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
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Shraddha Pai
Postdoctoral fellow, Petronis lab
The Krembil Family Epigenetics Research Laboratory
Centre for Addiction and Mental Health
250 College Street, Toronto, ON.
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