Hello Anke, Very glad to hear that the problem is resolved! Thank you for posting your reply back to the mailing list - it will likely be helpful for other users that run into a similar data misunderstanding.
Best regards, Jen UCSC Genome Browser Support On 7/12/10 12:26 PM, Anke Busch wrote: > Hello again, > > I just found my error. If the transcript is in the opposite orientation, > the START is the END and vice-versa. Thus, the names for the splice > sites also switch. On the negative strand, an alternative 3' splice site > refers to the end of the exon (specified in the list of all isoforms), > which is actually the start of the exon. > > Best regards, > Anke. > > > On Fri, Jul 9, 2010 at 5:31 PM, Anke Busch<[email protected] > <mailto:[email protected]>> wrote: > > Hello UCSC people, > > I extracted a list of all human alternative splicing events (assembly: > Feb. 2009 (GRCh37/hg19), track: Alt Events) and searched them in all > knownIsoforms. It seems to me that approximately 50% of the alternative > 3' splice site events (indicated by "altThreePrime") as well as of the > alternative 5' splice site events (indicated by "altFivePrime") are > wrongly annotated (real alt. 3' splice site events are indicated as alt. > 5' splice site events and the other way around). An example out of many > is the following: > > 585 chr1 18362 18379 altThreePrime 0 - > > If you search for this alternative splice site in the genome browser or > the list of knownIsoforms, you find an alternative ENDING of the exon > instead of an alternative START, which was expected according to the > "altThreePrime" annotation. An alternative ending has always to be > indicated as an "altFivePrime" event due to the general name convention > since the splice site is always given relative to the intron. > > Isoforms including alternative splice site 18362: > > 3 uc009viy.2 chr1 - 16606 29370 16606 16606 9 > 16606,16857,17232,17605,17914,18267,18496,24737,29320, > 16765,17055,17368,17742,18061,18362,18554,24891,29370, > 3 uc009vjf.2 chr1 - 17605 29370 17605 17605 7 > 17605,17914,18267,18496,18912,24737,29320, > 17742,18061,18362,18554,19139,24891,29370, > > Isoforms including alternative splice site 18379: > > 2 uc001aab.3 chr1 - 14362 24901 14362 14362 > 10 14362,14969,15795,16606,16853,17232,17605,17914,18267,24737, > 14829,15038,15947,16765,17055,17368,17742,18061,18379,24901, > 3 uc009viz.2 chr1 - 16606 29370 16606 16606 8 > 16606,16853,17232,17605,17914,18267,24737,29320, > 16765,17055,17368,17742,18061,18379,24891,29370, > 3 uc001aai.1 chr1 - 16857 19759 16857 16857 6 > 16857,17232,17605,17914,18267,18912, > 17055,17368,17742,18061,18379,19759, > 3 uc009vjb.1 chr1 - 16857 29961 16857 16857 7 > 16857,17232,17605,17914,18267,24737,29823, > 17055,17368,17742,18061,18379,24891,29961, > > Thanks for your help and best regards, > Anke. > > > _______________________________________________ > Genome maillist - [email protected] > <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
