Splice site coordinates: where to get them?

Question

[biostart]

Hello,

Is there an easy way to get from some database a BED file with splice site coordinates for mouse?

Thank you!

Answer 1

[Sean Davis]

You are looking for gtf files, most likely. The version from Ensembl is available here.

[biostart]

Thank you, I was aware of the Ensemble web site, but was hoping for something simpler and specifically listing splice sites,

Also, do you know how to convert the Ensembl gtf mm10 annotation to mm9? (Something like a liftover tool which deals with BED files).

[Sean Davis]

See Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api) and http://crossmap.sourceforge.net/.

[Sean Davis]

You may need to write some code. I do not know of a standard format for "splice sites".