synonym: insulator element
has OBO namespace: sequence
id: SO:0000627
in subset: SOFA
comment: moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.

Axiom
annotated source: insulator
annotated property: IAO_0000115
annotated target: 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.
has db xref: NCBI:cf
has db xref: PMID:12154228
has db xref: SO:regcreative

wiki
type: Axiom
annotated source: insulator
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Insulator_(genetics)

chromosomal_structural_element
type: Class
subclass of: chromosome_part
IAO_0000115: Regions of the chromosome that are important for structural elements.
has exact synonym: chromosomal structural element
has OBO namespace: sequence
id: SO:0000628
in subset: SOFA

antisense_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives from
  some values from: antisense_primary_transcript
IAO_0000115: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
has broad synonym: INSDC_feature:ncRNA
has db xref: http://en.wikipedia.org/wiki/Antisense_RNA
has exact synonym: INSDC_qualifier:antisense_RNA
has exact synonym: antisense RNA
has OBO namespace: sequence
id: SO:0000644
in subset: SOFA

Axiom
annotated source: antisense_RNA
annotated property: IAO_0000115
annotated target: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
has db xref: SO:ke

wiki
type: Axiom
annotated source: antisense_RNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Antisense_RNA

antisense_primary_transcript
type: Class
subclass of: primary_transcript
IAO_0000115: The reverse complement of the primary transcript.
has exact synonym: antisense primary transcript
has OBO namespace: sequence
id: SO:0000645
in subset: SOFA

Axiom
annotated source: antisense_primary_transcript
annotated property: IAO_0000115
annotated target: The reverse complement of the primary transcript.
has db xref: SO:ke

siRNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000115: 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.
has broad synonym: INSDC_feature:ncRNA
has db xref: http://en.wikipedia.org/wiki/SiRNA
has exact synonym: INSDC_qualifier:siRNA
has exact synonym: small interfering RNA
has OBO namespace: sequence
id: SO:0000646
in subset: SOFA

Axiom
annotated source: siRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: PMID:12592000

wiki
type: Axiom
annotated source: siRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/SiRNA

miRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
subclass of: Restriction
  on property: has part
  some values from: pre_miRNA
IAO_0000115: A primary transcript encoding a micro RNA.
has alternative id: SO:0000648
has exact synonym: miRNA primary transcript
has exact synonym: micro RNA primary transcript
has exact synonym: small temporal RNA primary transcript
has exact synonym: stRNA primary transcript
has exact synonym: stRNA_primary_transcript
has OBO namespace: sequence
id: SO:0000647

Axiom
annotated source: miRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a micro RNA.
has db xref: SO:ke

cytosolic_LSU_rRNA
type: Class
subclass of: cytosolic_rRNA
subclass of: Restriction
  on property: derives from
  some values from: rRNA_large_subunit_primary_transcript
IAO_0000115: Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
has exact synonym: cytosolic LSU RNA
has exact synonym: cytosolic LSU rRNA
has exact synonym: cytosolic large subunit rRNA
has OBO namespace: sequence
id: SO:0000651
in subset: SOFA
comment: Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_LSU_rRNA
annotated property: IAO_0000115
annotated target: Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
has db xref: SO:ke

ncRNA
type: Class
subclass of: mature_transcript
IAO_0000115: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
has broad synonym: INSDC_qualifier:other
has db xref: http://en.wikipedia.org/wiki/NcRNA
has db xref: http://www.gencodegenes.org/gencode_biotypes.html
has exact synonym: known_ncrna
has exact synonym: noncoding RNA
has OBO namespace: sequence
id: SO:0000655
in subset: SOFA
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.

Axiom
annotated source: ncRNA
annotated property: IAO_0000115
annotated target: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
has db xref: SO:ke

wiki
type: Axiom
annotated source: ncRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/NcRNA

GENCODE
type: Axiom
annotated source: ncRNA
annotated property: hasDbXref
annotated target: http://www.gencodegenes.org/gencode_biotypes.html

repeat_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: has part
  some values from: repeat_unit
IAO_0000115: A region of sequence containing one or more repeat units.
has broad synonym: INSDC_feature:repeat_region
has exact synonym: INSDC_qualifier:other
has exact synonym: repeat region
has OBO namespace: sequence
id: SO:0000657
in subset: SOFA

Axiom
annotated source: repeat_region
annotated property: IAO_0000115
annotated target: A region of sequence containing one or more repeat units.
has db xref: SO:ke

transcript
type: Class
subclass of: gene_member_region
subclass of: Restriction
  on property: overlaps
  some values from: unit_of_gene_expression
IAO_0000115: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
has broad synonym: INSDC_feature:misc_RNA
has db xref: http://en.wikipedia.org/wiki/RNA
has OBO namespace: sequence
id: SO:0000673
in subset: SOFA
comment: Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.

Axiom
annotated source: transcript
annotated property: IAO_0000115
annotated target: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
has db xref: SO:ma

wiki
type: Axiom
annotated source: transcript
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/RNA

junction
type: Class
subclass of: sequence_feature
IAO_0000115: A sequence_feature with an extent of zero.
has exact synonym: boundary
has exact synonym: breakpoint
has OBO namespace: sequence
id: SO:0000699
in subset: SOFA
comment: A junction is a boundary between regions. A boundary has an extent of zero.

Axiom
annotated source: junction
annotated property: IAO_0000115
annotated target: A sequence_feature with an extent of zero.
has db xref: SO:ke

gene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member of
  some values from: gene_group
IAO_0000115: 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.
has db xref: http://en.wikipedia.org/wiki/Gene
has exact synonym: INSDC_feature:gene
has OBO namespace: sequence
id: SO:0000704
in subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.

Axiom
annotated source: gene
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:immuno_workshop

wiki
type: Axiom
annotated source: gene
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Gene

DNA_motif
type: Class
subclass of: nucleotide_motif
IAO_0000115: A motif that is active in the DNA form of the sequence.
has db xref: http://en.wikipedia.org/wiki/DNA_motif
has exact synonym: DNA motif
has OBO namespace: sequence
id: SO:0000713

Axiom
annotated source: DNA_motif
annotated property: IAO_0000115
annotated target: A motif that is active in the DNA form of the sequence.
has db xref: SO:ke

wiki
type: Axiom
annotated source: DNA_motif
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/DNA_motif

nucleotide_motif
type: Class
subclass of: sequence_motif
IAO_0000115: A region of nucleotide sequence corresponding to a known motif.
has broad synonym: INSDC_feature:misc_feature
has exact synonym: INSDC_note:nucleotide_motif
has exact synonym: nucleotide motif
has OBO namespace: sequence
id: SO:0000714
in subset: SOFA

Axiom
annotated source: nucleotide_motif
annotated property: IAO_0000115
annotated target: A region of nucleotide sequence corresponding to a known motif.
has db xref: SO:ke

repeat_unit
type: Class
subclass of: biological_region
IAO_0000115: The simplest repeated component of a repeat region. A single repeat.
has db xref: http://www.insdc.org/files/feature_table.html
has exact synonym: repeat unit
has OBO namespace: sequence
id: SO:0000726
comment: Added to comply with the feature table. A single repeat.

Axiom
annotated source: repeat_unit
annotated property: IAO_0000115
annotated target: The simplest repeated component of a repeat region. A single repeat.
has db xref: SO:ke

cis_regulatory_module
type: Class
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: 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.
has exact synonym: CRM
has exact synonym: TF module
has exact synonym: cis regulatory module
has exact synonym: transcription factor module
has OBO namespace: sequence
id: SO:0000727
in subset: SOFA
comment: Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.

Axiom
annotated source: cis_regulatory_module
annotated property: IAO_0000115
annotated target: 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.
has db xref: PMID:19660565
has db xref: SO:SG

feature_attribute
type: Class
subclass of: sequence_attribute
IAO_0000115: An attribute describing a located_sequence_feature.
has exact synonym: feature attribute
has OBO namespace: sequence
id: SO:0000733

Axiom
annotated source: feature_attribute
annotated property: IAO_0000115
annotated target: An attribute describing a located_sequence_feature.
has db xref: SO:ke

chromosome_part
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part of
  some values from: chromosome
IAO_0000115: A region of a chromosome.
has exact synonym: chromosomal region
has exact synonym: chromosomal_region
has exact synonym: chromosome part
has OBO namespace: sequence
id: SO:0000830
in subset: SOFA
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.

Axiom
annotated source: chromosome_part
annotated property: IAO_0000115
annotated target: A region of a chromosome.
has db xref: SO:ke

gene_member_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member of
  some values from: gene
IAO_0000115: A region of a gene.
has exact synonym: gene member region
has OBO namespace: sequence
id: SO:0000831
in subset: SOFA
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.

Axiom
annotated source: gene_member_region
annotated property: IAO_0000115
annotated target: A region of a gene.
has db xref: SO:ke

transcript_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part of
  some values from: transcript
IAO_0000115: A region of a transcript.
has exact synonym: transcript region
has OBO namespace: sequence
id: SO:0000833
in subset: SOFA
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.

Axiom
annotated source: transcript_region
annotated property: IAO_0000115
annotated target: A region of a transcript.
has db xref: SO:ke

mature_transcript_region
type: Class
subclass of: transcript_region
IAO_0000115: A region of a mature transcript.
has exact synonym: mature transcript region
has OBO namespace: sequence
id: SO:0000834
in subset: SOFA
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.

Axiom
annotated source: mature_transcript_region
annotated property: IAO_0000115
annotated target: A region of a mature transcript.
has db xref: SO:ke

primary_transcript_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part of
  some values from: primary_transcript
IAO_0000115: A part of a primary transcript.
has exact synonym: primary transcript region
has OBO namespace: sequence
id: SO:0000835
in subset: SOFA
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.

Axiom
annotated source: primary_transcript_region
annotated property: IAO_0000115
annotated target: A part of a primary transcript.
has db xref: SO:ke

mRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part of
  some values from: mRNA
IAO_0000115: A region of an mRNA.
has exact synonym: mRNA region
has OBO namespace: sequence
id: SO:0000836
in subset: SOFA
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.

Axiom
annotated source: mRNA_region
annotated property: IAO_0000115
annotated target: A region of an mRNA.
has db xref: SO:cb

UTR_region
type: Class
subclass of: mRNA_region
IAO_0000115: A region of UTR.
has exact synonym: UTR region
has OBO namespace: sequence
id: SO:0000837
in subset: SOFA
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.

Axiom
annotated source: UTR_region
annotated property: IAO_0000115
annotated target: A region of UTR.
has db xref: SO:ke

polypeptide_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part of
  some values from: polypeptide
IAO_0000115: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
has alternative id: BS:00124
has alternative id: BS:00331
has narrow synonym: region
has narrow synonym: site
has OBO namespace: sequence
has related synonym: positional
has related synonym: positional polypeptide feature
has related synonym: region or site annotation
id: SO:0000839
in subset: SOFA
in subset: biosapiens
comment: Added to allow the polypeptide regions to have is_a paths back to the root.

Axiom
annotated source: polypeptide_region
annotated property: IAO_0000115
annotated target: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
has db xref: SO:GAR
has db xref: SO:ke

Axiom
annotated source: polypeptide_region
annotated property: hasNarrowSynonym
annotated target: region
has db xref: uniprot:feature_type

Axiom
annotated source: polypeptide_region
annotated property: hasNarrowSynonym
annotated target: site
has db xref: uniprot:feature_type

gene_component_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part of
  some values from: gene
IAO_0000115: A region of a gene that has a specific function.
has exact synonym: gene component region
has OBO namespace: sequence
id: SO:0000842
in subset: SOFA

capped_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: adjacent to
    some values from: cap
  intersection of: Restriction
    on property: has quality
    some values from: capped
subclass of: primary_transcript
subclass of: Restriction
  on property: adjacent to
  some values from: cap
subclass of: Restriction
  on property: has quality
  some values from: capped
IAO_0000115: A primary transcript that is capped.
has exact synonym: capped primary transcript
has OBO namespace: sequence
id: SO:0000861

Axiom
annotated source: capped_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript that is capped.
has db xref: SO:xp

capped_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent to
    some values from: cap
  intersection of: Restriction
    on property: has quality
    some values from: capped
subclass of: mRNA
subclass of: Restriction
  on property: adjacent to
  some values from: cap
subclass of: Restriction
  on property: has quality
  some values from: capped
IAO_0000115: An mRNA that is capped.
has exact synonym: capped mRNA
has OBO namespace: sequence
id: SO:0000862

Axiom
annotated source: capped_mRNA
annotated property: IAO_0000115
annotated target: An mRNA that is capped.
has db xref: SO:xp

epigenetically_modified_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has quality
    some values from: epigenetically_modified
subclass of: gene
subclass of: epigenetically_modified_region
subclass of: Restriction
  on property: has quality
  some values from: epigenetically_modified
IAO_0000115: A gene that is epigenetically modified.
has exact synonym: epigenetically modified gene
has OBO namespace: sequence
id: SO:0000898

Axiom
annotated source: epigenetically_modified_gene
annotated property: IAO_0000115
annotated target: A gene that is epigenetically modified.
has db xref: SO:ke

piRNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000115: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
has broad synonym: INSDC_feature:ncRNA
has db xref: http://en.wikipedia.org/wiki/PiRNA
has exact synonym: INSDC_qualifier:piRNA
has exact synonym: piwi-associated RNA
has OBO namespace: sequence
id: SO:0001035

Axiom
annotated source: piRNA
annotated property: IAO_0000115
annotated target: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
has db xref: SO:ke

wiki
type: Axiom
annotated source: piRNA
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/PiRNA

transcriptional_cis_regulatory_region
type: Class
subclass of: regulatory_region
IAO_0000115: A regulatory_region that modulates the transcription of a gene or genes.
has broad synonym: INSDC_feature:regulatory
has exact synonym: INSDC_qualifier:transcriptional_cis_regulatory_region
has exact synonym: transcription-control region
has exact synonym: transcriptional cis regulatory region
has OBO namespace: sequence
id: SO:0001055
in subset: SOFA
comment: Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: transcriptional_cis_regulatory_region
annotated property: IAO_0000115
annotated target: A regulatory_region that modulates the transcription of a gene or genes.
has db xref: PMID:9679020
has db xref: SO:regcreative

polypeptide_motif
type: Class
subclass of: polypeptide_conserved_region
IAO_0000115: 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.).
has alternative id: BS:00032
has broad synonym: motif
has exact synonym: polypeptide motif
has OBO namespace: sequence
id: SO:0001067
in subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_motif
annotated property: IAO_0000115
annotated target: 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.).
has db xref: EBIBS:GAR
has db xref: UniProt:curation_manual

Axiom
annotated source: polypeptide_motif
annotated property: hasBroadSynonym
annotated target: motif
has db xref: uniprot:feature_type

post_translationally_modified_region
type: Class
subclass of: biochemical_region_of_peptide
IAO_0000115: 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.
has alternative id: BS:00052
has db xref: http://en.wikipedia.org/wiki/Post_translational_modification
has exact synonym: mod_res
has exact synonym: modified residue
has exact synonym: post_translational_modification
has OBO namespace: sequence
id: SO:0001089
in subset: biosapiens
comment: Discrete.

Axiom
annotated source: post_translationally_modified_region
annotated property: IAO_0000115
annotated target: 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.
has db xref: EBIBS:GAR
has db xref: UniProt:curation_manual

wiki
type: Axiom
annotated source: post_translationally_modified_region
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Post_translational_modification

Axiom
annotated source: post_translationally_modified_region
annotated property: hasExactSynonym
annotated target: mod_res
has db xref: uniprot:feature_type

enzymatic
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
has OBO namespace: sequence
id: SO:0001185
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.

Axiom
annotated source: enzymatic
annotated property: IAO_0000115
annotated target: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
has db xref: RSC:cb

ribozymic
type: Class
subclass of: enzymatic
IAO_0000115: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
has OBO namespace: sequence
id: SO:0001186
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.

Axiom
annotated source: ribozymic
annotated property: IAO_0000115
annotated target: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
has db xref: RSC:cb

protein_coding_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has quality
    some values from: protein_coding
subclass of: gene
subclass of: Restriction
  on property: has quality
  some values from: protein_coding
IAO_0000115: A gene that codes for an RNA that can be translated into a protein.
has exact synonym: protein coding gene
has OBO namespace: sequence
id: SO:0001217
in subset: Alliance of Genome Resources

replicon
type: Class
subclass of: biological_region
IAO_0000115: A region containing at least one unique origin of replication and a unique termination site.
has db xref: http://en.wikipedia.org/wiki/Replicon_(genetics)
has OBO namespace: sequence
id: SO:0001235
in subset: SOFA

Axiom
annotated source: replicon
annotated property: IAO_0000115
annotated target: A region containing at least one unique origin of replication and a unique termination site.
has db xref: ISBN:0716719207

wiki
type: Axiom
annotated source: replicon
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Replicon_(genetics)

base
type: Class
subclass of: biological_region
IAO_0000115: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
has db xref: http://en.wikipedia.org/wiki/Nucleobase
has OBO namespace: sequence
id: SO:0001236
in subset: SOFA

Axiom
annotated source: base
annotated property: IAO_0000115
annotated target: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
has db xref: SO:ke

wiki
type: Axiom
annotated source: base
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Nucleobase

TSS_region
type: Class
IAO_0000115: The region of a gene from the 5' most TSS to the 3' TSS.
IAO_0100001: promoter
has exact synonym: TSS region
has OBO namespace: sequence
id: SO:0001240
comment: Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528
deprecated: true

Axiom
annotated source: TSS_region
annotated property: IAO_0000115
annotated target: The region of a gene from the 5' most TSS to the 3' TSS.
has db xref: BBOP:nw

miRNA_primary_transcript_region
type: Class
subclass of: primary_transcript_region
IAO_0000115: A part of an miRNA primary_transcript.
has exact synonym: miRNA primary transcript region
has OBO namespace: sequence
id: SO:0001243

Axiom
annotated source: miRNA_primary_transcript_region
annotated property: IAO_0000115
annotated target: A part of an miRNA primary_transcript.
has db xref: SO:ke

pre_miRNA
type: Class
subclass of: miRNA_primary_transcript_region
IAO_0000115: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
has exact synonym: pre-miRNA
has OBO namespace: sequence
id: SO:0001244

Axiom
annotated source: pre_miRNA
annotated property: IAO_0000115
annotated target: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
has db xref: SO:ke

ncRNA_gene
type: Class
subclass of: gene
IAO_0000115: A gene that encodes a non-coding RNA.
has exact synonym: ncRNA gene
has exact synonym: non-coding RNA gene
has OBO namespace: sequence
id: SO:0001263
in subset: Alliance of Genome Resources

experimental_feature
type: Class
subclass of: region
IAO_0000115: A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
has exact synonym: experimental output artefact
has exact synonym: experimental_output_artefact
has OBO namespace: sequence
has related synonym: analysis feature
id: SO:0001410
in subset: SOFA

Axiom
annotated source: experimental_feature
annotated property: IAO_0000115
annotated target: A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
has db xref: SO:cb

biological_region
type: Class
subclass of: region
IAO_0000115: A region defined by its disposition to be involved in a biological process.
has broad synonym: INSDC_misc_feature
has exact synonym: INSDC_note:biological_region
has exact synonym: biological region
has OBO namespace: sequence
id: SO:0001411
in subset: SOFA

Axiom
annotated source: biological_region
annotated property: IAO_0000115
annotated target: A region defined by its disposition to be involved in a biological process.
has db xref: SO:cb

topologically_defined_region
type: Class
subclass of: region
IAO_0000115: A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
has exact synonym: topologically defined region
has OBO namespace: sequence
id: SO:0001412
in subset: SOFA

Axiom
annotated source: topologically_defined_region
annotated property: IAO_0000115
annotated target: A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
has db xref: PMID:32782014
has db xref: SO:cb

rRNA_gene
type: Class
subclass of: ncRNA_gene
IAO_0000115: A gene that encodes for ribosomal RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:10:32Z
has exact synonym: rDNA
has exact synonym: rRNA gene
has OBO namespace: sequence
id: SO:0001637
comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).

Axiom
annotated source: rRNA_gene
annotated property: IAO_0000115
annotated target: A gene that encodes for ribosomal RNA.
has db xref: SO:ke

genetic_marker
type: Class
subclass of: biological_region
IAO_0000115: A measurable sequence feature that varies within a population.
created by: kareneilbeck
creation date: 2010-05-28T02:33:07Z
has OBO namespace: sequence
has related synonym: genetic marker
id: SO:0001645

Axiom
annotated source: genetic_marker
annotated property: IAO_0000115
annotated target: A measurable sequence feature that varies within a population.
has db xref: SO:db

nucleotide_to_protein_binding_site
type: Class
subclass of: protein_binding_site
IAO_0000115: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
created by: kareneilbeck
creation date: 2010-08-03T12:26:05Z
has OBO namespace: sequence
has related synonym: nucleotide to protein binding site
id: SO:0001654
in subset: SOFA

Axiom
annotated source: nucleotide_to_protein_binding_site
annotated property: IAO_0000115
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
has db xref: SO:ke

promoter_element
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: overlaps
  some values from: TF_binding_site
subclass of: Restriction
  on property: part of
  some values from: promoter
IAO_0000115: An element that can exist within the promoter region of a gene.
created by: kareneilbeck
creation date: 2010-10-01T11:48:32Z
has exact synonym: promoter element
has OBO namespace: sequence
id: SO:0001659
comment: Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.

RNApol_II_core_promoter
type: Class
subclass of: RNApol_II_promoter
IAO_0000115: The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
created by: kareneilbeck
creation date: 2010-10-01T03:13:41Z
has exact synonym: RNApol II core promoter
has OBO namespace: sequence
id: SO:0001669

Axiom
annotated source: RNApol_II_core_promoter
annotated property: IAO_0000115
annotated target: The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
has db xref: PMID:16858867

sequence_motif
type: Class
subclass of: biological_region
IAO_0000115: A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
created by: kareneilbeck
creation date: 2010-10-14T04:13:22Z
has db xref: http://en.wikipedia.org/wiki/Sequence_motif
has OBO namespace: sequence
has related synonym: sequence motif
id: SO:0001683
in subset: SOFA

Axiom
annotated source: sequence_motif
annotated property: IAO_0000115
annotated target: A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
has db xref: http://en.wikipedia.org/wiki/Sequence_motif

wikipedia
type: Axiom
annotated source: sequence_motif
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Sequence_motif

histone_modification
type: Class
equivalent class: Class
  intersection of: post_translationally_modified_region
  intersection of: Restriction
    on property: has quality
    some values from: epigenetically_modified
subclass of: post_translationally_modified_region
subclass of: epigenetically_modified_region
subclass of: Restriction
  on property: has quality
  some values from: epigenetically_modified
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2010-03-31T10:22:08Z
has exact synonym: histone modification
has OBO namespace: sequence
has related synonym: histone modification site
id: SO:0001700

Axiom
annotated source: histone_modification
annotated property: IAO_0000115
annotated target: 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.
has db xref: http:en.wikipedia.org/wiki/Histone

epigenetically_modified_region
type: Class
equivalent class: Class
  intersection of: biological_region
  intersection of: Restriction
    on property: has quality
    some values from: epigenetically_modified
subclass of: regulatory_region
subclass of: Restriction
  on property: has quality
  some values from: epigenetically_modified
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2010-03-27T12:02:29Z
has OBO namespace: sequence
has related synonym: epigenetically modified region
id: SO:0001720
in subset: SOFA
comment: Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.

Axiom
annotated source: epigenetically_modified_region
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:ke
has db xref: http://en.wikipedia.org/wiki/Epigenetics

regional_centromere
type: Class
subclass of: centromere
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2011-05-31T12:43:07Z
has exact synonym: regional centromere
has OBO namespace: sequence
id: SO:0001795

Axiom
annotated source: regional_centromere
annotated property: IAO_0000115
annotated target: 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.
has db xref: PMID:7502067
has db xref: SO:vw

regional_centromere_central_core
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part of
  some values from: regional_centromere
IAO_0000115: A conserved region within the central region of a modular centromere, where the kinetochore is formed.
created by: kareneilbeck
creation date: 2011-05-31T12:56:30Z
has exact synonym: regional centromere central core
has OBO namespace: sequence
id: SO:0001796

Axiom
annotated source: regional_centromere_central_core
annotated property: IAO_0000115
annotated target: A conserved region within the central region of a modular centromere, where the kinetochore is formed.
has db xref: SO:vw

centromeric_repeat
type: Class
subclass of: repeat_region
IAO_0000115: A repeat region found within the modular centromere.
created by: kareneilbeck
creation date: 2011-05-31T12:59:27Z
has broad synonym: INSDC_feature:repeat_region
has exact synonym: INSDC_qualifier:centromeric_repeat
has exact synonym: centromeric repeat
has OBO namespace: sequence
id: SO:0001797

Axiom
annotated source: centromeric_repeat
annotated property: IAO_0000115
annotated target: A repeat region found within the modular centromere.
has db xref: SO:ke

regional_centromere_inner_repeat_region
type: Class
subclass of: centromeric_repeat
subclass of: Restriction
  on property: part of
  some values from: regional_centromere
subclass of: Restriction
  on property: part of
  some values from: regional_centromere_central_core
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2011-05-31T01:01:08Z
has exact synonym: lmr repeat
has exact synonym: lmr1L
has exact synonym: lmr1R
has exact synonym: regional centromere inner repeat region
has OBO namespace: sequence
id: SO:0001798

Axiom
annotated source: regional_centromere_inner_repeat_region
annotated property: IAO_0000115
annotated target: 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.
has db xref: SO:vw

tasiRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a tasiRNA.
created by: kareneilbeck
creation date: 2011-05-31T03:27:35Z
has exact synonym: tasiRNA primary transcript
has OBO namespace: sequence
id: SO:0001801

Axiom
annotated source: tasiRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a tasiRNA.
has db xref: PMID:16145017

lncRNA
type: Class
subclass of: ncRNA
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2012-02-14T05:18:01Z
has broad synonym: INSDC_feature:ncRNA
has db xref: http://www.gencodegenes.org/gencode_biotypes.html
has exact synonym: INSDC_qualifier:lncRNA
has exact synonym: lncRNA_transcript
has exact synonym: long non-coding RNA
has OBO namespace: sequence
id: SO:0001877
comment: Updated the definition of lncRNA (SO:0001877) from "A non-coding RNA over 200nucleotides in length." to "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." See GitHub Issue #575

Axiom
annotated source: lncRNA
annotated property: IAO_0000115
annotated target: 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.
has db xref: HGNC:mw
comment: PMID:33353982

GENCODE
type: Axiom
annotated source: lncRNA
annotated property: hasDbXref
annotated target: http://www.gencodegenes.org/gencode_biotypes.html

rDNA_replication_fork_barrier
type: Class
subclass of: DNA_motif
IAO_0000115: A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
created by: kareneilbeck
creation date: 2012-06-11T02:55:02Z
has exact synonym: DNA spacer replication fork barrier
has exact synonym: RFB
has exact synonym: RTS1 barrier
has exact synonym: RTS1 element
has exact synonym: rDNA replication fork barrier
has OBO namespace: sequence
id: SO:0001914
comment: Requested by Midori - June 2012.

Axiom
annotated source: rDNA_replication_fork_barrier
annotated property: IAO_0000115
annotated target: A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
has db xref: PMID:14645529

telomeric_transcript
type: Class
subclass of: ncRNA
IAO_0000115: A non-coding transcript derived from the transcript of the telomere.
created by: kareneilbeck
creation date: 2012-10-31T01:42:15Z
has exact synonym: telomeric transcript
has OBO namespace: sequence
id: SO:0001927

Axiom
annotated source: telomeric_transcript
annotated property: IAO_0000115
annotated target: A non-coding transcript derived from the transcript of the telomere.
has db xref: PMID:22139915

subtelomere
type: Class
subclass of: chromosomal_structural_element
IAO_0000115: 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.
created by: kareneilbeck
creation date: 2014-01-05T07:02:01Z
has OBO namespace: sequence
id: SO:0001997

Axiom
annotated source: subtelomere
annotated property: IAO_0000115
annotated target: 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.
has db xref: POMBE:al

lncRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a lncRNA.
created by: kareneilbeck
creation date: 2015-01-09T15:23:03Z
has exact synonym: lncRNA primary transcript
has OBO namespace: sequence
id: SO:0002035

Axiom
annotated source: lncRNA_primary_transcript
annotated property: IAO_0000115
annotated target: A primary transcript encoding a lncRNA.
has db xref: SO:ke

early_origin_of_replication
type: Class
subclass of: origin_of_replication
IAO_0000115: An origin of replication that initiates early in S phase.
created by: nicole
creation date: 2016-09-15T15:53:36Z
has exact synonym: early origin
has exact synonym: early origin of replication
has exact synonym: early replication origin
has OBO namespace: sequence
id: SO:0002140

Axiom
annotated source: early_origin_of_replication
annotated property: IAO_0000115
annotated target: An origin of replication that initiates early in S phase.
has db xref: PMID:23348837
has db xref: PMID:9115207

late_origin_of_replication
type: Class
subclass of: origin_of_replication
IAO_0000115: An origin of replication that initiates late in S phase.
created by: nicole
creation date: 2016-09-15T15:56:07Z
has exact synonym: late origin
has exact synonym: late origin of replication
has exact synonym: late replication origin
has OBO namespace: sequence
id: SO:0002141

Axiom
annotated source: late_origin_of_replication
annotated property: IAO_0000115
annotated target: An origin of replication that initiates late in S phase.
has db xref: PMID:23348837
has db xref: PMID:9115207

eukaryotic_promoter
type: Class
subclass of: promoter
IAO_0000115: 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.
created by: david
creation date: 2019-07-31T14:01:20Z
has exact synonym: Eukaryotic promoter
has OBO namespace: sequence
id: SO:0002221

prokaryotic_promoter
type: Class
subclass of: promoter
IAO_0000115: 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.
created by: david
creation date: 2019-07-31T14:02:26Z
has exact synonym: Prokaryotic promoter
has OBO namespace: sequence
id: SO:0002222

Axiom
annotated source: prokaryotic_promoter
annotated property: IAO_0000115
annotated target: 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.
has db xref: PMID:32665585

pumilio_response_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part of
  some values from: three_prime_UTR
IAO_0000115: A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).
created by: david
creation date: 2020-04-14T10:40:30Z
has exact synonym: PRE binding RNA
has exact synonym: pumilio response element
has OBO namespace: sequence
id: SO:0002234
comment: Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455)

Axiom
annotated source: pumilio_response_element
annotated property: IAO_0000115
annotated target: A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).
has db xref: PMID:30601114

cytosolic_rRNA_5_8S_gene
type: Class
subclass of: cytosolic_LSU_rRNA_gene
IAO_0000115: 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.
created by: david
creation date: 2020-05-07T16:12:30Z
has exact synonym: 5.8S rRNA gene
has exact synonym: 5_8S rRNA gene
has exact synonym: 5_8S_rRNA_gene
has OBO namespace: sequence
id: SO:0002240
comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).

sncRNA
type: Class
subclass of: ncRNA
IAO_0000115: A non-coding RNA less than 200 nucleotides in length.
created by: david
creation date: 2020-05-13T11:07:30Z
has exact synonym: Small noncoding RNA
has OBO namespace: sequence
id: SO:0002247
comment: Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)

Axiom
annotated source: sncRNA
annotated property: IAO_0000115
annotated target: A non-coding RNA less than 200 nucleotides in length.
has db xref: PMID:30069443

unit_of_gene_expression
type: Class
subclass of: biological_region
IAO_0000115: Transcription units or transcribed coding sequences.
created by: david
creation date: 2020-08-05T11:49:30Z
has exact synonym: unit of gene expression
has OBO namespace: sequence
id: SO:0002300
comment: Added as per Mejia-Almonte et.al PMID:32665585

Axiom
annotated source: unit_of_gene_expression
annotated property: IAO_0000115
annotated target: Transcription units or transcribed coding sequences.
has db xref: Bacterial_regulation_working_group:CMA
has db xref: PMID:32665585

topologically_associated_domain
type: Class
subclass of: topologically_defined_region
IAO_0000115: An instance of a self-interacting DNA region flanked by left and right TAD boundaries.
created by: david
creation date: 2020-08-12T14:01:30Z
has exact synonym: TAD
has exact synonym: topologically associated domain
has OBO namespace: sequence
id: SO:0002304
comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative.

Axiom
annotated source: topologically_associated_domain
annotated property: IAO_0000115
annotated target: An instance of a self-interacting DNA region flanked by left and right TAD boundaries.
has db xref: GREEKC:cl
has db xref: PMID:32782014

topologically_associated_domain_boundary
type: Class
subclass of: junction
subclass of: Restriction
  on property: part of
  some values from: topologically_associated_domain
IAO_0000115: A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.
created by: david
creation date: 2020-08-12T14:01:30Z
has exact synonym: TAD boundary
has exact synonym: TAD_boundary
has exact synonym: topologically associated domain boundary
has OBO namespace: sequence
id: SO:0002305
comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative.

Axiom
annotated source: topologically_associated_domain_boundary
annotated property: IAO_0000115
annotated target: A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.
has db xref: GREEKC:cl
has db xref: PMID:32782014

DNA_loop
type: Class
subclass of: chromosome_part
subclass of: Restriction
  on property: overlaps
  some values from: topologically_associated_domain
IAO_0000115: A region of DNA between two loop anchor positions that are held in close physical proximity.
created by: david
creation date: 2020-08-12T14:01:30Z
has exact synonym: DNA loop
has OBO namespace: sequence
id: SO:0002307
comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.

Axiom
annotated source: DNA_loop
annotated property: IAO_0000115
annotated target: A region of DNA between two loop anchor positions that are held in close physical proximity.
has db xref: GREEKC:cl
has db xref: PMID:32782014

DNA_loop_anchor
type: Class
subclass of: cis_regulatory_module
subclass of: Restriction
  on property: part of
  some values from: DNA_loop
IAO_0000115: 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.
created by: david
creation date: 2020-08-12T14:01:30Z
has exact synonym: DNA loop anchor
has OBO namespace: sequence
id: SO:0002308
comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.

Axiom
annotated source: DNA_loop_anchor
annotated property: IAO_0000115
annotated target: 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.
has db xref: GREEKC:cl
has db xref: PMID:32782014

core_promoter_element
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part of
  some values from: promoter
IAO_0000115: 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.
created by: david
creation date: 2020-08-12T14:01:30Z
has exact synonym: core promoter element
has OBO namespace: sequence
id: SO:0002309
comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative.

Axiom
annotated source: core_promoter_element
annotated property: IAO_0000115
annotated target: 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.
has db xref: GREEKC:rl

cytosolic_rRNA
type: Class
subclass of: rRNA
IAO_0000115: Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.
created by: david
creation date: 2021-06-10T16:45:30Z
has exact synonym: cytosolic rRNA
has exact synonym: cytosolic ribosomal RNA
has OBO namespace: sequence
id: SO:0002343
comment: Added as a request from EBI. See GitHub Issue #493

Axiom
annotated source: cytosolic_rRNA
annotated property: IAO_0000115
annotated target: Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.
has db xref: PMID:3044395

cytosolic_rRNA_gene
type: Class
subclass of: rRNA_gene
IAO_0000115: A gene that codes for cytosolic rRNA.
created by: evan
creation date: 2021-11-19T04:30:40Z
has OBO namespace: sequence
id: SO:0002360
comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).

cytosolic_LSU_rRNA_gene
type: Class
subclass of: cytosolic_rRNA_gene
IAO_0000115: A gene that codes for cytosolic LSU rRNA.
created by: evan
creation date: 2021-11-19T04:32:20Z
has exact synonym: cytosolic large subunit rRNA gene
has OBO namespace: sequence
id: SO:0002361
comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).

regulatory_region
type: Class
subclass of: gene_member_region
IAO_0000115: A region of sequence that is involved in the control of a biological process.
has broad synonym: INSDC_feature:regulatory
has db xref: http://en.wikipedia.org/wiki/Regulatory_region
has exact synonym: INSDC_qualifier:other
has exact synonym: regulatory region
has OBO namespace: sequence
id: SO:0005836
in subset: SOFA

Axiom
annotated source: regulatory_region
annotated property: IAO_0000115
annotated target: A region of sequence that is involved in the control of a biological process.
has db xref: SO:ke

wiki
type: Axiom
annotated source: regulatory_region
annotated property: hasDbXref
annotated target: http://en.wikipedia.org/wiki/Regulatory_region

gene_group
type: Class
subclass of: biological_region
IAO_0000115: A collection of related genes.
has exact synonym: gene group
has OBO namespace: sequence
id: SO:0005855
in subset: SOFA

Axiom
annotated source: gene_group
annotated property: IAO_0000115
annotated target: A collection of related genes.
has db xref: SO:ma

biochemical_region_of_peptide
type: Class
subclass of: polypeptide_motif
IAO_0000115: A region of a peptide that is involved in a biochemical function.
has exact synonym: biochemical motif
has exact synonym: biochemical region of peptide
has OBO namespace: sequence
has related synonym: biochemical_region
id: SO:0100001
in subset: biosapiens
comment: Range.

Axiom
annotated source: biochemical_region_of_peptide
annotated property: IAO_0000115
annotated target: A region of a peptide that is involved in a biochemical function.
has db xref: EBIBS:GAR

polypeptide_conserved_region
type: Class
subclass of: polypeptide_region
IAO_0000115: 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.
has exact synonym: polypeptide conserved region
has OBO namespace: sequence
id: SO:0100021
in subset: biosapiens

Axiom
annotated source: polypeptide_conserved_region
annotated property: IAO_0000115
annotated target: 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.
has db xref: EBIBS:GAR

gene_segment
type: Class
subclass of: gene_component_region
IAO_0000115: A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
has exact synonym: gene segment
has OBO namespace: sequence
id: SO:3000000
comment: Requested by tracker 2021594, July 2008, by Alex.

Axiom
annotated source: gene_segment
annotated property: IAO_0000115
annotated target: A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
has db xref: GOC:add