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Splice site coordinates: where to get them?

Hello,

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

Thank you!

rna-seq chip-seq sequence next-gen
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updated by Sean Davis Sean Davis • written by biostart biostart

1 answer

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

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updated by Ram Ram • written by Sean Davis Sean Davis

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).

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written by biostart biostart

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

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updated by Ram Ram • written by Sean Davis Sean Davis

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