transgene [SO_0000902]

A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. On the relationship between ’transgenic insertions’, ’transgenes’, and ‘alleles’ Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a ‘sequence alteration’ (sensu SO) which creates a ‘variant gene allele’. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene’s sequence has been altered to create an allele. For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach.

Open transgene in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/SO_0000902",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0000902",
            "label": "transgene"
        },
        "description": [
            "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome)."
        ],
        "comment": [
            "Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors.  What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome.  For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome.",
            "On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species  as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome.  In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome.  But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene  traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference.  An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele.  \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion.  The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains.  The model of the Flybase example HERE illustrates this approach."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/SO_0000704",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0000704",
            "label": "gene"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/so#has_quality",
                "label": "has_quality",
                "type": "has_quality"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/SO_0000781",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "SO_0000781",
                "label": "transgenic"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}