start_retained_variant [SO_0002019]

A sequence variant where at least one base in the start codon is changed, but the start remains. Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.

Open start_retained_variant in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/SO_0002019",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0002019",
            "label": "start_retained_variant"
        },
        "description": [
            "A sequence variant where at least one base in the start codon is changed, but the start remains."
        ],
        "comment": [
            "Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/SO_0001582",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0001582",
            "label": "Initiating Methionine"
        },
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/SO_0001819",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0001819",
            "label": "wiki"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [
        {
            "synonym": {
                "scope": "has_exact_synonym",
                "label": "snpEff:SYNONYMOUS_START",
                "type": ""
            },
            "pub": {
                "core": {
                    "symbol": "",
                    "iri": "http://flybase.org/reports/Unattributed",
                    "types": [
                        "Entity",
                        "Individual",
                        "pub"
                    ],
                    "short_form": "Unattributed",
                    "label": ""
                },
                "FlyBase": "",
                "PubMed": "",
                "DOI": ""
            }
        }
    ],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}