Dear sir,
Thanks for your time and effort on the detail explaination. I have another question on this gene related to the position: Why the position info on UCSC differ from that on NCBI? The info for this Gene on NCBI is: chr17 position : 62396775 ~ 62404856. Sincerely, hongwei On 10/21/2011 9:52 AM, Wang, Hongwei wrote: > Dear Luvina Guruvadoo, > > Thanks for your time and effort on the detail explaination. I have > another question on this gene related to the position: > Why the position info on UCSC differ from that on NCBI? > The info for this Gene on NCBI is: chr17 position : 62396775 ~ > 62404856. > > Sincerely, > > hongwei > > -----Original Message----- > From: Luvina Guruvadoo [mailto:[email protected]] > Sent: Thursday, October 20, 2011 11:11 AM > To: Wang, Hongwei > Cc: [email protected] > Subject: Re: [Genome] gene-PECAM1 position > > 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
