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SEQUENCE ONTOLOGY - ANNOTATIONS

The Sequence Types and Features Ontology (SO) is downloaded weekly from the SourceForge CVS repository at http://song.cvs.sourceforge.net/viewvc/song/ontology/. For more information about this ontology, see the Sequence Ontology Home Page at http://www.sequenceontology.org/.
Term:initiator_codon_variant
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Accession:SO:0001582 term browser browse the term
Definition:A codon variant that changes at least one base of the first codon of a transcript.
Comment: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.
Synonyms:exact_synonym: Jannovar:initiator_codon_variant;   VAT:startOverlap;   initiatior codon variant;   initiator codon change
 related_synonym: snpEff:NON_SYNONYMOUS_START
 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html;   http://snpeff.sourceforge.net/SnpEff_manual.html;   http://vat.gersteinlab.org/formats.php "VAT";   loinc:LA6695-6 "Initiating Methionine"

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  SO ontology 0
    sequence_variant 0
      structural_variant 0
        feature_variant 0
          gene_variant 0
            transcript_variant 0
              coding_transcript_variant 0
                coding_sequence_variant 0
                  initiator_codon_variant 0
                    start_lost 0
                    start_retained_variant 0
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