finding exons for a gene, having the coding sequence only - (Mar/14/2011 )

Hi there,

I was wondering if you knew of a way to get the total mRNA for a gene, including all exons. I only have the coding sequence for my gene and I am interested in finding regulatory regions upstream (or downstream). The mouse genome is not annotated around that region (I checked the UCSC genome browser).

Thanks for your help!

D

-dfe-

Did you try BLAT?

-bob1-

Yes I tried.. nothing. Any other idea?

bob1 on Mon Mar 14 21:08:22 2011 said:

Did you try BLAT?

-dfe-

You can use the Emsembl database at http://uswest.ensembl.org/ to retrieve your mRNA sequence plus upstream and down stream sequences. It is very convenient. For example this link brings you to mouse bcl2 gene in the database http://uswest.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000057329;r=1:108434755-108610851;t=ENSMUST00000112751

then click "Sequence" on the left, the genome sequence for bcl2 will be displayed with exons marked in red. Click "Configure this page" on the left more options are available including much much 5' and 3' flanking sequence to include in the display.

-pcrman-

Thanks pcrman, this is helpful. However, my gene is not annotated and somehow, only the coding sequence is available. If I look at the corresponding region on Ensembl, there is no information about exons.
My question was whether there is a way to find exons from genomic DNA..

pcrman on Tue Mar 15 02:08:03 2011 said:

-dfe-