[ensembl-dev] Question regarding UTR retrieval from database

Steve Moss gawbul at gmail.com
Tue Apr 14 14:47:25 BST 2015

Dear Duarte,

Just looking at the transcript/exon information here
it appears as though some of the coordinates you have given correspond to
exons? What EnsEMBL release are you using? I'm not sure if I understand
correctly, but is it the 5 prime + 3 prime UTRs and the intron sequences
that you want?

You can use $transcript->get_all_Introns() to retrieve the non-coding
regions between the exons (implicitly defined as introns). The coordinates
from the beginning of the gene, e.g. $gene->start() to the beginning of the
transcript, e.g. $transcript->start() should be the 5 prime UTR sequence
(which should be the same as 5' UTR start and end you used - so not sure
why you were getting the other values?), and the $transcript->end() to
$gene->end() should be the 3 prime UTR coordinates.

Is that what you want?



On 14 April 2015 at 13:40, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear Developers
> Please consider the transcript :
> ENST00000470357
> I am trying to retrieve the coordinates of UTR regions of this transcript
> To this end I have a script that basicaly starts with the transcript
> feature object $transcript
> my $five_prime  = $transcript->five_prime_utr_Feature;
> $feature_params->{start} = $five_prime->start;
> $feature_params->{end}  = $five_prime->end;
> However, in this case the script will output the coordinates from the
> start of the 1st non_coding exon to the end of the non-coding portion of
> the 3rd exon (chr1 7772707 7777171).
> How can I change this so that the script will only output the coordinates
> of the non-coding exon portions?
> In this case I would like to output:
> chr1 7772707 7773198
> chr1 7773442 7773511
> chr1 7777160 7777171
> This there a simple way of achieving this?
> Many thanks
> Duarte
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