[ensembl-dev] slice from 3'UTR

[ian Longden]

You can use the following methods on the Transcript object:-

$transcript->cdna_coding_start;
$transcript->start;

$transcript->cdna_coding_end;
$transcript->end;

To get the info you need

Please note cdna_coding_start retrieves the position of the coding
start of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs).

Similarly for cdna_coding_end.

HTH,
Ian.

On Wed, Oct 6, 2010 at 5:06 PM, Anna Terry <anna.terry at csc.mrc.ac.uk> wrote:
> Hi,
>
> Is it possible to get a slice(coordinates of) the 5' and 3' UTRs of a
> transcript, as opposed to just the sequence using $transcrpt->five_prime_utr
>
> Cheers
> Anna
>
>
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