Hi Hongwei, The data incorporated into the hg19 UCSC Genes track was from October of 2009. In contrast, the RefSeq Genes track was last updated on October 20th of this year. So, I believe the difference you're seeing is because the NCBI record has been updated since the creation of the UCSC Genes track.
The new version of the UCSC Genes track on hg19 is currently undergoing quality review. On our genome-preview web site, you can see the new version of UCSC Genes and see that the PECAM1 is much more similar to the RefSeq Genes version. Genome-preview (http://genome-preview.ucsc.edu/) allows users to preview tracks/data before they have been through our quality assurance process. Because genome-preview contains pre-release data, please use discretion when downloading and viewing data from genome-preview as it may still be undergoing changes and improvements. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/21/11 9:55 AM, Wang, Hongwei wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
