Hi Vinay, I spoke to one of our developers about this gap in uc010kps.1. The gap appears to be a polymorphism in the last exon. If you turn on the mRNA track alongside the UCSC Genes track, you will see several mRNAs with unaligned sequence in those 6 bases (and some that do align to those 6 bases). UCSC Genes is based in part on the mRNA track, and it looks like the uc010kps.1 annotation is showing the polymorphism from the mRNAs that don't have aligning sequence in those 6 bases.
So, this gap should be considered a region with unaligned sequence, not an intron. The last two blocks in uc010kps.1 represent only one exon. It seems that our UCSC Genes process should have closed this gap. We will add this case to our list of things to examine in for future UCSC Gene builds. -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/25/10 10:17, Mittal, Vinay K wrote: > Hi, I was looking at the transcript uc010kps.1 (from hg18 assembly) > and found that its 8th exon is spliced with a 6 bps gap. I am a bit > skeptical about it because splice sites for this spliced region are > not canonical. Could you please have a look at it. > > Thanks. > > Sincerely, V. > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
