Hi Hongwei, One of our developers looked into this and in summary, has this to say: If you look at this gene on hg18 (Build36), and turn on the "Hg19 Diff" track (located in Mapping and Sequencing Tracks), you will see that a contig covering most of the gene was dropped from the assembly from hg18 to hg19; the original sequence is no longer in hg19 and the gene lands where the exons are mapped. If you look at this gene on hg19 and turn on the "GRC Patch Release" track, it appears the hg19 sequence has been replaced by the patch sequence. Take the protein sequence from genbank, blat to hg18 and hg19. It matches hg18 much better than it matches hg19. If you blat it to the patch5 sequence (only possible on our test server) you find it matches 100% perfectly .As it turns out, the gene is located in the sequence AC234063.4 - which is not in any genome assembly yet.
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/12/2011 4:53 PM, Wang, Hongwei wrote: > Dear Sir, > > > > I have a question on PECAM1 gene position for Human genome between > Build36 and Build37. > > In Build36, this gene position is on chr17 from 59753595 to 59817743 > based on UCSC . The gene length is about 64kb. > > In Build37, the gene position is from 62399864 to 62401205. The gene > length is about 1.3kb. > > Could you please tell me why the gene length is different so much > between different Build? Thanks. > > > > Sincerely, > > Hongwei Wang > > Fred Hutchinson Cancer Research Center > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
