[ensembl-dev] slice from 3'UTR

Anna Terry anna.terry at csc.mrc.ac.uk
Mon Oct 11 13:40:59 BST 2010


Hi,

Thanks for thinking about this for me.  After thinking about why this 
information is not readily available I realise that the sequence is 
actually the best option for what I am doing.  I don't actually want any 
intronic sequence!

Many thanks for the help
Anna

On 07/10/10 08:52, ian Longden wrote:
> 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
>>
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>>      

-- 
Anna Terry
Lymphocyte Development
MRC Clinical Sciences Centre
Imperial College Faculty of Medicine
Hammersmith Hospital
Du Cane Road
London W12 0NN

Tel:	0208 3832140
	0208 3832145
Email: anna.terry at csc.mrc.ac.uk





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