[ensembl-dev] chromosomal location of a gene

[Bert Overduin]

Hello Thomas,

The Ensembl gene start and end coordinates correspond to the outermost
transcript start and end coordinates. These can be part of the same
transcript or belong to two different transcripts. An example of the latter
is the human BRCA2 gene (
http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805),
where the start coordinate corresponds to the start coordinate of transcript
ENST00000380152 (BRCA2-001) and the end coordinate to the end coordinate of
transcript ENST00000544455 (BRCA2-201).

Also note that by definition the start coordinate is always less than the
end coordinate, so for reverse strand genes the start coordinate corresponds
to the 3' end of the gene, not the 5' end!

Absolute genomic start and end coordinates you can retrieve using
seq_region_start and seq_region_end.

Hope this helps,
Bert

On Tue, Sep 27, 2011 at 10:40 AM, Thomas Juettemann <juettemann at gmail.com>wrote:

> Dear All,
>
> I was wondering how the chromosomal location of a gene is defined in
> Ensembl.
> Are start and end the lowest and highest start coordinate found in all
> of the genes transcripts?
> And does the function  "seq_region_end()" from the Perl API return these
> values?
>
> Many thanks,
> Thomas
>
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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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