[ensembl-dev] mapping miRBase -> Ensembl

[Andy Yates]

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
> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/