Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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initiator_codon_variant

SO:0001582

Definition: A codon variant that changes at least one base of the first codon of a transcript.

Comments and references

This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.

Definition references: SO:ke

Synonyms

ScopeValue
exactJannovar:initiator_codon_variant
exactVAT:startOverlap
exactinitiatior codon variant
exactinitiator codon change
relatedsnpEff:NON_SYNONYMOUS_START

Identifiers and subsets

Accession: SO:0001582

Persistent URL: http://purl.obolibrary.org/obo/SO_0001582

Alternate IDs: None

Subsets: None

Cross references: http://snpeff.sourceforge.net/SnpEff_manual.html, http://vat.gersteinlab.org/formats.php, loinc:LA6695-6

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: 2022-04-25 in commit 476626e

Number of changes: 2

Ontology neighborhood diagram

Ontology neighborhood for SO:0001582 Ontology neighborhood graph for SO:0001582 initiator_codon_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0001580 coding_sequence_variant SO:0001580 coding_sequence_variant SO:0001582 initiator_codon_variant SO:0001582 initiator_codon_variant SO:0002019 start_retained_variant SO:0002019 start_retained_variant SO:0002012 start_lost SO:0002012 start_lost
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
2022-04-25xref removedCross reference removed: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html476626e
2016-12-05createdTerm introduced into the editable ontology history
Initial label: initiator_codon_variant
Initial definition captured.
Initial parent: SO:0001580
92e3cae