[BioC] exon genomic coordinates

Hans-Rudolf Hotz hrh at fmi.ch
Thu Nov 21 14:38:31 CET 2013

Hi John

You can use the BioMart database, which you can access with the biomaRt 
package to get all exons for all transcripts for a given giene, eg:

ensembl = useMart("ensembl")
#assuming you are interested in mouse
mouse.ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl)

getBM(attributes = 
filters = 'mgi_symbol', values=c("KIT"),mart=mouse.ensembl)

Hope this helps


On 11/21/2013 09:14 AM, array chip wrote:
> Hi,
> Can anyone suggest how to retrieve the genomic coordinates for all exons for a given gene by say gene symbol? For example, how to retrieve the coordinates for all 21 exons for gene KIT?
> Thanks
> John
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