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
