definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

amino acid modification
type: AnnotationProperty
sub property of: synonym_type_property

Alliance of Genome Resources
type: AnnotationProperty
sub property of: synonym_type_property

Alliance of Genome Resources
type: AnnotationProperty
comment: Alliance of Genome Resources Gene Biotype Slim
sub property of: subset_property

biosapiens
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
comment: database of genomic structural variation
sub property of: subset_property

RNA modification
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

SOFA
type: AnnotationProperty
comment: SO feature annotation
sub property of: subset_property

variant annotation term
type: AnnotationProperty
sub property of: synonym_type_property

amino acid 1 letter code
type: AnnotationProperty
sub property of: synonym_type_property

amino acid 3 letter code
type: AnnotationProperty
sub property of: synonym_type_property

biosapiens
type: AnnotationProperty
comment: biosapiens protein feature ontology
sub property of: subset_property

dbsnp variant terms
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
sub property of: synonym_type_property

ensembl variant terms
type: AnnotationProperty
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

adjacent_to
type: ObjectProperty
definition: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
has_obo_namespace: sequence
id: adjacent_to
in_subset: SOFA

Axiom
annotated source: adjacent_to
annotated property: definition
annotated target: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
database_cross_reference: PMID:20226267
database_cross_reference: SO:ke

associated_with
type: ObjectProperty
has_obo_namespace: sequence
id: associated_with
comment: This relationship is vague and up for discussion.

complete_evidence_for_feature
type: ObjectProperty
sub property of: evidence_for_feature
type: TransitiveProperty
definition: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
has_obo_namespace: sequence
id: complete_evidence_for_feature
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: complete_evidence_for_feature
annotated property: definition
annotated target: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
database_cross_reference: SO:ke

connects_on
type: ObjectProperty
definition: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
created by: kareneilbeck
creation date: 2010-10-14T01:38:51Z
has_obo_namespace: sequence
id: connects_on
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.

Axiom
annotated source: connects_on
annotated property: definition
annotated target: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
database_cross_reference: PMID:20226267

contained_by
type: ObjectProperty
type: TransitiveProperty
definition: X contained_by Y iff X starts after start of Y and X ends before end of Y.
created by: kareneilbeck
creation date: 2010-10-14T01:26:16Z
has_obo_namespace: sequence
id: contained_by
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.

Axiom
annotated source: contained_by
annotated property: definition
annotated target: X contained_by Y iff X starts after start of Y and X ends before end of Y.
database_cross_reference: PMID:20226267

contains
type: ObjectProperty
type: TransitiveProperty
definition: The inverse of contained_by.
created by: kareneilbeck
creation date: 2010-10-14T01:32:15Z
has_obo_namespace: sequence
id: contains
comment: Example: pre_miRNA contains miRNA_loop.

Axiom
annotated source: contains
annotated property: definition
annotated target: The inverse of contained_by.
database_cross_reference: PMID:20226267

derives_from
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: sequence
id: derives_from
in_subset: SOFA

disconnected_from
type: ObjectProperty
definition: X is disconnected_from Y iff it is not the case that X overlaps Y.
created by: kareneilbeck
creation date: 2010-10-14T01:42:10Z
has_obo_namespace: sequence
id: disconnected_from

Axiom
annotated source: disconnected_from
annotated property: definition
annotated target: X is disconnected_from Y iff it is not the case that X overlaps Y.
database_cross_reference: PMID:20226267

edited_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:19:45Z
has_obo_namespace: sequence
id: edited_from

edited_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:19:11Z
has_obo_namespace: sequence
id: edited_to

evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
definition: B is evidence_for_feature A, if an instance of B supports the existence of A.
has_obo_namespace: sequence
id: evidence_for_feature
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: evidence_for_feature
annotated property: definition
annotated target: B is evidence_for_feature A, if an instance of B supports the existence of A.
database_cross_reference: SO:ke

exemplar_of
type: ObjectProperty
definition: X is exemplar of Y if X is the best evidence for Y.
has_obo_namespace: sequence
id: exemplar_of
comment: Tracker id: 2594157.

Axiom
annotated source: exemplar_of
annotated property: definition
annotated target: X is exemplar of Y if X is the best evidence for Y.
database_cross_reference: SO:ke

finished_by
type: ObjectProperty
definition: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:45:45Z
has_obo_namespace: sequence
id: finished_by
comment: Example CDS finished_by stop_codon.

Axiom
annotated source: finished_by
annotated property: definition
annotated target: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
database_cross_reference: PMID:20226267

finishes
type: ObjectProperty
definition: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
created by: kareneilbeck
creation date: 2010-10-14T02:17:53Z
has_obo_namespace: sequence
id: finishes
comment: Example: stop_codon finishes CDS.

Axiom
annotated source: finishes
annotated property: definition
annotated target: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
database_cross_reference: PMID:20226267

gained
type: ObjectProperty
definition: X gained Y if X is a variant_of X' and Y part of X but not X'.
created by: kareneilbeck
creation date: 2011-06-28T12:51:10Z
has_obo_namespace: sequence
id: gained
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may gain a stop codon not present in the reference sequence.

Axiom
annotated source: gained
annotated property: definition
annotated target: X gained Y if X is a variant_of X' and Y part of X but not X'.
database_cross_reference: SO:ke

genome_of
type: ObjectProperty
has_obo_namespace: sequence
id: genome_of

guided_by
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:27:04Z
has_obo_namespace: sequence
id: guided_by

guides
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:27:24Z
has_obo_namespace: sequence
id: guides

has_integral_part
type: ObjectProperty
sub property of: has_part
definition: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
created by: kareneilbeck
creation date: 2009-08-19T12:01:46Z
has_obo_namespace: sequence
id: has_integral_part
comment: Example: mRNA has_integral_part CDS.

Axiom
annotated source: has_integral_part
annotated property: definition
annotated target: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

has_origin
type: ObjectProperty
has_obo_namespace: sequence
id: has_origin

has_part
type: ObjectProperty
definition: Inverse of part_of.
has_obo_namespace: sequence
id: has_part
comment: Example: operon has_part gene.

Axiom
annotated source: has_part
annotated property: definition
annotated target: Inverse of part_of.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

has_quality
type: ObjectProperty
has_obo_namespace: sequence
id: has_quality
comment: The relationship between a feature and an attribute.

homologous_to
type: ObjectProperty
sub property of: similar_to
type: SymmetricProperty
has_obo_namespace: sequence
id: homologous_to
in_subset: SOFA

integral_part_of
type: ObjectProperty
sub property of: part_of
definition: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
created by: kareneilbeck
creation date: 2009-08-19T12:03:28Z
has_obo_namespace: sequence
id: integral_part_of
comment: Example: exon integral_part_of transcript.

Axiom
annotated source: integral_part_of
annotated property: definition
annotated target: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

is_consecutive_sequence_of
type: ObjectProperty
definition: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
created by: kareneilbeck
creation date: 2010-10-14T02:19:48Z
has_obo_namespace: sequence
id: is_consecutive_sequence_of
comment: Example: region is consecutive_sequence of base.

Axiom
annotated source: is_consecutive_sequence_of
annotated property: definition
annotated target: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
database_cross_reference: PMID:20226267

lost
type: ObjectProperty
definition: X lost Y if X is a variant_of X' and Y part of X' but not X.
created by: kareneilbeck
creation date: 2011-06-28T12:53:16Z
has_obo_namespace: sequence
id: lost
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may have lost a stop codon present in the reference sequence.

Axiom
annotated source: lost
annotated property: definition
annotated target: X lost Y if X is a variant_of X' and Y part of X' but not X.
database_cross_reference: SO:ke

maximally_overlaps
type: ObjectProperty
definition: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
created by: kareneilbeck
creation date: 2010-10-14T01:34:48Z
has_obo_namespace: sequence
id: maximally_overlaps
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.

Axiom
annotated source: maximally_overlaps
annotated property: definition
annotated target: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
database_cross_reference: PMID:20226267

member_of
type: ObjectProperty
sub property of: part_of
type: TransitiveProperty
has_obo_namespace: sequence
id: member_of
in_subset: SOFA
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.

non_functional_homolog_of
type: ObjectProperty
sub property of: homologous_to
definition: A relationship between a pseudogenic feature and its functional ancestor.
has_obo_namespace: sequence
id: non_functional_homolog_of
in_subset: SOFA

Axiom
annotated source: non_functional_homolog_of
annotated property: definition
annotated target: A relationship between a pseudogenic feature and its functional ancestor.
database_cross_reference: SO:ke

orthologous_to
type: ObjectProperty
sub property of: homologous_to
type: SymmetricProperty
has_obo_namespace: sequence
id: orthologous_to
in_subset: SOFA

overlaps
type: ObjectProperty
definition: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
created by: kareneilbeck
creation date: 2010-10-14T01:33:15Z
has_obo_namespace: sequence
id: overlaps
comment: Example: coding_exon overlaps CDS.

Axiom
annotated source: overlaps
annotated property: definition
annotated target: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
database_cross_reference: PMID:20226267

paralogous_to
type: ObjectProperty
sub property of: homologous_to
type: SymmetricProperty
has_obo_namespace: sequence
id: paralogous_to
in_subset: SOFA

part_of
type: ObjectProperty
type: TransitiveProperty
definition: X part_of Y if X is a subregion of Y.
has_obo_namespace: sequence
id: part_of
in_subset: SOFA
comment: Example: amino_acid part_of polypeptide.

Axiom
annotated source: part_of
annotated property: definition
annotated target: X part_of Y if X is a subregion of Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

partial_evidence_for_feature
type: ObjectProperty
sub property of: evidence_for_feature
definition: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
has_obo_namespace: sequence
id: partial_evidence_for_feature

Axiom
annotated source: partial_evidence_for_feature
annotated property: definition
annotated target: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
database_cross_reference: SO:ke

position_of
type: ObjectProperty
has_obo_namespace: sequence
id: position_of

processed_from
type: ObjectProperty
definition: Inverse of processed_into.
created by: kareneilbeck
creation date: 2009-08-19T12:14:00Z
has_obo_namespace: sequence
id: processed_from
comment: Example: miRNA processed_from miRNA_primary_transcript.

Axiom
annotated source: processed_from
annotated property: definition
annotated target: Inverse of processed_into.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

processed_into
type: ObjectProperty
definition: X is processed_into Y if a region X is modified to create Y.
created by: kareneilbeck
creation date: 2009-08-19T12:15:02Z
has_obo_namespace: sequence
id: processed_into
comment: Example: miRNA_primary_transcript processed into miRNA.

Axiom
annotated source: processed_into
annotated property: definition
annotated target: X is processed_into Y if a region X is modified to create Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

recombined_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:21:03Z
has_obo_namespace: sequence
id: recombined_from

recombined_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:20:07Z
has_obo_namespace: sequence
id: recombined_to

sequence_of
type: ObjectProperty
has_obo_namespace: sequence
id: sequence_of

similar_to
type: ObjectProperty
type: SymmetricProperty
has_obo_namespace: sequence
id: similar_to
in_subset: SOFA

started_by
type: ObjectProperty
definition: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:43:55Z
has_obo_namespace: sequence
id: started_by
comment: Example: CDS started_by start_codon.

Axiom
annotated source: started_by
annotated property: definition
annotated target: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
database_cross_reference: PMID:20226267

starts
type: ObjectProperty
definition: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:47:53Z
has_obo_namespace: sequence
id: starts
comment: Example: start_codon starts CDS.

Axiom
annotated source: starts
annotated property: definition
annotated target: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
database_cross_reference: PMID:20226267

trans_spliced_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:22:14Z
has_obo_namespace: sequence
id: trans_spliced_from

trans_spliced_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:22:00Z
has_obo_namespace: sequence
id: trans_spliced_to

transcribed_from
type: ObjectProperty
definition: X is transcribed_from Y if X is synthesized from template Y.
created by: kareneilbeck
creation date: 2009-08-19T12:05:39Z
has_obo_namespace: sequence
id: transcribed_from
comment: Example: primary_transcript transcribed_from gene.

Axiom
annotated source: transcribed_from
annotated property: definition
annotated target: X is transcribed_from Y if X is synthesized from template Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

transcribed_to
type: ObjectProperty
definition: Inverse of transcribed_from.
created by: kareneilbeck
creation date: 2009-08-19T12:08:24Z
has_obo_namespace: sequence
id: transcribed_to
comment: Example: gene transcribed_to primary_transcript.

Axiom
annotated source: transcribed_to
annotated property: definition
annotated target: Inverse of transcribed_from.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

translates_to
type: ObjectProperty
definition: Inverse of translation _of.
created by: kareneilbeck
creation date: 2009-08-19T12:11:53Z
has_obo_namespace: sequence
id: translates_to
comment: Example: codon translates_to amino_acid.

Axiom
annotated source: translates_to
annotated property: definition
annotated target: Inverse of translation _of.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

translation_of
type: ObjectProperty
definition: X is translation of Y if Y is translated by ribosome to create X.
created by: kareneilbeck
creation date: 2009-08-19T12:09:59Z
has_obo_namespace: sequence
id: translation_of
comment: Example: Polypeptide translation_of CDS.

Axiom
annotated source: translation_of
annotated property: definition
annotated target: X is translation of Y if Y is translated by ribosome to create X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

variant_of
type: ObjectProperty
definition: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
has_obo_namespace: sequence
id: variant_of
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.

Axiom
annotated source: variant_of
annotated property: definition
annotated target: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
database_cross_reference: SO:immuno_workshop

Sequence_Ontology
type: Class
has_obo_namespace: sequence
id: SO:0000000
in_subset: SOFA
deprecated: true

region
type: Class
subclass of: sequence_feature
definition: 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: definition
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.
database_cross_reference: SO:ke

interior_coding_exon
type: Class
subclass of: coding_exon
definition: A coding exon that is not the most 3-prime or the most 5-prime in a given transcript.
has_exact_synonym: interior coding exon
has_obo_namespace: sequence
id: SO:0000004
in_subset: SOFA

satellite_DNA
type: Class
subclass of: tandem_repeat
definition: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Satellite_DNA
has_exact_synonym: INSDC_qualifier:satellite
has_exact_synonym: satellite DNA
has_obo_namespace: sequence
id: SO:0000005
in_subset: SOFA

Axiom
annotated source: satellite_DNA
annotated property: definition
annotated target: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: satellite_DNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Satellite_DNA

PCR_product
type: Class
subclass of: reagent
definition: A region amplified by a PCR reaction.
database_cross_reference: http://en.wikipedia.org/wiki/RAPD
has_exact_synonym: PCR product
has_obo_namespace: sequence
has_related_synonym: amplicon
id: SO:0000006
in_subset: SOFA
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.

Axiom
annotated source: PCR_product
annotated property: definition
annotated target: A region amplified by a PCR reaction.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: PCR_product
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/RAPD

read_pair
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: contig
subclass of: Restriction
  on property: part_of
  some values from: paired_end_fragment
definition: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
has_exact_synonym: mate pair
has_exact_synonym: read-pair
has_obo_namespace: sequence
id: SO:0000007
in_subset: SOFA

Axiom
annotated source: read_pair
annotated property: definition
annotated target: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
database_cross_reference: SO:ls

scRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: nc_primary_transcript
definition: A small non coding RNA sequence, present in the cytoplasm.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:scRNA
has_exact_synonym: small cytoplasmic RNA
has_obo_namespace: sequence
id: SO:0000013
in_subset: SOFA

Axiom
annotated source: scRNA
annotated property: definition
annotated target: A small non coding RNA sequence, present in the cytoplasm.
database_cross_reference: SO:ke

match_set
type: Class
definition: A collection of match parts.
has_obo_namespace: sequence
id: SO:0000038
in_subset: SOFA
deprecated: true

Axiom
annotated source: match_set
annotated property: definition
annotated target: A collection of match parts.
database_cross_reference: SO:ke

match_part
type: Class
subclass of: experimental_feature
subclass of: Restriction
  on property: part_of
  some values from: match
definition: A part of a match, for example an hsp from blast is a match_part.
has_exact_synonym: match part
has_obo_namespace: sequence
id: SO:0000039
in_subset: SOFA

Axiom
annotated source: match_part
annotated property: definition
annotated target: A part of a match, for example an hsp from blast is a match_part.
database_cross_reference: SO:ke

gene_part
type: Class
definition: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
has_obo_namespace: sequence
id: SO:0000050
in_subset: SOFA
deprecated: true

Axiom
annotated source: gene_part
annotated property: definition
annotated target: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
database_cross_reference: SO:ke

operator
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: http://en.wikipedia.org/wiki/Operator_(biology)#Operator
has_exact_synonym: operator segment
has_obo_namespace: sequence
id: SO:0000057
in_subset: SOFA
comment: Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.

Axiom
annotated source: operator
annotated property: definition
annotated target: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: operator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Operator_(biology)#Operator

nuclease_binding_site
type: Class
subclass of: nucleotide_to_protein_binding_site
definition: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
has_exact_synonym: nuclease binding site
has_obo_namespace: sequence
id: SO:0000059
in_subset: SOFA

Axiom
annotated source: nuclease_binding_site
annotated property: definition
annotated target: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
database_cross_reference: SO:cb

transposable_element
type: Class
subclass of: integrated_mobile_genetic_element
definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
database_cross_reference: http://en.wikipedia.org/wiki/Transposable_element
has_exact_synonym: transposable element
has_exact_synonym: transposon
has_obo_namespace: sequence
id: SO:0000101
in_subset: SOFA

Axiom
annotated source: transposable_element
annotated property: definition
annotated target: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
database_cross_reference: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html

wiki
type: Axiom
annotated source: transposable_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Transposable_element

expressed_sequence_match
type: Class
subclass of: nucleotide_match
definition: A match to an EST or cDNA sequence.
has_exact_synonym: expressed sequence match
has_obo_namespace: sequence
id: SO:0000102
in_subset: SOFA

Axiom
annotated source: expressed_sequence_match
annotated property: definition
annotated target: A match to an EST or cDNA sequence.
database_cross_reference: SO:ke

clone_insert_end
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
definition: The end of the clone insert.
has_exact_synonym: clone insert end
has_obo_namespace: sequence
id: SO:0000103
in_subset: SOFA

Axiom
annotated source: clone_insert_end
annotated property: definition
annotated target: The end of the clone insert.
database_cross_reference: SO:ke

polypeptide
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: derives_from
  some values from: CDS
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: SO:ma

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

sequence_variant_obs
type: Class
definition: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
has_obo_namespace: sequence
has_related_synonym: mutation
id: SO:0000109
in_subset: SOFA
deprecated: true

Axiom
annotated source: sequence_variant_obs
annotated property: definition
annotated target: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
database_cross_reference: SO:ke

sequence_feature
type: Class
definition: 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: definition
annotated target: Any extent of continuous biological sequence.
database_cross_reference: LAMHDI:mb
database_cross_reference: SO:ke

primer
type: Class
subclass of: ss_oligo
definition: An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
database_cross_reference: http://en.wikipedia.org/wiki/Primer_(molecular_biology)
has_exact_synonym: DNA primer
has_exact_synonym: primer oligonucleotide
has_exact_synonym: primer polynucleotide
has_exact_synonym: primer sequence
has_obo_namespace: sequence
id: SO:0000112
in_subset: SOFA

Axiom
annotated source: primer
annotated property: definition
annotated target: An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: primer
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Primer_(molecular_biology)

proviral_region
type: Class
subclass of: integrated_mobile_genetic_element
definition: A viral sequence which has integrated into a host genome.
has_exact_synonym: proviral region
has_obo_namespace: sequence
has_related_synonym: proviral sequence
id: SO:0000113
in_subset: SOFA

Axiom
annotated source: proviral_region
annotated property: definition
annotated target: A viral sequence which has integrated into a host genome.
database_cross_reference: SO:ke

methylated_cytosine
type: Class
subclass of: methylated_DNA_base_feature
definition: A methylated deoxy-cytosine.
has_exact_synonym: methylated C
has_exact_synonym: methylated cytosine
has_exact_synonym: methylated cytosine base
has_exact_synonym: methylated cytosine residue
has_exact_synonym: methylated_C
has_obo_namespace: sequence
id: SO:0000114
in_subset: SOFA

Axiom
annotated source: methylated_cytosine
annotated property: definition
annotated target: A methylated deoxy-cytosine.
database_cross_reference: SO:ke

protein_coding_primary_transcript
type: Class
subclass of: primary_transcript
definition: A primary transcript that, at least in part, encodes one or more proteins.
has_exact_synonym: protein coding primary transcript
has_obo_namespace: sequence
has_related_synonym: pre mRNA
id: SO:0000120
in_subset: SOFA
comment: May contain introns.

Axiom
annotated source: protein_coding_primary_transcript
annotated property: definition
annotated target: A primary transcript that, at least in part, encodes one or more proteins.
database_cross_reference: SO:ke

ribosome_entry_site
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: five_prime_UTR
definition: Region in mRNA where ribosome assembles.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:ribosome_binding_site
has_exact_synonym: ribosome entry site
has_obo_namespace: sequence
id: SO:0000139
in_subset: SOFA

Axiom
annotated source: ribosome_entry_site
annotated property: definition
annotated target: Region in mRNA where ribosome assembles.
database_cross_reference: SO:ke

attenuator
type: Class
subclass of: regulatory_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Attenuator
has_exact_synonym: INSDC_qualifier:attenuator
has_exact_synonym: attenuator sequence
has_obo_namespace: sequence
id: SO:0000140
in_subset: SOFA

Axiom
annotated source: attenuator
annotated property: definition
annotated target: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
database_cross_reference: SO:as

wiki
type: Axiom
annotated source: attenuator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Attenuator

terminator
type: Class
subclass of: transcriptional_cis_regulatory_region
subclass of: Restriction
  on property: part_of
  some values from: transcript
definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Terminator_(genetics)
has_exact_synonym: INSDC_qualifier:terminator
has_exact_synonym: terminator sequence
has_obo_namespace: sequence
id: SO:0000141
in_subset: SOFA
comment: 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: terminator
annotated property: definition
annotated target: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: terminator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Terminator_(genetics)

assembly_component
type: Class
subclass of: experimental_feature
definition: A region of known length which may be used to manufacture a longer region.
has_exact_synonym: assembly component
has_obo_namespace: sequence
id: SO:0000143
in_subset: SOFA

Axiom
annotated source: assembly_component
annotated property: definition
annotated target: A region of known length which may be used to manufacture a longer region.
database_cross_reference: SO:ke

exon
type: Class
subclass of: transcript_region
definition: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
database_cross_reference: http://en.wikipedia.org/wiki/Exon
has_exact_synonym: INSDC_feature:exon
has_obo_namespace: sequence
id: SO:0000147
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: exon
annotated property: definition
annotated target: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: exon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Exon

supercontig
type: Class
subclass of: sequence_assembly
subclass of: Restriction
  on property: part_of
  some values from: ultracontig
definition: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
has_obo_namespace: sequence
has_related_synonym: scaffold
id: SO:0000148
in_subset: SOFA

Axiom
annotated source: supercontig
annotated property: definition
annotated target: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
database_cross_reference: SO:ls

contig
type: Class
subclass of: assembly_component
subclass of: sequence_assembly
subclass of: Restriction
  on property: part_of
  some values from: supercontig
definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
database_cross_reference: http://en.wikipedia.org/wiki/Contig
has_obo_namespace: sequence
id: SO:0000149
in_subset: SOFA

Axiom
annotated source: contig
annotated property: definition
annotated target: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
database_cross_reference: SO:ls

wiki
type: Axiom
annotated source: contig
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Contig

read
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: contig
definition: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
has_obo_namespace: sequence
id: SO:0000150
in_subset: SOFA

Axiom
annotated source: read
annotated property: definition
annotated target: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
database_cross_reference: SO:rd

clone
type: Class
subclass of: reagent
definition: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
database_cross_reference: http:http://en.wikipedia.org/wiki/Clone_(genetics)
has_obo_namespace: sequence
id: SO:0000151
in_subset: SOFA

Axiom
annotated source: clone
annotated property: definition
annotated target: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: clone
annotated property: database_cross_reference
annotated target: http:http://en.wikipedia.org/wiki/Clone_(genetics)

deletion
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: The point at which one or more contiguous nucleotides were excised.
has_alternative_id: SO:1000033
database_cross_reference: http://en.wikipedia.org/wiki/Nucleotide_deletion
database_cross_reference: loinc:LA6692-3
has_exact_synonym: deleted_sequence
has_exact_synonym: nucleotide deletion
has_exact_synonym: nucleotide_deletion
has_obo_namespace: sequence
id: SO:0000159
in_subset: SOFA

Axiom
annotated source: deletion
annotated property: definition
annotated target: The point at which one or more contiguous nucleotides were excised.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: deletion
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nucleotide_deletion

Deletion
type: Axiom
annotated source: deletion
annotated property: database_cross_reference
annotated target: loinc:LA6692-3

methylated_adenine
type: Class
subclass of: methylated_DNA_base_feature
definition: A modified base in which adenine has been methylated.
has_exact_synonym: methylated A
has_exact_synonym: methylated adenine
has_exact_synonym: methylated adenine base
has_exact_synonym: methylated adenine residue
has_exact_synonym: methylated_A
has_obo_namespace: sequence
id: SO:0000161
in_subset: SOFA

Axiom
annotated source: methylated_adenine
annotated property: definition
annotated target: A modified base in which adenine has been methylated.
database_cross_reference: SO:ke

splice_site
type: Class
subclass of: primary_transcript_region
definition: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
database_cross_reference: http://en.wikipedia.org/wiki/Splice_site
has_exact_synonym: splice site
has_obo_namespace: sequence
id: SO:0000162
in_subset: SOFA
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.

Axiom
annotated source: splice_site
annotated property: definition
annotated target: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: splice_site
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Splice_site

five_prime_cis_splice_site
type: Class
subclass of: cis_splice_site
definition: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
has_exact_synonym: 5' splice site
has_exact_synonym: donor splice site
has_exact_synonym: five prime splice site
has_exact_synonym: splice donor site
has_obo_namespace: sequence
has_related_synonym: donor
id: SO:0000163
in_subset: SOFA

Axiom
annotated source: five_prime_cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

three_prime_cis_splice_site
type: Class
subclass of: cis_splice_site
definition: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
has_exact_synonym: acceptor splice site
has_exact_synonym: splice acceptor site
has_exact_synonym: three prime splice site
has_obo_namespace: sequence
has_related_synonym: 3' splice site
has_related_synonym: acceptor
id: SO:0000164
in_subset: SOFA

Axiom
annotated source: three_prime_cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

enhancer
type: Class
subclass of: cis_regulatory_module
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

promoter
type: Class
subclass of: gene_component_region
subclass of: transcriptional_cis_regulatory_region
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: SO:regcreative

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

cross_genome_match
type: Class
subclass of: nucleotide_match
definition: A nucleotide match against a sequence from another organism.
has_exact_synonym: cross genome match
has_obo_namespace: sequence
id: SO:0000177
in_subset: SOFA

Axiom
annotated source: cross_genome_match
annotated property: definition
annotated target: A nucleotide match against a sequence from another organism.
database_cross_reference: SO:ma

operon
type: Class
subclass of: gene_group
definition: The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
database_cross_reference: http://en.wikipedia.org/wiki/Operon
has_exact_synonym: INSDC_feature:operon
has_obo_namespace: sequence
id: SO:0000178
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020.

Axiom
annotated source: operon
annotated property: definition
annotated target: The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: operon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Operon

clone_insert_start
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
definition: The start of the clone insert.
has_exact_synonym: clone insert start
has_obo_namespace: sequence
id: SO:0000179
in_subset: SOFA

Axiom
annotated source: clone_insert_start
annotated property: definition
annotated target: The start of the clone insert.
database_cross_reference: SO:ke

translated_nucleotide_match
type: Class
subclass of: nucleotide_match
definition: A match against a translated sequence.
has_exact_synonym: translated nucleotide match
has_obo_namespace: sequence
id: SO:0000181
in_subset: SOFA

Axiom
annotated source: translated_nucleotide_match
annotated property: definition
annotated target: A match against a translated sequence.
database_cross_reference: SO:ke

non_transcribed_region
type: Class
subclass of: gene_component_region
definition: A region of the gene which is not transcribed.
has_exact_synonym: non transcribed region
has_exact_synonym: non-transcribed sequence
has_exact_synonym: nontranscribed region
has_exact_synonym: nontranscribed sequence
has_obo_namespace: sequence
id: SO:0000183
in_subset: SOFA

Axiom
annotated source: non_transcribed_region
annotated property: definition
annotated target: A region of the gene which is not transcribed.
database_cross_reference: SO:ke

primary_transcript
type: Class
subclass of: transcript
definition: A transcript that in its initial state requires modification to be functional.
database_cross_reference: 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: definition
annotated target: A transcript that in its initial state requires modification to be functional.
database_cross_reference: SO:ma

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

repeat_family
type: Class
definition: A group of characterized repeat sequences.
has_obo_namespace: sequence
id: SO:0000187
in_subset: SOFA
deprecated: true

Axiom
annotated source: repeat_family
annotated property: definition
annotated target: A group of characterized repeat sequences.
database_cross_reference: SO:ke

intron
type: Class
subclass of: primary_transcript_region
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

RFLP_fragment
type: Class
subclass of: restriction_fragment
definition: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
database_cross_reference: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
has_exact_synonym: RFLP
has_exact_synonym: RFLP fragment
has_exact_synonym: restriction fragment length polymorphism
has_obo_namespace: sequence
id: SO:0000193
in_subset: SOFA

Axiom
annotated source: RFLP_fragment
annotated property: definition
annotated target: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
database_cross_reference: GOC:pj

wiki
type: Axiom
annotated source: RFLP_fragment
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

coding_exon
type: Class
subclass of: exon
definition: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
has_exact_synonym: coding exon
has_obo_namespace: sequence
id: SO:0000195
in_subset: SOFA

Axiom
annotated source: coding_exon
annotated property: definition
annotated target: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
database_cross_reference: SO:ke

five_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
definition: The sequence of the five_prime_coding_exon that codes for protein.
has_exact_synonym: five prime exon coding region
has_obo_namespace: sequence
id: SO:0000196
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon_coding_region
annotated property: definition
annotated target: The sequence of the five_prime_coding_exon that codes for protein.
database_cross_reference: SO:cjm

three_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: coding_exon
definition: The sequence of the three_prime_coding_exon that codes for protein.
has_exact_synonym: three prime exon coding region
has_obo_namespace: sequence
id: SO:0000197
in_subset: SOFA

Axiom
annotated source: three_prime_coding_exon_coding_region
annotated property: definition
annotated target: The sequence of the three_prime_coding_exon that codes for protein.
database_cross_reference: SO:cjm

noncoding_exon
type: Class
subclass of: exon
definition: An exon that does not contain any codons.
has_exact_synonym: noncoding exon
has_obo_namespace: sequence
id: SO:0000198
in_subset: SOFA

Axiom
annotated source: noncoding_exon
annotated property: definition
annotated target: An exon that does not contain any codons.
database_cross_reference: SO:ke

five_prime_coding_exon
type: Class
subclass of: coding_exon
definition: The 5' most coding exon.
has_exact_synonym: 5' coding exon
has_exact_synonym: five prime coding exon
has_obo_namespace: sequence
id: SO:0000200
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon
annotated property: definition
annotated target: The 5' most coding exon.
database_cross_reference: SO:ke

UTR
type: Class
subclass of: mRNA_region
definition: 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: definition
annotated target: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
database_cross_reference: SO:ke

five_prime_UTR
type: Class
subclass of: UTR
definition: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
database_cross_reference: http://en.wikipedia.org/wiki/5'_UTR
has_exact_synonym: 5' UTR
has_exact_synonym: INSDC_feature:5'UTR
has_exact_synonym: five prime UTR
has_exact_synonym: five_prime_untranslated_region
has_obo_namespace: sequence
id: SO:0000204
in_subset: SOFA

Axiom
annotated source: five_prime_UTR
annotated property: definition
annotated target: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: five_prime_UTR
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5'_UTR

three_prime_UTR
type: Class
subclass of: UTR
definition: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
database_cross_reference: 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: definition
annotated target: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

rRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: 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: definition
annotated target: A primary transcript encoding a ribosomal RNA.
database_cross_reference: SO:ke

mature_transcript
type: Class
subclass of: transcript
subclass of: Restriction
  on property: derives_from
  some values from: primary_transcript
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: SO:ke

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

mRNA
type: Class
subclass of: mature_transcript
definition: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
database_cross_reference: http://en.wikipedia.org/wiki/MRNA
database_cross_reference: 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: definition
annotated target: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
database_cross_reference: SO:ma

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

GENCODE
type: Axiom
annotated source: mRNA
annotated property: database_cross_reference
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
definition: 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: definition
annotated target: A DNA site where a transcription factor binds.
database_cross_reference: SO:ke

ORF
type: Class
subclass of: reading_frame
definition: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
has_exact_synonym: open reading frame
has_obo_namespace: sequence
id: SO:0000236
in_subset: SOFA
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ORF
annotated property: definition
annotated target: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
database_cross_reference: SGD:rb
database_cross_reference: SO:ma

flanking_region
type: Class
subclass of: topologically_defined_region
definition: The sequences extending on either side of a specific region.
has_exact_synonym: flanking region
has_obo_namespace: sequence
id: SO:0000239
in_subset: SOFA

Axiom
annotated source: flanking_region
annotated property: definition
annotated target: The sequences extending on either side of a specific region.
database_cross_reference: SO:ke

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_primary_transcript
definition: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
has_broad_synonym: INSDC_qualifier:unknown
database_cross_reference: 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: definition
annotated target: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
database_cross_reference: ISBN:0198506732
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

tRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: nc_primary_transcript
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: ISBN:0198506732
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

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

snRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: nc_primary_transcript
definition: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: 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: definition
annotated target: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
database_cross_reference: PMID:11733745
database_cross_reference: WB:ems
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

snoRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: nc_primary_transcript
definition: 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: definition
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.
database_cross_reference: GOC:kgc
database_cross_reference: PMID:31828325

miRNA
type: Class
subclass of: small_regulatory_ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: primary_transcript_region
definition: 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
database_cross_reference: http://en.wikipedia.org/wiki/MiRNA
database_cross_reference: 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: definition
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.
database_cross_reference: PMID:11081512
database_cross_reference: PMID:12592000

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

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

microsatellite
type: Class
subclass of: satellite_DNA
definition: A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Microsatellite
has_exact_synonym: INSDC_qualifier:microsatellite
has_exact_synonym: STR
has_exact_synonym: microsatellite locus
has_exact_synonym: microsatellite marker
has_exact_synonym: short tandem repeat
has_obo_namespace: sequence
id: SO:0000289
in_subset: SOFA

Axiom
annotated source: microsatellite
annotated property: definition
annotated target: A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
database_cross_reference: NCBI:th
database_cross_reference: http://www.informatics.jax.org/silver/glossary.shtml

wiki
type: Axiom
annotated source: microsatellite
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Microsatellite

Axiom
annotated source: microsatellite
annotated property: has_exact_synonym
annotated target: STR
database_cross_reference: http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/

inverted_repeat
type: Class
subclass of: repeat_region
definition: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Inverted_repeat
has_exact_synonym: INSDC_qualifier:inverted
has_exact_synonym: inverted repeat
has_exact_synonym: inverted repeat sequence
has_obo_namespace: sequence
id: SO:0000294
in_subset: SOFA

Axiom
annotated source: inverted_repeat
annotated property: definition
annotated target: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: inverted_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Inverted_repeat

origin_of_replication
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: replicon
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: NCBI:cf
database_cross_reference: http://www.insdc.org/files/feature_table.html

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

clip
type: Class
subclass of: primary_transcript_region
definition: Part of the primary transcript that is clipped off during processing.
has_obo_namespace: sequence
id: SO:0000303
in_subset: SOFA

Axiom
annotated source: clip
annotated property: definition
annotated target: Part of the primary transcript that is clipped off during processing.
database_cross_reference: SO:ke

modified_DNA_base
type: Class
subclass of: base
subclass of: epigenetically_modified_region
definition: 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: definition
annotated target: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
database_cross_reference: http://www.insdc.org/files/feature_table.html

methylated_DNA_base_feature
type: Class
subclass of: modified_DNA_base
definition: A nucleotide modified by methylation.
has_exact_synonym: methylated base feature
has_obo_namespace: sequence
id: SO:0000306
in_subset: SOFA

Axiom
annotated source: methylated_DNA_base_feature
annotated property: definition
annotated target: A nucleotide modified by methylation.
database_cross_reference: SO:ke

CpG_island
type: Class
subclass of: biological_region
definition: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
database_cross_reference: http://en.wikipedia.org/wiki/CpG_island
has_exact_synonym: CG island
has_exact_synonym: CpG island
has_obo_namespace: sequence
id: SO:0000307
in_subset: SOFA

Axiom
annotated source: CpG_island
annotated property: definition
annotated target: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
database_cross_reference: SO:rd

wiki
type: Axiom
annotated source: CpG_island
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/CpG_island

direct_repeat
type: Class
subclass of: repeat_region
definition: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Direct_repeat
has_exact_synonym: INSDC_qualifier:direct
has_exact_synonym: direct repeat
has_obo_namespace: sequence
id: SO:0000314
in_subset: SOFA

Axiom
annotated source: direct_repeat
annotated property: definition
annotated target: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: direct_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Direct_repeat

TSS
type: Class
subclass of: nucleotide_motif
subclass of: primary_transcript_region
subclass of: Restriction
  on property: overlaps
  some values from: TF_binding_site
subclass of: Restriction
  on property: part_of
  some values from: promoter
definition: 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: definition
annotated target: The first base where RNA polymerase begins to synthesize the RNA transcript.
database_cross_reference: SO:ke

CDS
type: Class
subclass of: mRNA_region
definition: 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: definition
annotated target: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
database_cross_reference: SO:ma

start_codon
type: Class
subclass of: codon
definition: First codon to be translated by a ribosome.
database_cross_reference: http://en.wikipedia.org/wiki/Start_codon
has_exact_synonym: initiation codon
has_exact_synonym: start codon
has_obo_namespace: sequence
id: SO:0000318
in_subset: SOFA

Axiom
annotated source: start_codon
annotated property: definition
annotated target: First codon to be translated by a ribosome.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: start_codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Start_codon

stop_codon
type: Class
subclass of: codon
definition: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
database_cross_reference: http://en.wikipedia.org/wiki/Stop_codon
has_exact_synonym: stop codon
has_obo_namespace: sequence
id: SO:0000319
in_subset: SOFA

Axiom
annotated source: stop_codon
annotated property: definition
annotated target: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: stop_codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Stop_codon

tag
type: Class
subclass of: oligo
definition: A nucleotide sequence that may be used to identify a larger sequence.
has_obo_namespace: sequence
id: SO:0000324
in_subset: SOFA

Axiom
annotated source: tag
annotated property: definition
annotated target: A nucleotide sequence that may be used to identify a larger sequence.
database_cross_reference: SO:ke

rRNA_large_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
definition: 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: definition
annotated target: A primary transcript encoding a large ribosomal subunit RNA.
database_cross_reference: SO:ke

SAGE_tag
type: Class
subclass of: tag
definition: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
has_exact_synonym: SAGE tag
has_obo_namespace: sequence
id: SO:0000326
in_subset: SOFA

Axiom
annotated source: SAGE_tag
annotated property: definition
annotated target: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
database_cross_reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

conserved_region
type: Class
subclass of: experimental_feature
definition: Region of sequence similarity by descent from a common ancestor.
has_broad_synonym: INSDC_feature:misc_feature
database_cross_reference: 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: definition
annotated target: Region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

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

STS
type: Class
subclass of: tag
definition: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
has_exact_synonym: INSDC_feature:STS
has_exact_synonym: sequence tag site
has_obo_namespace: sequence
id: SO:0000331
in_subset: SOFA

Axiom
annotated source: STS
annotated property: definition
annotated target: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
database_cross_reference: http://www.biospace.com

coding_conserved_region
type: Class
subclass of: conserved_region
definition: Coding region of sequence similarity by descent from a common ancestor.
has_exact_synonym: coding conserved region
has_obo_namespace: sequence
id: SO:0000332
in_subset: SOFA

Axiom
annotated source: coding_conserved_region
annotated property: definition
annotated target: Coding region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

exon_junction
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
definition: The boundary between two exons in a processed transcript.
has_exact_synonym: exon junction
has_obo_namespace: sequence
id: SO:0000333
in_subset: SOFA

Axiom
annotated source: exon_junction
annotated property: definition
annotated target: The boundary between two exons in a processed transcript.
database_cross_reference: SO:ke

nc_conserved_region
type: Class
subclass of: conserved_region
definition: Non-coding region of sequence similarity by descent from a common ancestor.
has_exact_synonym: conserved non-coding element
has_exact_synonym: conserved non-coding sequence
has_exact_synonym: nc conserved region
has_exact_synonym: noncoding conserved region
has_obo_namespace: sequence
id: SO:0000334
in_subset: SOFA

Axiom
annotated source: nc_conserved_region
annotated property: definition
annotated target: Non-coding region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

pseudogene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: gene
definition: 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
database_cross_reference: 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: definition
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).
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

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

RNAi_reagent
type: Class
subclass of: ds_oligo
definition: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
has_exact_synonym: RNAi reagent
has_obo_namespace: sequence
id: SO:0000337
in_subset: SOFA

Axiom
annotated source: RNAi_reagent
annotated property: definition
annotated target: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
database_cross_reference: SO:rd

chromosome
type: Class
subclass of: replicon
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: SO:ma

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

chromosome_band
type: Class
subclass of: chromosome_part
definition: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
database_cross_reference: http://en.wikipedia.org/wiki/Cytological_band
has_exact_synonym: chromosome band
has_exact_synonym: cytoband
has_exact_synonym: cytological band
has_obo_namespace: sequence
id: SO:0000341
in_subset: SOFA

Axiom
annotated source: chromosome_band
annotated property: definition
annotated target: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: chromosome_band
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Cytological_band

match
type: Class
subclass of: experimental_feature
definition: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
has_obo_namespace: sequence
id: SO:0000343
in_subset: SOFA

Axiom
annotated source: match
annotated property: definition
annotated target: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
database_cross_reference: SO:ke

splice_enhancer
type: Class
subclass of: splicing_regulatory_region
definition: Region of a transcript that regulates splicing.
has_exact_synonym: splice enhancer
has_obo_namespace: sequence
id: SO:0000344
in_subset: SOFA

Axiom
annotated source: splice_enhancer
annotated property: definition
annotated target: Region of a transcript that regulates splicing.
database_cross_reference: SO:ke

EST
type: Class
subclass of: tag
subclass of: Restriction
  on property: derives_from
  some values from: mRNA
definition: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
has_exact_synonym: expressed sequence tag
has_obo_namespace: sequence
id: SO:0000345
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: EST
annotated property: definition
annotated target: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
database_cross_reference: SO:ke

nucleotide_match
type: Class
subclass of: match
definition: A match against a nucleotide sequence.
has_exact_synonym: nucleotide match
has_obo_namespace: sequence
id: SO:0000347
in_subset: SOFA

Axiom
annotated source: nucleotide_match
annotated property: definition
annotated target: A match against a nucleotide sequence.
database_cross_reference: SO:ke

protein_match
type: Class
subclass of: match
definition: A match against a protein sequence.
has_exact_synonym: protein match
has_obo_namespace: sequence
id: SO:0000349
in_subset: SOFA

Axiom
annotated source: protein_match
annotated property: definition
annotated target: A match against a protein sequence.
database_cross_reference: SO:ke

sequence_assembly
type: Class
subclass of: assembly
definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
database_cross_reference: http://en.wikipedia.org/wiki/Sequence_assembly
has_exact_synonym: sequence assembly
has_obo_namespace: sequence
id: SO:0000353
in_subset: SOFA

Axiom
annotated source: sequence_assembly
annotated property: definition
annotated target: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: sequence_assembly
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Sequence_assembly

codon
type: Class
subclass of: CDS_region
definition: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
database_cross_reference: http://en.wikipedia.org/wiki/Codon
has_obo_namespace: sequence
id: SO:0000360
in_subset: SOFA

Axiom
annotated source: codon
annotated property: definition
annotated target: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Codon

insertion_site
type: Class
subclass of: junction
definition: The junction where an insertion occurred.
has_exact_synonym: insertion site
has_obo_namespace: sequence
id: SO:0000366
in_subset: SOFA

Axiom
annotated source: insertion_site
annotated property: definition
annotated target: The junction where an insertion occurred.
database_cross_reference: SO:ke

transposable_element_insertion_site
type: Class
subclass of: insertion_site
definition: The junction in a genome where a transposable_element has inserted.
has_exact_synonym: transposable element insertion site
has_obo_namespace: sequence
id: SO:0000368
in_subset: SOFA

Axiom
annotated source: transposable_element_insertion_site
annotated property: definition
annotated target: The junction in a genome where a transposable_element has inserted.
database_cross_reference: SO:ke

small_regulatory_ncRNA
type: Class
subclass of: ncRNA
definition: 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: definition
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).
database_cross_reference: PMID:28541282
database_cross_reference: PomBase:al
database_cross_reference: SO:ma

enzymatic_RNA
type: Class
subclass of: ncRNA
definition: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
has_exact_synonym: enzymatic RNA
has_obo_namespace: sequence
id: SO:0000372
in_subset: SOFA
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: enzymatic_RNA
annotated property: definition
annotated target: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
database_cross_reference: RSC:cb

ribozyme
type: Class
subclass of: enzymatic_RNA
definition: An RNA with catalytic activity.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Ribozyme
has_exact_synonym: INSDC_qualifier:ribozyme
has_obo_namespace: sequence
id: SO:0000374
in_subset: SOFA

Axiom
annotated source: ribozyme
annotated property: definition
annotated target: An RNA with catalytic activity.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: ribozyme
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Ribozyme

cytosolic_5_8S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: 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: definition
annotated target: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: https://rfam.xfam.org/family/RF00002

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

hammerhead_ribozyme
type: Class
subclass of: RNA_motif
definition: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Hammerhead_ribozyme
has_exact_synonym: INSDC_qualifier:hammerhead_ribozyme
has_exact_synonym: hammerhead ribozyme
has_obo_namespace: sequence
id: SO:0000380
in_subset: SOFA

Axiom
annotated source: hammerhead_ribozyme
annotated property: definition
annotated target: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
database_cross_reference: PMID:2436805

wiki
type: Axiom
annotated source: hammerhead_ribozyme
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hammerhead_ribozyme

RNase_MRP_RNA
type: Class
subclass of: enzymatic_RNA
definition: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:RNase_MRP_RNA
has_exact_synonym: RNase MRP RNA
has_obo_namespace: sequence
id: SO:0000385
in_subset: SOFA
comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: RNase_MRP_RNA
annotated property: definition
annotated target: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

RNase_P_RNA
type: Class
subclass of: enzymatic_RNA
definition: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:RNase_P_RNA
has_exact_synonym: RNase P RNA
has_obo_namespace: sequence
id: SO:0000386
in_subset: SOFA
comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.

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

telomerase_RNA
type: Class
subclass of: ncRNA
definition: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Telomerase_RNA
has_exact_synonym: INSDC_qualifier:telomerase_RNA
has_exact_synonym: telomerase RNA
has_obo_namespace: sequence
id: SO:0000390
in_subset: SOFA

Axiom
annotated source: telomerase_RNA
annotated property: definition
annotated target: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: telomerase_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Telomerase_RNA

U1_snRNA
type: Class
subclass of: snRNA
definition: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
database_cross_reference: http://en.wikipedia.org/wiki/U1_snRNA
has_exact_synonym: U1 small nuclear RNA
has_exact_synonym: U1 snRNA
has_exact_synonym: small nuclear RNA U1
has_exact_synonym: snRNA U1
has_obo_namespace: sequence
id: SO:0000391
in_subset: SOFA

Axiom
annotated source: U1_snRNA
annotated property: definition
annotated target: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U1_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U1_snRNA

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: U1 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U1
database_cross_reference: RSC:cb

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U1
database_cross_reference: RSC:cb

U2_snRNA
type: Class
subclass of: snRNA
definition: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
database_cross_reference: http://en.wikipedia.org/wiki/U2_snRNA
has_exact_synonym: U2 small nuclear RNA
has_exact_synonym: U2 snRNA
has_exact_synonym: small nuclear RNA U2
has_exact_synonym: snRNA U2
has_obo_namespace: sequence
id: SO:0000392
in_subset: SOFA

Axiom
annotated source: U2_snRNA
annotated property: definition
annotated target: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U2_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U2_snRNA

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: U2 small nuclear RNA
database_cross_reference: RSC:CB

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U2
database_cross_reference: RSC:CB

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U2
database_cross_reference: RSC:CB

U4_snRNA
type: Class
subclass of: snRNA
definition: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
database_cross_reference: http://en.wikipedia.org/wiki/U4_snRNA
has_exact_synonym: U4 small nuclear RNA
has_exact_synonym: U4 snRNA
has_exact_synonym: small nuclear RNA U4
has_exact_synonym: snRNA U4
has_obo_namespace: sequence
id: SO:0000393
in_subset: SOFA

Axiom
annotated source: U4_snRNA
annotated property: definition
annotated target: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U4_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U4_snRNA

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: U4 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U4
database_cross_reference: RSC:cb

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U4
database_cross_reference: RSC:cb

U4atac_snRNA
type: Class
subclass of: snRNA
definition: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
has_exact_synonym: U4atac small nuclear RNA
has_exact_synonym: U4atac snRNA
has_exact_synonym: small nuclear RNA U4atac
has_exact_synonym: snRNA U4atac
has_obo_namespace: sequence
id: SO:0000394
in_subset: SOFA

Axiom
annotated source: U4atac_snRNA
annotated property: definition
annotated target: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
database_cross_reference: PMID:12409455

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: U4atac small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U4atac
database_cross_reference: RSC:cb

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U4atac
database_cross_reference: RSC:cb

U5_snRNA
type: Class
subclass of: snRNA
definition: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
database_cross_reference: http://en.wikipedia.org/wiki/U5_snRNA
has_exact_synonym: U5 small nuclear RNA
has_exact_synonym: U5 snRNA
has_exact_synonym: small nuclear RNA U5
has_exact_synonym: snRNA U5
has_obo_namespace: sequence
id: SO:0000395
in_subset: SOFA

Axiom
annotated source: U5_snRNA
annotated property: definition
annotated target: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U5_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U5_snRNA

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: U5 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U5
database_cross_reference: RSC:cb

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U5
database_cross_reference: RSC:cb

U6_snRNA
type: Class
subclass of: snRNA
definition: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
database_cross_reference: http://en.wikipedia.org/wiki/U6_snRNA
has_exact_synonym: U6 small nuclear RNA
has_exact_synonym: U6 snRNA
has_exact_synonym: small nuclear RNA U6
has_exact_synonym: snRNA U6
has_obo_namespace: sequence
id: SO:0000396
in_subset: SOFA

Axiom
annotated source: U6_snRNA
annotated property: definition
annotated target: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U6_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U6_snRNA

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: U6 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U6
database_cross_reference: RSC:cb

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U6
database_cross_reference: RSC:cb

U6atac_snRNA
type: Class
subclass of: snRNA
definition: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
has_exact_synonym: U6atac small nuclear RNA
has_exact_synonym: U6atac snRNA
has_exact_synonym: snRNA U6atac
has_obo_namespace: sequence
id: SO:0000397
in_subset: SOFA

Axiom
annotated source: U6atac_snRNA
annotated property: definition
annotated target: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
database_cross_reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: U6atac small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: U6atac snRNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U6atac
database_cross_reference: RSC:cb

U11_snRNA
type: Class
subclass of: snRNA
definition: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
database_cross_reference: http://en.wikipedia.org/wiki/U11_snRNA
has_exact_synonym: U11 small nuclear RNA
has_exact_synonym: U11 snRNA
has_exact_synonym: small nuclear RNA U11
has_exact_synonym: snRNA U11
has_obo_namespace: sequence
id: SO:0000398
in_subset: SOFA

Axiom
annotated source: U11_snRNA
annotated property: definition
annotated target: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
database_cross_reference: PMID:9622129

wiki
type: Axiom
annotated source: U11_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U11_snRNA

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: U11 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U11
database_cross_reference: RSC:cb

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U11
database_cross_reference: RSC:cb

U12_snRNA
type: Class
subclass of: snRNA
definition: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
database_cross_reference: http://en.wikipedia.org/wiki/U12_snRNA
has_exact_synonym: U12 small nuclear RNA
has_exact_synonym: U12 snRNA
has_exact_synonym: small nuclear RNA U12
has_exact_synonym: snRNA U12
has_obo_namespace: sequence
id: SO:0000399
in_subset: SOFA

Axiom
annotated source: U12_snRNA
annotated property: definition
annotated target: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U12_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U12_snRNA

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: U12 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U12
database_cross_reference: RSC:cb

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U12
database_cross_reference: RSC:cb

U14_snoRNA
type: Class
subclass of: C_D_box_snoRNA
definition: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
has_alternative_id: SO:0005839
has_exact_synonym: U14 small nucleolar RNA
has_exact_synonym: U14 snoRNA
has_exact_synonym: small nucleolar RNA U14
has_exact_synonym: snoRNA U14
has_obo_namespace: sequence
id: SO:0000403
in_subset: SOFA
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.

Axiom
annotated source: U14_snoRNA
annotated property: definition
annotated target: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
database_cross_reference: PMID:2551119
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

vault_RNA
type: Class
subclass of: ncRNA
definition: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Vault_RNA
has_exact_synonym: INSDC_qualifier:vault_RNA
has_exact_synonym: vault RNA
has_obo_namespace: sequence
id: SO:0000404
in_subset: SOFA

Axiom
annotated source: vault_RNA
annotated property: definition
annotated target: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: vault_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Vault_RNA

Y_RNA
type: Class
subclass of: ncRNA
definition: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Y_RNA
has_exact_synonym: INSDC_qualifier:Y_RNA
has_exact_synonym: Y RNA
has_obo_namespace: sequence
id: SO:0000405
in_subset: SOFA

Axiom
annotated source: Y_RNA
annotated property: definition
annotated target: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: Y_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Y_RNA

cytosolic_18S_rRNA
type: Class
subclass of: cytosolic_SSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/18S_ribosomal_RNA
has_exact_synonym: cytosolic 18S rRNA
has_exact_synonym: cytosolic 18S ribosomal RNA
has_exact_synonym: cytosolic rRNA 18S
has_obo_namespace: sequence
id: SO:0000407
in_subset: SOFA
comment: Renamed to cytosolic_18S_rRNA from rRNA_18S 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_18S_rRNA
annotated property: definition
annotated target: Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_18S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/18S_ribosomal_RNA

binding_site
type: Class
subclass of: biological_region
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:ke

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

protein_binding_site
type: Class
subclass of: binding_site
definition: 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: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
database_cross_reference: SO:ke

restriction_fragment
type: Class
subclass of: assembly_component
definition: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
database_cross_reference: http://en.wikipedia.org/wiki/Restriction_fragment
has_exact_synonym: restriction fragment
has_obo_namespace: sequence
id: SO:0000412
in_subset: SOFA

Axiom
annotated source: restriction_fragment
annotated property: definition
annotated target: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: restriction_fragment
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Restriction_fragment

sequence_difference
type: Class
subclass of: remark
definition: A region where the sequence differs from that of a specified sequence.
has_exact_synonym: INSDC_feature:misc_difference
has_exact_synonym: sequence difference
has_obo_namespace: sequence
id: SO:0000413
in_subset: SOFA

Axiom
annotated source: sequence_difference
annotated property: definition
annotated target: A region where the sequence differs from that of a specified sequence.
database_cross_reference: SO:ke

signal_peptide
type: Class
subclass of: peptide_localization_signal
subclass of: Restriction
  on property: derives_from
  some values from: CDS_region
subclass of: Restriction
  on property: part_of
  some values from: cleaved_peptide_region
definition: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
has_alternative_id: BS:00159
database_cross_reference: http://en.wikipedia.org/wiki/Signal_peptide
has_exact_synonym: INSDC_feature:sig_peptide
has_exact_synonym: signal peptide
has_exact_synonym: signal peptide coding sequence
has_obo_namespace: sequence
has_related_synonym: signal
id: SO:0000418
in_subset: SOFA
in_subset: biosapiens
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.

Axiom
annotated source: signal_peptide
annotated property: definition
annotated target: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: signal_peptide
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Signal_peptide

Axiom
annotated source: signal_peptide
annotated property: has_related_synonym
annotated target: signal
database_cross_reference: uniprot:feature_type

mature_protein_region
type: Class
subclass of: polypeptide_region
subclass of: Restriction
  on property: derives_from
  some values from: CDS_region
subclass of: Restriction
  on property: part_of
  some values from: immature_peptide_region
definition: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
has_alternative_id: BS:00149
has_exact_synonym: INSDC_feature:mat_peptide
has_exact_synonym: mature protein region
has_obo_namespace: sequence
has_related_synonym: chain
has_related_synonym: mature peptide
id: SO:0000419
in_subset: SOFA
in_subset: biosapiens
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.

Axiom
annotated source: mature_protein_region
annotated property: definition
annotated target: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb
database_cross_reference: http://www.insdc.org/files/feature_table.html

Axiom
annotated source: mature_protein_region
annotated property: has_related_synonym
annotated target: chain
database_cross_reference: uniprot:feature_type

ARS
type: Class
subclass of: origin_of_replication
definition: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
has_exact_synonym: autonomously replicating sequence
has_obo_namespace: sequence
id: SO:0000436
in_subset: SOFA

Axiom
annotated source: ARS
annotated property: definition
annotated target: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
database_cross_reference: SO:ma

ss_oligo
type: Class
subclass of: oligo
definition: A single stranded oligonucleotide.
has_exact_synonym: single strand oligo
has_exact_synonym: single strand oligonucleotide
has_exact_synonym: single stranded oligonucleotide
has_exact_synonym: ss oligo
has_exact_synonym: ss oligonucleotide
has_obo_namespace: sequence
id: SO:0000441
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ss_oligo
annotated property: definition
annotated target: A single stranded oligonucleotide.
database_cross_reference: SO:ke

ds_oligo
type: Class
subclass of: oligo
definition: A double stranded oligonucleotide.
has_exact_synonym: double stranded oligonucleotide
has_exact_synonym: ds oligo
has_exact_synonym: ds-oligonucleotide
has_obo_namespace: sequence
id: SO:0000442
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ds_oligo
annotated property: definition
annotated target: A double stranded oligonucleotide.
database_cross_reference: SO:ke

rasiRNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:rasiRNA
has_exact_synonym: repeat associated small interfering RNA
has_obo_namespace: sequence
id: SO:0000454
in_subset: SOFA
comment: Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573.

Axiom
annotated source: rasiRNA
annotated property: definition
annotated target: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
database_cross_reference: PMID:18032451
database_cross_reference: http://www.developmentalcell.com/content/article/abstract

pseudogenic_region
type: Class
subclass of: biological_region
definition: A non-functional descendant of a functional entity.
has_exact_synonym: pseudogenic region
has_obo_namespace: sequence
id: SO:0000462
in_subset: SOFA

Axiom
annotated source: pseudogenic_region
annotated property: definition
annotated target: A non-functional descendant of a functional entity.
database_cross_reference: SO:cjm

decayed_exon
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: exon
definition: A non-functional descendant of an exon.
has_exact_synonym: decayed exon
has_obo_namespace: sequence
id: SO:0000464
in_subset: SOFA
comment: Does not have to be part of a pseudogene.

Axiom
annotated source: decayed_exon
annotated property: definition
annotated target: A non-functional descendant of an exon.
database_cross_reference: SO:ke

golden_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: golden_path
definition: One of the pieces of sequence that make up a golden path.
has_exact_synonym: golden path fragment
has_obo_namespace: sequence
id: SO:0000468
in_subset: SOFA

Axiom
annotated source: golden_path_fragment
annotated property: definition
annotated target: One of the pieces of sequence that make up a golden path.
database_cross_reference: SO:rd

tiling_path
type: Class
subclass of: sequence_assembly
definition: A set of regions which overlap with minimal polymorphism to form a linear sequence.
has_exact_synonym: tiling path
has_obo_namespace: sequence
id: SO:0000472
in_subset: SOFA

Axiom
annotated source: tiling_path
annotated property: definition
annotated target: A set of regions which overlap with minimal polymorphism to form a linear sequence.
database_cross_reference: SO:cjm

tiling_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: tiling_path
definition: A piece of sequence that makes up a tiling_path (SO:0000472).
has_exact_synonym: tiling path fragment
has_obo_namespace: sequence
id: SO:0000474
in_subset: SOFA

Axiom
annotated source: tiling_path_fragment
annotated property: definition
annotated target: A piece of sequence that makes up a tiling_path (SO:0000472).
database_cross_reference: SO:ke

nc_primary_transcript
type: Class
subclass of: primary_transcript
definition: 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: definition
annotated target: A primary transcript that is never translated into a protein.
database_cross_reference: SO:ke

three_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: coding_exon
definition: The sequence of the 3' exon that is not coding.
has_exact_synonym: three prime coding exon noncoding region
has_exact_synonym: three_prime_exon_noncoding_region
has_obo_namespace: sequence
id: SO:0000484
in_subset: SOFA

Axiom
annotated source: three_prime_coding_exon_noncoding_region
annotated property: definition
annotated target: The sequence of the 3' exon that is not coding.
database_cross_reference: SO:ke

five_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
definition: The sequence of the 5' exon preceding the start codon.
has_exact_synonym: five prime coding exon noncoding region
has_exact_synonym: five_prime_exon_noncoding_region
has_obo_namespace: sequence
id: SO:0000486
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon_noncoding_region
annotated property: definition
annotated target: The sequence of the 5' exon preceding the start codon.
database_cross_reference: SO:ke

virtual_sequence
type: Class
subclass of: sequence_assembly
definition: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
has_exact_synonym: virtual sequence
has_obo_namespace: sequence
id: SO:0000499
in_subset: SOFA

Axiom
annotated source: virtual_sequence
annotated property: definition
annotated target: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
database_cross_reference: SO:ke

transcribed_region
type: Class
definition: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
has_obo_namespace: sequence
id: SO:0000502
in_subset: SOFA
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
deprecated: true

Axiom
annotated source: transcribed_region
annotated property: definition
annotated target: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
database_cross_reference: SO:ke

polyA_signal_sequence
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:polyA_signal_sequence
has_exact_synonym: poly(A) signal
has_exact_synonym: polyA signal sequence
has_exact_synonym: polyadenylation termination signal
has_obo_namespace: sequence
id: SO:0000551
in_subset: SOFA
comment: 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: polyA_signal_sequence
annotated property: definition
annotated target: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
database_cross_reference: http://www.insdc.org/files/feature_table.html

polyA_site
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
definition: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
has_alternative_id: SO:0001430
has_exact_synonym: INSDC_feature:polyA_site
has_exact_synonym: polyA cleavage site
has_exact_synonym: polyA junction
has_exact_synonym: polyA site
has_exact_synonym: polyA_junction
has_obo_namespace: sequence
has_related_synonym: polyadenylation site
id: SO:0000553
in_subset: SOFA

Axiom
annotated source: polyA_site
annotated property: definition
annotated target: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
database_cross_reference: http://www.insdc.org/files/feature_table.html

centromere
type: Class
subclass of: chromosomal_structural_element
definition: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
database_cross_reference: 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: definition
annotated target: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
database_cross_reference: SO:ke

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

cap
type: Class
subclass of: biological_region
definition: 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.
database_cross_reference: http://en.wikipedia.org/wiki/5%27_cap
has_obo_namespace: sequence
id: SO:0000581
in_subset: SOFA

Axiom
annotated source: cap
annotated property: definition
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.
database_cross_reference: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html

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

group_I_intron
type: Class
subclass of: autocatalytically_spliced_intron
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

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

autocatalytically_spliced_intron
type: Class
subclass of: intron
definition: 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: definition
annotated target: A self spliced intron.
database_cross_reference: SO:ke

SRP_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: nc_primary_transcript
definition: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:SRP_RNA
has_exact_synonym: SRP RNA
has_obo_namespace: sequence
has_related_synonym: 7S RNA
has_related_synonym: signal recognition particle RNA
id: SO:0000590
in_subset: SOFA

Axiom
annotated source: SRP_RNA
annotated property: definition
annotated target: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

C_D_box_snoRNA
type: Class
subclass of: snoRNA
definition: 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: definition
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'.
database_cross_reference: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

Axiom
annotated source: C_D_box_snoRNA
annotated property: has_exact_synonym
annotated target: SNORD
database_cross_reference: PMID:31828325

guide_RNA
type: Class
subclass of: ncRNA
definition: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Guide_RNA
has_exact_synonym: INSDC_qualifier:guide_RNA
has_exact_synonym: gRNA
has_exact_synonym: guide RNA
has_obo_namespace: sequence
id: SO:0000602
in_subset: SOFA

Axiom
annotated source: guide_RNA
annotated property: definition
annotated target: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
database_cross_reference: http://www.rna.ucla.edu/index.html

wiki
type: Axiom
annotated source: guide_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Guide_RNA

group_II_intron
type: Class
subclass of: autocatalytically_spliced_intron
definition: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
database_cross_reference: http://en.wikipedia.org/wiki/Group_II_intron
has_exact_synonym: group II intron
has_obo_namespace: sequence
id: SO:0000603
in_subset: SOFA
comment: GO:0000373.

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

wiki
type: Axiom
annotated source: group_II_intron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Group_II_intron

intergenic_region
type: Class
subclass of: biological_region
definition: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
database_cross_reference: http://en.wikipedia.org/wiki/Intergenic_region
has_exact_synonym: intergenic region
has_obo_namespace: sequence
id: SO:0000605
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: intergenic_region
annotated property: definition
annotated target: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
database_cross_reference: SO:cjm

wiki
type: Axiom
annotated source: intergenic_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Intergenic_region

polyA_sequence
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: adjacent_to
  some values from: mRNA
definition: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
has_exact_synonym: polyA sequence
has_obo_namespace: sequence
id: SO:0000610
in_subset: SOFA

Axiom
annotated source: polyA_sequence
annotated property: definition
annotated target: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
database_cross_reference: SO:ke

branch_site
type: Class
subclass of: spliceosomal_intron_region
definition: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
has_exact_synonym: branch point
has_exact_synonym: branch site
has_exact_synonym: branch_point
has_obo_namespace: sequence
id: SO:0000611
in_subset: SOFA

Axiom
annotated source: branch_site
annotated property: definition
annotated target: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
database_cross_reference: SO:ke

polypyrimidine_tract
type: Class
subclass of: spliceosomal_intron_region
definition: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
database_cross_reference: http://en.wikipedia.org/wiki/Polypyrimidine_tract
has_exact_synonym: polypyrimidine tract
has_obo_namespace: sequence
id: SO:0000612
in_subset: SOFA

Axiom
annotated source: polypyrimidine_tract
annotated property: definition
annotated target: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
database_cross_reference: http://nar.oupjournals.org/cgi/content/full/25/4/888

wiki
type: Axiom
annotated source: polypyrimidine_tract
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Polypyrimidine_tract

transcription_end_site
type: Class
subclass of: primary_transcript_region
definition: The base where transcription ends.
has_exact_synonym: transcription end site
has_obo_namespace: sequence
id: SO:0000616
in_subset: SOFA

Axiom
annotated source: transcription_end_site
annotated property: definition
annotated target: The base where transcription ends.
database_cross_reference: SO:ke

telomere
type: Class
subclass of: chromosomal_structural_element
definition: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
database_cross_reference: 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: definition
annotated target: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
database_cross_reference: SO:ma

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

silencer
type: Class
subclass of: cis_regulatory_module
definition: 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
database_cross_reference: 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: definition
annotated target: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
database_cross_reference: SO:ke

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

insulator
type: Class
subclass of: cis_regulatory_module
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: NCBI:cf
database_cross_reference: PMID:12154228
database_cross_reference: SO:regcreative

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

chromosomal_structural_element
type: Class
subclass of: chromosome_part
definition: 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

minisatellite
type: Class
subclass of: satellite_DNA
definition: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Minisatellite
has_exact_synonym: INSDC_qualifier:minisatellite
has_exact_synonym: VNTR
has_obo_namespace: sequence
id: SO:0000643
in_subset: SOFA

Axiom
annotated source: minisatellite
annotated property: definition
annotated target: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
database_cross_reference: http://www.informatics.jax.org/silver/glossary.shtml

wiki
type: Axiom
annotated source: minisatellite
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Minisatellite

Axiom
annotated source: minisatellite
annotated property: has_exact_synonym
annotated target: VNTR
database_cross_reference: http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/

antisense_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: antisense_primary_transcript
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: SO:ke

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

antisense_primary_transcript
type: Class
subclass of: primary_transcript
definition: 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: definition
annotated target: The reverse complement of the primary transcript.
database_cross_reference: SO:ke

siRNA
type: Class
subclass of: small_regulatory_ncRNA
definition: 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
database_cross_reference: 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: definition
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.
database_cross_reference: PMID:12592000

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

cytosolic_SSU_rRNA
type: Class
subclass of: rRNA
definition: Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
has_exact_synonym: cytosolic SSU rRNA
has_exact_synonym: cytosolic SSU ribosomal RNA
has_exact_synonym: cytosolic small subunit rRNA
has_obo_namespace: sequence
id: SO:0000650
in_subset: SOFA
comment: Renamed to cytosolic_SSU_rRNA from small_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_SSU_rRNA
annotated property: definition
annotated target: Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
database_cross_reference: SO:ke

cytosolic_LSU_rRNA
type: Class
subclass of: rRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_large_subunit_primary_transcript
definition: 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: definition
annotated target: Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
database_cross_reference: SO:ke

cytosolic_5S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/5S_ribosomal_RNA
has_exact_synonym: cytosolic 5S LSU rRNA
has_exact_synonym: cytosolic 5S rRNA
has_exact_synonym: cytosolic 5S ribosomal RNA
has_exact_synonym: cytosolic rRNA 5S
has_obo_namespace: sequence
id: SO:0000652
in_subset: SOFA
comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 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_5S_rRNA
annotated property: definition
annotated target: Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: cytosolic_5S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5S_ribosomal_RNA

cytosolic_28S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/28S_ribosomal_RNA
has_exact_synonym: cytosolic 28S LSU rRNA
has_exact_synonym: cytosolic 28S rRNA
has_exact_synonym: cytosolic 28S ribosomal RNA
has_exact_synonym: cytosolic rRNA 28S
has_obo_namespace: sequence
id: SO:0000653
in_subset: SOFA
comment: Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 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_28S_rRNA
annotated property: definition
annotated target: Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_28S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/28S_ribosomal_RNA

ncRNA
type: Class
subclass of: mature_transcript
definition: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
has_broad_synonym: INSDC_qualifier:other
database_cross_reference: http://en.wikipedia.org/wiki/NcRNA
database_cross_reference: 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: definition
annotated target: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
database_cross_reference: SO:ke

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

GENCODE
type: Axiom
annotated source: ncRNA
annotated property: database_cross_reference
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: biological_region
definition: 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: definition
annotated target: A region of sequence containing one or more repeat units.
database_cross_reference: SO:ke

dispersed_repeat
type: Class
subclass of: repeat_region
definition: A repeat that is located at dispersed sites in the genome.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Interspersed_repeat
has_exact_synonym: INSDC_qualifier:dispersed
has_exact_synonym: dispersed repeat
has_exact_synonym: interspersed repeat
has_obo_namespace: sequence
id: SO:0000658
in_subset: SOFA

Axiom
annotated source: dispersed_repeat
annotated property: definition
annotated target: A repeat that is located at dispersed sites in the genome.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: dispersed_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Interspersed_repeat

spliceosomal_intron
type: Class
subclass of: intron
definition: An intron which is spliced by the spliceosome.
has_exact_synonym: spliceosomal intron
has_obo_namespace: sequence
id: SO:0000662
in_subset: SOFA
comment: GO:0000398.

Axiom
annotated source: spliceosomal_intron
annotated property: definition
annotated target: An intron which is spliced by the spliceosome.
database_cross_reference: SO:ke

insertion
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
has_alternative_id: SO:1000034
database_cross_reference: loinc:LA6687-3
has_exact_synonym: insertion
has_exact_synonym: nucleotide insertion
has_exact_synonym: nucleotide_insertion
has_obo_namespace: sequence
id: SO:0000667
in_subset: DBVAR
in_subset: SOFA

Axiom
annotated source: insertion
annotated property: definition
annotated target: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
database_cross_reference: SO:ke

Insertion
type: Axiom
annotated source: insertion
annotated property: database_cross_reference
annotated target: loinc:LA6687-3

Axiom
annotated source: insertion
annotated property: has_exact_synonym
annotated target: insertion
database_cross_reference: http://www.ncbi.nlm.nih.gov/dbvar/
has_synonym_type: DBVAR

EST_match
type: Class
subclass of: expressed_sequence_match
definition: A match against an EST sequence.
has_exact_synonym: EST match
has_obo_namespace: sequence
id: SO:0000668
in_subset: SOFA

Axiom
annotated source: EST_match
annotated property: definition
annotated target: A match against an EST sequence.
database_cross_reference: SO:ke

transcript
type: Class
subclass of: gene_member_region
subclass of: Restriction
  on property: overlaps
  some values from: biological_region
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
has_broad_synonym: INSDC_feature:misc_RNA
database_cross_reference: 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: definition
annotated target: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
database_cross_reference: SO:ma

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

nuclease_sensitive_site
type: Class
subclass of: nuclease_binding_site
definition: A region of nucleotide sequence targeted by a nuclease enzyme.
has_exact_synonym: nuclease sensitive site
has_obo_namespace: sequence
id: SO:0000684
in_subset: SOFA

Axiom
annotated source: nuclease_sensitive_site
annotated property: definition
annotated target: A region of nucleotide sequence targeted by a nuclease enzyme.
database_cross_reference: SO:ma

deletion_junction
type: Class
subclass of: junction
definition: The space between two bases in a sequence which marks the position where a deletion has occurred.
has_exact_synonym: deletion junction
has_obo_namespace: sequence
id: SO:0000687
in_subset: SOFA

Axiom
annotated source: deletion_junction
annotated property: definition
annotated target: The space between two bases in a sequence which marks the position where a deletion has occurred.
database_cross_reference: SO:ke

golden_path
type: Class
subclass of: sequence_assembly
definition: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
has_exact_synonym: golden path
has_obo_namespace: sequence
id: SO:0000688
in_subset: SOFA

Axiom
annotated source: golden_path
annotated property: definition
annotated target: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
database_cross_reference: SO:ls

cDNA_match
type: Class
subclass of: expressed_sequence_match
definition: A match against cDNA sequence.
has_exact_synonym: cDNA match
has_obo_namespace: sequence
id: SO:0000689
in_subset: SOFA

Axiom
annotated source: cDNA_match
annotated property: definition
annotated target: A match against cDNA sequence.
database_cross_reference: SO:ke

SNP
type: Class
subclass of: SNV
definition: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
has_exact_synonym: single nucleotide polymorphism
has_obo_namespace: sequence
id: SO:0000694
in_subset: SOFA

Axiom
annotated source: SNP
annotated property: definition
annotated target: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
database_cross_reference: SO:cb

reagent
type: Class
subclass of: biomaterial_region
definition: A sequence used in experiment.
has_obo_namespace: sequence
id: SO:0000695
in_subset: SOFA
comment: Requested by Lynn Crosby, jan 2006.

Axiom
annotated source: reagent
annotated property: definition
annotated target: A sequence used in experiment.
database_cross_reference: SO:ke

oligo
type: Class
subclass of: reagent
definition: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
database_cross_reference: http://en.wikipedia.org/wiki/Oligonucleotide
has_exact_synonym: oligonucleotide
has_obo_namespace: sequence
id: SO:0000696
in_subset: SOFA

Axiom
annotated source: oligo
annotated property: definition
annotated target: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Oligonucleotide

junction
type: Class
subclass of: sequence_feature
definition: 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: definition
annotated target: A sequence_feature with an extent of zero.
database_cross_reference: SO:ke

remark
type: Class
subclass of: experimental_feature
definition: A comment about the sequence.
has_obo_namespace: sequence
id: SO:0000700
in_subset: SOFA

Axiom
annotated source: remark
annotated property: definition
annotated target: A comment about the sequence.
database_cross_reference: SO:ke

possible_base_call_error
type: Class
subclass of: sequence_difference
definition: A region of sequence where the validity of the base calling is questionable.
has_exact_synonym: possible base call error
has_obo_namespace: sequence
id: SO:0000701
in_subset: SOFA

Axiom
annotated source: possible_base_call_error
annotated property: definition
annotated target: A region of sequence where the validity of the base calling is questionable.
database_cross_reference: SO:ke

possible_assembly_error
type: Class
subclass of: sequence_difference
definition: A region of sequence where there may have been an error in the assembly.
has_exact_synonym: possible assembly error
has_obo_namespace: sequence
id: SO:0000702
in_subset: SOFA

Axiom
annotated source: possible_assembly_error
annotated property: definition
annotated target: A region of sequence where there may have been an error in the assembly.
database_cross_reference: SO:ke

experimental_result_region
type: Class
subclass of: remark
definition: A region of sequence implicated in an experimental result.
has_exact_synonym: experimental result region
has_obo_namespace: sequence
id: SO:0000703
in_subset: SOFA

Axiom
annotated source: experimental_result_region
annotated property: definition
annotated target: A region of sequence implicated in an experimental result.
database_cross_reference: SO:ke

gene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member_of
  some values from: gene_group
definition: 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.
database_cross_reference: 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: definition
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.
database_cross_reference: SO:immuno_workshop

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

tandem_repeat
type: Class
subclass of: repeat_region
definition: Two or more adjacent copies of a region (of length greater than 1).
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Tandem_repeat
database_cross_reference: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
has_exact_synonym: INSDC_qualifier:tandem
has_exact_synonym: tandem repeat
has_obo_namespace: sequence
id: SO:0000705
in_subset: SOFA

Axiom
annotated source: tandem_repeat
annotated property: definition
annotated target: Two or more adjacent copies of a region (of length greater than 1).
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: tandem_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Tandem_repeat

trans_splice_acceptor_site
type: Class
subclass of: trans_splice_site
definition: The 3' splice site of the acceptor primary transcript.
has_exact_synonym: trans splice acceptor site
has_obo_namespace: sequence
has_related_synonym: 3' trans splice site
id: SO:0000706
in_subset: SOFA
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.

Axiom
annotated source: trans_splice_acceptor_site
annotated property: definition
annotated target: The 3' splice site of the acceptor primary transcript.
database_cross_reference: SO:ke

nucleotide_motif
type: Class
subclass of: sequence_motif
definition: 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: definition
annotated target: A region of nucleotide sequence corresponding to a known motif.
database_cross_reference: SO:ke

RNA_motif
type: Class
subclass of: nucleotide_motif
definition: A motif that is active in RNA sequence.
has_exact_synonym: RNA motif
has_obo_namespace: sequence
id: SO:0000715
in_subset: SOFA

Axiom
annotated source: RNA_motif
annotated property: definition
annotated target: A motif that is active in RNA sequence.
database_cross_reference: SO:ke

reading_frame
type: Class
subclass of: experimental_feature
definition: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
database_cross_reference: http://en.wikipedia.org/wiki/Reading_frame
has_exact_synonym: reading frame
has_obo_namespace: sequence
id: SO:0000717
in_subset: SOFA
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.

Axiom
annotated source: reading_frame
annotated property: definition
annotated target: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
database_cross_reference: SGD:rb

wiki
type: Axiom
annotated source: reading_frame
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Reading_frame

ultracontig
type: Class
subclass of: sequence_assembly
definition: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
has_exact_synonym: pseudochromosome
has_obo_namespace: sequence
has_related_synonym: superscaffold
id: SO:0000719
in_subset: SOFA

Axiom
annotated source: ultracontig
annotated property: definition
annotated target: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
database_cross_reference: FB:WG

oriT
type: Class
subclass of: origin_of_replication
definition: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: http://en.wikipedia.org/wiki/Origin_of_transfer
has_exact_synonym: INSDC_feature:oriT
has_exact_synonym: origin of transfer
has_obo_namespace: sequence
id: SO:0000724
in_subset: SOFA

Axiom
annotated source: oriT
annotated property: definition
annotated target: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: oriT
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Origin_of_transfer

transit_peptide
type: Class
subclass of: peptide_localization_signal
subclass of: Restriction
  on property: derives_from
  some values from: CDS_region
definition: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
has_alternative_id: BS:00055
has_exact_synonym: INSDC_feature:transit_peptide
has_exact_synonym: transit peptide
has_obo_namespace: sequence
has_related_synonym: signal
has_related_synonym: transit
id: SO:0000725
in_subset: SOFA
in_subset: biosapiens
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.

Axiom
annotated source: transit_peptide
annotated property: definition
annotated target: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
database_cross_reference: http://www.insdc.org/files/feature_table.html

Axiom
annotated source: transit_peptide
annotated property: has_related_synonym
annotated target: transit
database_cross_reference: uniprot:feature_type

cis_regulatory_module
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: 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: definition
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.
database_cross_reference: PMID:19660565
database_cross_reference: SO:SG

gap
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: sequence_assembly
definition: A gap in the sequence of known length. The unknown bases are filled in with N's.
has_exact_synonym: INSDC_feature:gap
has_narrow_synonym: INSDC_feature:assembly_gap
has_obo_namespace: sequence
id: SO:0000730
in_subset: SOFA

Axiom
annotated source: gap
annotated property: definition
annotated target: A gap in the sequence of known length. The unknown bases are filled in with N's.
database_cross_reference: SO:ke

gene_group_regulatory_region
type: Class
definition: A region that is involved in the regulation of transcription of a group of regulated genes.
term replaced by: SO:0001055
has_exact_synonym: gene group regulatory region
has_obo_namespace: sequence
id: SO:0000752
in_subset: SOFA
comment: Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529.
deprecated: true

clone_insert
type: Class
subclass of: reagent
subclass of: Restriction
  on property: part_of
  some values from: clone
definition: The region of sequence that has been inserted and is being propagated by the clone.
has_exact_synonym: clone insert
has_obo_namespace: sequence
id: SO:0000753
in_subset: SOFA

Axiom
annotated source: clone_insert
annotated property: definition
annotated target: The region of sequence that has been inserted and is being propagated by the clone.
database_cross_reference: SO:ke

pseudogenic_rRNA
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: transcript
subclass of: Restriction
  on property: part_of
  some values from: pseudogene
definition: A non functional descendant of an rRNA.
has_broad_synonym: INSDC_feature:rRNA
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: pseudogenic rRNA
has_obo_namespace: sequence
id: SO:0000777
in_subset: SOFA
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.

Axiom
annotated source: pseudogenic_rRNA
annotated property: definition
annotated target: A non functional descendant of an rRNA.
database_cross_reference: SO:ke

pseudogenic_tRNA
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: transcript
subclass of: Restriction
  on property: part_of
  some values from: pseudogene
definition: A non functional descendent of a tRNA.
has_broad_synonym: INSDC_feature:tRNA
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: pseudogenic tRNA
has_obo_namespace: sequence
id: SO:0000778
in_subset: SOFA
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.

Axiom
annotated source: pseudogenic_tRNA
annotated property: definition
annotated target: A non functional descendent of a tRNA.
database_cross_reference: SO:ke

chromosome_part
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: chromosome
definition: 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: definition
annotated target: A region of a chromosome.
database_cross_reference: SO:ke

gene_member_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member_of
  some values from: gene
definition: 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: definition
annotated target: A region of a gene.
database_cross_reference: SO:ke

transcript_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: transcript
definition: 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: definition
annotated target: A region of a transcript.
database_cross_reference: SO:ke

mature_transcript_region
type: Class
subclass of: transcript_region
definition: 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: definition
annotated target: A region of a mature transcript.
database_cross_reference: SO:ke

primary_transcript_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: primary_transcript
definition: 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: definition
annotated target: A part of a primary transcript.
database_cross_reference: SO:ke

mRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: 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: definition
annotated target: A region of an mRNA.
database_cross_reference: SO:cb

UTR_region
type: Class
subclass of: mRNA_region
definition: 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: definition
annotated target: A region of UTR.
database_cross_reference: SO:ke

polypeptide_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: polypeptide
definition: 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: definition
annotated target: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
database_cross_reference: SO:GAR
database_cross_reference: SO:ke

Axiom
annotated source: polypeptide_region
annotated property: has_narrow_synonym
annotated target: region
database_cross_reference: uniprot:feature_type

Axiom
annotated source: polypeptide_region
annotated property: has_narrow_synonym
annotated target: site
database_cross_reference: uniprot:feature_type

spliceosomal_intron_region
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: spliceosomal_intron
definition: A region within an intron.
has_exact_synonym: spliceosomal intron region
has_obo_namespace: sequence
id: SO:0000841
in_subset: SOFA
comment: A terms added to allow the parts of introns to have is_a paths to the root.

Axiom
annotated source: spliceosomal_intron_region
annotated property: definition
annotated target: A region within an intron.
database_cross_reference: SO:ke

gene_component_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: gene
definition: 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

CDS_region
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: CDS
definition: A region of a CDS.
has_exact_synonym: CDS region
has_obo_namespace: sequence
id: SO:0000851
in_subset: SOFA

Axiom
annotated source: CDS_region
annotated property: definition
annotated target: A region of a CDS.
database_cross_reference: SO:cb

exon_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: exon
definition: A region of an exon.
has_exact_synonym: exon region
has_obo_namespace: sequence
id: SO:0000852
in_subset: SOFA

Axiom
annotated source: exon_region
annotated property: definition
annotated target: A region of an exon.
database_cross_reference: RSC:cb

cytosolic_16S_rRNA
type: Class
subclass of: cytosolic_SSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/16S_ribosomal_RNA
has_exact_synonym: cytosolic 16S SSU RNA
has_exact_synonym: cytosolic 16S ribosomal RNA
has_exact_synonym: cytosolic rRNA 16S
has_obo_namespace: sequence
has_related_synonym: cytosolic 16S rRNA
id: SO:0001000
in_subset: SOFA
comment: Renamed to cytosolic_16S_rRNA from rRNA_16S 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_16S_rRNA
annotated property: definition
annotated target: Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_16S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/16S_ribosomal_RNA

cytosolic_23S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.
has_exact_synonym: cytosolic 23S LSU rRNA
has_exact_synonym: cytosolic 23S rRNA
has_exact_synonym: cytosolic rRNA 23S
has_obo_namespace: sequence
has_related_synonym: cytosolic 23S ribosomal RNA
id: SO:0001001
in_subset: SOFA
comment: Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 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_23S_rRNA
annotated property: definition
annotated target: Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: SO:ke

cytosolic_25S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: gene
definition: Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.
has_exact_synonym: cytosolic 25S LSU rRNA
has_exact_synonym: cytosolic 25S rRNA
has_exact_synonym: cytosolic 25S ribosomal RNA
has_exact_synonym: cytosolic rRNA 25S
has_obo_namespace: sequence
id: SO:0001002
in_subset: SOFA
comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 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_25S_rRNA
annotated property: definition
annotated target: Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.
database_cross_reference: PMID:15493135
database_cross_reference: PMID:2100998
database_cross_reference: RSC:cb

copy_number_variation
type: Class
subclass of: sequence_alteration
definition: A variation that increases or decreases the copy number of a given region.
database_cross_reference: http://en.wikipedia.org/wiki/Copy_number_variation
has_exact_synonym: CNP
has_exact_synonym: CNV
has_exact_synonym: copy number polymorphism
has_exact_synonym: copy number variation
has_obo_namespace: sequence
id: SO:0001019
in_subset: SOFA

Axiom
annotated source: copy_number_variation
annotated property: definition
annotated target: A variation that increases or decreases the copy number of a given region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: copy_number_variation
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Copy_number_variation

mobile_genetic_element
type: Class
subclass of: biological_region
definition: A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
database_cross_reference: http://en.wikipedia.org/wiki/Mobile_genetic_element
has_exact_synonym: INSDC_feature:mobile_element
has_exact_synonym: MGE
has_exact_synonym: mobile genetic element
has_obo_namespace: sequence
id: SO:0001037
in_subset: SOFA

Axiom
annotated source: mobile_genetic_element
annotated property: definition
annotated target: A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
database_cross_reference: PMID:14681355

wiki
type: Axiom
annotated source: mobile_genetic_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mobile_genetic_element

integrated_mobile_genetic_element
type: Class
subclass of: mobile_genetic_element
definition: An MGE that is integrated into the host chromosome.
has_exact_synonym: integrated mobile genetic element
has_obo_namespace: sequence
id: SO:0001039
in_subset: SOFA

Axiom
annotated source: integrated_mobile_genetic_element
annotated property: definition
annotated target: An MGE that is integrated into the host chromosome.
database_cross_reference: SO:ke

transcriptional_cis_regulatory_region
type: Class
subclass of: regulatory_region
definition: 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: definition
annotated target: A regulatory_region that modulates the transcription of a gene or genes.
database_cross_reference: PMID:9679020
database_cross_reference: SO:regcreative

splicing_regulatory_region
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory_region that modulates splicing.
has_exact_synonym: splicing regulatory region
has_obo_namespace: sequence
id: SO:0001056
in_subset: SOFA
comment: 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: splicing_regulatory_region
annotated property: definition
annotated target: A regulatory_region that modulates splicing.
database_cross_reference: SO:ke

sequence_alteration
type: Class
subclass of: sequence_feature
definition: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
has_alternative_id: SO:1000004
has_alternative_id: SO:1000007
has_broad_synonym: INSDC_feature:misc_feature
has_exact_synonym: INSDC_feature:variation
has_exact_synonym: INSDC_note:sequence_alteration
has_exact_synonym: sequence alteration
has_narrow_synonym: partially characterised change in DNA sequence
has_narrow_synonym: partially_characterised_change_in_DNA_sequence
has_narrow_synonym: uncharacterised_change_in_nucleotide_sequence
has_obo_namespace: sequence
has_related_synonym: sequence variation
id: SO:0001059
in_subset: SOFA
comment: Merged with partially characterized change in nucleotide sequence.

Axiom
annotated source: sequence_alteration
annotated property: definition
annotated target: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
database_cross_reference: SO:ke

immature_peptide_region
type: Class
subclass of: polypeptide_region
definition: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
has_alternative_id: BS:00129
has_exact_synonym: immature peptide region
has_obo_namespace: sequence
id: SO:0001063
in_subset: SOFA
in_subset: biosapiens
comment: Range.

Axiom
annotated source: immature_peptide_region
annotated property: definition
annotated target: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
database_cross_reference: EBIBS:GAR

noncoding_region_of_exon
type: Class
subclass of: exon_region
definition: The maximal intersection of exon and UTR.
has_exact_synonym: noncoding region of exon
has_obo_namespace: sequence
id: SO:0001214
in_subset: SOFA
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.

Axiom
annotated source: noncoding_region_of_exon
annotated property: definition
annotated target: The maximal intersection of exon and UTR.
database_cross_reference: SO:ke

coding_region_of_exon
type: Class
subclass of: exon_region
definition: The region of an exon that encodes for protein sequence.
has_exact_synonym: coding region of exon
has_obo_namespace: sequence
id: SO:0001215
in_subset: SOFA
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.

Axiom
annotated source: coding_region_of_exon
annotated property: definition
annotated target: The region of an exon that encodes for protein sequence.
database_cross_reference: SO:ke

replicon
type: Class
subclass of: biological_region
definition: A region containing at least one unique origin of replication and a unique termination site.
database_cross_reference: http://en.wikipedia.org/wiki/Replicon_(genetics)
has_obo_namespace: sequence
id: SO:0001235
in_subset: SOFA

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

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

base
type: Class
subclass of: biological_region
definition: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
database_cross_reference: http://en.wikipedia.org/wiki/Nucleobase
has_obo_namespace: sequence
id: SO:0001236
in_subset: SOFA

Axiom
annotated source: base
annotated property: definition
annotated target: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
database_cross_reference: SO:ke

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

assembly
type: Class
subclass of: experimental_feature
definition: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
database_cross_reference: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
has_obo_namespace: sequence
id: SO:0001248
in_subset: SOFA

Axiom
annotated source: assembly
annotated property: definition
annotated target: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: assembly
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly

biomaterial_region
type: Class
subclass of: region
definition: A region which is intended for use in an experiment.
has_exact_synonym: biomaterial region
has_obo_namespace: sequence
id: SO:0001409
in_subset: SOFA

Axiom
annotated source: biomaterial_region
annotated property: definition
annotated target: A region which is intended for use in an experiment.
database_cross_reference: SO:cb

experimental_feature
type: Class
subclass of: region
definition: 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: definition
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.
database_cross_reference: SO:cb

biological_region
type: Class
subclass of: region
definition: 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: definition
annotated target: A region defined by its disposition to be involved in a biological process.
database_cross_reference: SO:cb

topologically_defined_region
type: Class
subclass of: region
definition: 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: definition
annotated target: A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
database_cross_reference: PMID:32782014
database_cross_reference: SO:cb

cis_splice_site
type: Class
subclass of: splice_site
definition: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
has_exact_synonym: cis splice site
has_obo_namespace: sequence
id: SO:0001419
in_subset: SOFA

Axiom
annotated source: cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke

trans_splice_site
type: Class
subclass of: splice_site
definition: Primary transcript region bordering trans-splice junction.
has_exact_synonym: trans splice site
has_obo_namespace: sequence
id: SO:0001420
in_subset: SOFA

Axiom
annotated source: trans_splice_site
annotated property: definition
annotated target: Primary transcript region bordering trans-splice junction.
database_cross_reference: SO:ke

SNV
type: Class
subclass of: substitution
definition: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
created by: kareneilbeck
creation date: 2009-10-08T11:37:49Z
has_exact_synonym: single nucleotide variant
has_obo_namespace: sequence
id: SO:0001483
in_subset: SOFA

Axiom
annotated source: SNV
annotated property: definition
annotated target: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
database_cross_reference: SO:bm

peptide_localization_signal
type: Class
subclass of: polypeptide_region
definition: A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
created by: kareneilbeck
creation date: 2010-03-11T02:15:05Z
has_exact_synonym: peptide localization signal
has_obo_namespace: sequence
has_related_synonym: localization signal
id: SO:0001527
in_subset: SOFA

Axiom
annotated source: peptide_localization_signal
annotated property: definition
annotated target: A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
database_cross_reference: SO:ke

kozak_sequence
type: Class
subclass of: ribosome_entry_site
definition: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
created by: kareneilbeck
creation date: 2010-06-07T03:12:20Z
database_cross_reference: http://en.wikipedia.org/wiki/Kozak_consensus_sequence
has_exact_synonym: kozak consensus
has_exact_synonym: kozak consensus sequence
has_exact_synonym: kozak sequence
has_obo_namespace: sequence
id: SO:0001647
in_subset: SOFA

Axiom
annotated source: kozak_sequence
annotated property: definition
annotated target: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: kozak_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Kozak_consensus_sequence

nucleotide_to_protein_binding_site
type: Class
subclass of: protein_binding_site
definition: 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: definition
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
database_cross_reference: SO:ke

transcription_regulatory_region
type: Class
definition: A regulatory region that is involved in the control of the process of transcription.
created by: kareneilbeck
creation date: 2010-10-12T03:49:35Z
has_exact_synonym: transcription regulatory region
has_obo_namespace: sequence
id: SO:0001679
in_subset: SOFA
comment: Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527.
deprecated: true

Axiom
annotated source: transcription_regulatory_region
annotated property: definition
annotated target: A regulatory region that is involved in the control of the process of transcription.
database_cross_reference: SO:ke

sequence_motif
type: Class
subclass of: biological_region
definition: 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
database_cross_reference: 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: definition
annotated target: A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
database_cross_reference: http://en.wikipedia.org/wiki/Sequence_motif

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

epigenetically_modified_region
type: Class
subclass of: regulatory_region
definition: 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: definition
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.
database_cross_reference: SO:ke
database_cross_reference: http://en.wikipedia.org/wiki/Epigenetics

paired_end_fragment
type: Class
subclass of: assembly_component
definition: An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
created by: kareneilbeck
creation date: 2011-04-14T01:48:20Z
has_exact_synonym: paired end fragment
has_obo_namespace: sequence
id: SO:0001790
in_subset: SOFA

Axiom
annotated source: paired_end_fragment
annotated property: definition
annotated target: An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
database_cross_reference: SO:ke

regulatory_region
type: Class
subclass of: gene_member_region
definition: A region of sequence that is involved in the control of a biological process.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: 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: definition
annotated target: A region of sequence that is involved in the control of a biological process.
database_cross_reference: SO:ke

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

gene_group
type: Class
subclass of: biological_region
definition: 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: definition
annotated target: A collection of related genes.
database_cross_reference: SO:ma

cleaved_peptide_region
type: Class
subclass of: polypeptide_region
subclass of: Restriction
  on property: part_of
  some values from: immature_peptide_region
definition: The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
has_exact_synonym: cleaved peptide region
has_obo_namespace: sequence
id: SO:0100011
in_subset: SOFA
in_subset: biosapiens
comment: Range.

Axiom
annotated source: cleaved_peptide_region
annotated property: definition
annotated target: The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
database_cross_reference: EBIBS:GAR

substitution
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: A sequence alteration where the length of the change in the variant is the same as that of the reference.
database_cross_reference: loinc:LA6690-7
has_obo_namespace: sequence
id: SO:1000002
in_subset: SOFA

Axiom
annotated source: substitution
annotated property: definition
annotated target: A sequence alteration where the length of the change in the variant is the same as that of the reference.
database_cross_reference: SO:ke

Substitution
type: Axiom
annotated source: substitution
annotated property: database_cross_reference
annotated target: loinc:LA6690-7

complex_substitution
type: Class
subclass of: substitution
definition: When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
has_exact_synonym: complex substitution
has_obo_namespace: sequence
id: SO:1000005
in_subset: SOFA

Axiom
annotated source: complex_substitution
annotated property: definition
annotated target: When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
database_cross_reference: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html

point_mutation
type: Class
subclass of: SNV
definition: A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Point_mutation
has_exact_synonym: point mutation
has_obo_namespace: sequence
id: SO:1000008
in_subset: SOFA

Axiom
annotated source: point_mutation
annotated property: definition
annotated target: A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: point_mutation
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Point_mutation

inversion
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: A continuous nucleotide sequence is inverted in the same position.
database_cross_reference: loinc:LA6689-9
has_exact_synonym: inversion
has_obo_namespace: sequence
id: SO:1000036
in_subset: DBVAR
in_subset: SOFA

Axiom
annotated source: inversion
annotated property: definition
annotated target: A continuous nucleotide sequence is inverted in the same position.
database_cross_reference: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html

Inversion
type: Axiom
annotated source: inversion
annotated property: database_cross_reference
annotated target: loinc:LA6689-9

Axiom
annotated source: inversion
annotated property: has_exact_synonym
annotated target: inversion
database_cross_reference: http://www.ncbi.nlm.nih.gov/dbvar/
has_synonym_type: DBVAR

regulon
type: Class
subclass of: gene_group
subclass of: Restriction
  on property: has_part
  some values from: biological_region
definition: A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products.
database_cross_reference: http://en.wikipedia.org/wiki/Regulon
has_obo_namespace: sequence
id: SO:1001284
in_subset: SOFA
comment: Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300

Axiom
annotated source: regulon
annotated property: definition
annotated target: A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products.
database_cross_reference: ISBN:0198506732
database_cross_reference: PMID:32665585

wiki
type: Axiom
annotated source: regulon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Regulon

databank_entry
type: Class
subclass of: reagent
definition: The sequence referred to by an entry in a databank such as GenBank or SwissProt.
has_exact_synonym: databank entry
has_obo_namespace: sequence
has_related_synonym: accession
id: SO:2000061
in_subset: SOFA

Axiom
annotated source: databank_entry
annotated property: definition
annotated target: The sequence referred to by an entry in a databank such as GenBank or SwissProt.
database_cross_reference: SO:ke