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Old 10-07-2010, 06:21 AM   #8
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Location: Southern France

Join Date: Aug 2009
Posts: 269

A quick and dirty way, all from the UCSC Tables, group="Genes and gene prediction tracks", output format="BED".

Promoter (kind of): select "Upstream by"= 500 or 1Kb or whatever you want. Of course, consider the limitations described in the posts above.

Splice sites: select "Introns" and extract their extremities once downloaded (or send it to Galaxy from the previous screen to do it online). I find it easier to get splice sites from introns than from exons -no need to filter TSSs and polyA sites.
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