Hi Shraddha, Here is a previous mailing list question that may help you find a way to use our Table Browser to answer your question (please note that it also explains that refGene doesn't contain alternate transcripts):
https://lists.soe.ucsc.edu/pipermail/genome/2007-September/014705.html Also, have you looked at the SIB Alt-Splicing track on mm8? It seems like it could be useful: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm8&g=sibTxGraph I hope this information is helpful. Please feel free to contact the mailing list if you require further assistance. Best, Mary --------------------------- Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Shraddha Pai" <[email protected]> To: [email protected] Sent: Thursday, May 20, 2010 6:57:26 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Best way to extract alternatively-spliced exons for mouse? Hi, I would like to extract a list of all alternatively spliced exons for a given chromosome for database mm8. The best way seems to me is the following (needs a script): 1. process the refGenes table 2. group items by the name2 field ("gene symbol") 3. And find the exon start/stops that don't occur in all entries of a particular gene symbol. Such exons are ones that define the different splice isoforms. Is there a better way to achieve such a list? Are the alternative spliceforms in this list curated ones (ie, we know they genuinely exist rather than being predictions)? A quick look through your mailing list suggests there used to be an "AltEvents" table that had this information, but there isn't such a track now. (although I do see one in the human database, hg18). Your guidance would be great. I tried to download the AltSplice flatfile from an ENSEMBL website but the data won't be for NCBI build 36 (mm8), which is what I need. Thanks in advance and thank you for this wonderful resource! Shraddha ------------------------------------------------------ Shraddha Pai Postdoctoral fellow, Petronis lab The Krembil Family Epigenetics Research Laboratory Centre for Addiction and Mental Health 250 College Street, Toronto, ON. ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
