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The Sequence Types and Features Ontology (SO) is downloaded weekly from the SourceForge CVS repository at For more information about this ontology, see the Sequence Ontology Home Page at

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Accession:SO:0002011 term browser browse the term
Definition:A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.
Comment:Requested by Pablo Cingolani, for use in SnpEff.
Synonyms:exact_synonym: Jannovar:intragenic_variant;   intragenic variant;   snpEff:INTRAGENIC

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  SO ontology 0
    sequence_variant 0
      structural_variant 0
        feature_variant 0
          gene_variant 0
            transcript_variant 0
              intragenic_variant 0
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