Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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stop_lost

SO:0001578

Definition: A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.

Comments and references

EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.

Definition references: SO:ke

Synonyms

ScopeValue
exactANNOVAR:stoploss
exactJannovar:stop_lost
exactSeattleseq:stop-lost
exactVAAST:stop_lost
exactVAT:removedStop
exactVEP:stop_lost
exactsnpEff:STOP_LOST
exactstop codon lost
exactstop lost
relatedSeattleseq:stop-lost-near-splice

Identifiers and subsets

Accession: SO:0001578

Persistent URL: http://purl.obolibrary.org/obo/SO_0001578

Alternate IDs: None

Subsets: None

Cross references: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp, http://snpeff.sourceforge.net/SnpEff_manual.html, http://vat.gersteinlab.org/formats.php, http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences

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:0001578 Ontology neighborhood graph for SO:0001578 stop_lost. Parent, child, and related nodes can be activated to open their term pages. SO:0001907 feature_elongation SO:0001907 feature_elongation SO:0001992 nonsynonymous_variant SO:0001992 nonsynonymous_variant SO:0001590 terminator_codon_variant SO:0001590 terminator_codon_variant SO:0001578 stop_lost SO:0001578 stop_lost
The local DAG shows nearby parent, child, and related terms. Each node links to its own term page.

Relationships

Parents

Children

None recorded in the current release neighborhood.

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: stop_lost
Initial definition captured.
Initial parents: SO:0001590, SO:0001907, SO:0001992
92e3cae