[ensembl-dev] mapping miRBase -> Ensembl

[Julien Roux]

Thanks Andy for the answer
Yes you're right...
Then I find it strange that it is not possible to retrieve this info 
from Biomart
Am I missing something?

Le 25.11.10 16:12, Andy Yates a écrit :
> Hi Julien,
>
> It seems that the mirBase accession is available from the transcript and not the gene.
>
> http://www.ensembl.org/Danio_rerio/Transcript/Similarity?db=core;g=ENSDARG00000082738;r=25:1688203-1688297;t=ENSDART00000116791
>
> Andy
>
> On 25 Nov 2010, at 15:02, Julien Roux wrote:
>
>> Dear Ensembl team
>>
>> For zebrafish Ensembl genes, it does not seem possible to retrieve the miRbase Accessions via Biomart. nothing appears in the "External References" section.
>> However I checked that it is possible for other species (human, mouse etc)
>> How does it come?
>> Is there another way to retrieve this mapping?
>> The data seem to be in Ensembl since the description of some genes mention the mirBase accession (http://www.ensembl.org/Danio_rerio/Gene/Summary?db=core;g=ENSDARG00000082738 for example)
>> Thnaks for your help
>> Julien
>> -- 
>> Julien Roux, PhD
>>
>> http://www.unil.ch/dee/page38327.html
>>
>> Keller group, Department of Ecology and Evolution
>> Biophore, University of Lausanne, 1015 Lausanne, Switzerland
>> tel: +41 21 692 4221    fax: +41 21 692 4165
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev


-- 
Julien Roux, PhD
http://www.unil.ch/dee/page38327.html
Keller group, Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4221    fax: +41 21 692 4165