Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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splice_site_variant

SO:0001629

Definition: A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.

Comments and references

EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.

Definition references: http://ensembl.org/info/docs/variation/index.html

Synonyms

ScopeValue
exactVAT:spliceOverlap
exactessential_splice_site
exactsplice site variant

Identifiers and subsets

Accession: SO:0001629

Persistent URL: http://purl.obolibrary.org/obo/SO_0001629

Alternate IDs: None

Subsets: None

Cross references: http://vat.gersteinlab.org/formats.php

History summary

Term history is reconstructed from the Git-era ontology files by comparing ontology classes across revisions. Earlier SVN-era changes will be added at a future date.

First seen in Git-era editable history: 2016-12-05 in commit 92e3cae

Most recent Git-era change: 2016-12-05 in commit 92e3cae

Number of changes: 1

Ontology neighborhood diagram

Ontology neighborhood for SO:0001629 Ontology neighborhood graph for SO:0001629 splice_site_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0001568 splicing_variant SO:0001568 splicing_variant SO:0001627 intron_variant SO:0001627 intron_variant SO:0001629 splice_site_variant SO:0001629 splice_site_variant SO:0001787 splice_donor_5th_base_variant SO:0001787 splice_donor_5th_base_variant SO:0001574 splice_acceptor_variant SO:0001574 splice_acceptor_variant SO:0001575 splice_donor_variant SO:0001575 splice_donor_variant
The local DAG shows nearby parent, child, and related terms. Each node links to its own term page.

Relationships

Parents

Children

Change history

This timeline summarizes changes identified in SO’s GitHub commit history, including updates to labels, definitions, parent terms, synonyms, subsets, and obsoletion status. It is a best-effort reconstruction and may not include every change to a term. Since only history from GitHub is included at the moment, any term added before the migration from SVN to Git will show as being created in 2016. This will be addressed once SVN history is incorporated.

DateChangeSummaryEvidence
2016-12-05createdTerm introduced into the editable ontology history
Initial label: splice_site_variant
Initial definition captured.
Initial parents: SO:0001568, SO:0001627
92e3cae