[Genome] mutually exclusive exons

[Ann Zweig]

Hello Pete,

	We have only enumerated the following alternative splicing and other 
events in the knownAlt table:

     * Alternate Promoter (altPromoter) - Transcription starts at 
multiple places.
     * Alternate Finish Site (altFinish) - Transcription ends at 
multiple places.
     * Cassette Exon (cassetteExon) - Exon is present in some 
transcripts but not others. These are found by looking for exons that 
overlap an intron in the same transcript.
     * Retained Intron (retainedIntron) - Introns are spliced out in 
some transcripts but not others. In some cases, particularly when the 
intron is near the 3' end, this can reflect an incompletely processed 
transcript rather than a true alt-splicing event.
     * Overlapping Exon (bleedingExon) - Initial or terminal exons 
overlap in an intron in another transcript. These often are associated 
with incompletely processed transcripts.
     * Alternate 3' End (altThreePrime) - Variations on the 3' end of an 
intron.
     * Alternate 5' End (altFivePrime) - Variations on the 5' end of an 
intron.
     * Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends 
rather than the usual GT/AG. These are associated with the minor 
spliceosome.
     * Strange Intron Ends (strangeSplice) - An intron with ends that 
are not GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort 
due to sequencing error or polymorphism.


	Depending on exactly what output you are trying to get, you might be 
able to create this on your own using the Custom Track tool.  You can 
read about it here: 
http://genome.cse.ucsc.edu/goldenPath/help/customTrack.html


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Pete Shepard wrote:
> Dear Genome Browser Folks,
> 
> I am wondering if you have a field for mutually exclusive exons in your
> knownAlt table.
> 
> Thanks
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome