On Fri, Jun 26, 2009 at 3:53 AM, Gad Abraham
<gabraham@csse.unimelb.edu.au>wrote:

> On 26/6/09 2:15 PM, Steve Lianoglou wrote:
>
>> Hi,
>>
>> On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote:
>>
>>  Hi,
>>>
>>> Is it possible to get RefSeq summaries for a given gene using biomaRt
>>> (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq
>>> Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID.
>>>
>>> Specifically, I'm looking for mentions of alternative splicing (e.g.,
>>> "Alternatively spliced transcript variants encoding different isoforms
>>> have been described").
>>>
>>
>>
>> Would the presence of multiple ensembl_transcript_id's for one gene give
>> you the information you need?
>>
>> For example:
>>
>> R> getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id',
>> 'refseq_dna', 'transcript_start', 'transcript_end'),
>> filters='hgnc_symbol', value='AKNA', mart=hmart)
>> hgnc_symbol ensembl_transcript_id refseq_dna transcript_start
>> transcript_end
>> 1 AKNA ENST00000223791 116138266 116179065
>> 2 AKNA ENST00000320310 116136257 116162197
>> 3 AKNA ENST00000374074 116138266 116179736
>> 4 AKNA ENST00000312033 116161188 116190182
>> 5 AKNA ENST00000394574 116178067 116196506
>> 6 AKNA ENST00000374075 116136257 116196506
>> 7 AKNA ENST00000394582 116136257 116190037
>> 8 AKNA ENST00000374088 NM_030767 116138228 116190064
>> 9 AKNA ENST00000307564 116136257 116196506
>> 10 AKNA ENST00000374079 116136257 116196506
>>
>
> Thanks Steve,
>
> As far as I understand, having multiple splice variants doesn't in itself
> necessarily indicate that alternative splicing is important for the gene's
> function. My plan was to find such genes through the RefSeq description, and
> then if there is known alternative splicing, get the variants.


Hi, Gad.  I'm not sure what your goal is for looking for such genes, but I
think it likely that nearly all genes undergo alternative splicing under the
right conditions, so any gene that has multiple transcripts in a database
like RefSeq (or Ensembl) is likely to be a viable candidate.  See here for
details, as an example.

http://www.nature.com/nature/journal/v456/n7221/full/nature07509.html

Hope that helps.

Sean

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