Hi Kevin, The discrepancy between the CCDS and RefSeq txstart and txend coordinates exits because CCDS does not annotate untranslated regions (UTR), it only annotates protein-coding regions, and RefSeq does annotate UTR.
I have created a session (click on the link below) with the CCDS and RefSeq tracks open to F8. In this session you can see how the two tracks differ in their annotation of F8. If you zoom into either end of F8, you can more easily see the coordinate differences. http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Katrina&hgS_otherUserSessionName=F8refSeqVsCCDS I hope this is helpful! Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Ann Zweig wrote: > Reposting to list. > > > >> ------------------------------------------------------------------------ >> >> *From:* Viel, Kevin >> *Sent:* Wednesday, September 30, 2009 2:48 PM >> *To:* [email protected] >> *Subject:* txstart and start discrepancy >> >> >> >> Hello, >> >> >> >> I obtained the “Genes and Gene Prediction Tracks” for the Feb. 2009 >> Human Genome, which contains these data: >> >> >> >> name txstart txend >> >> CCDS35457.1 154065871 154250827 >> >> >> >> >> >> This record corresponds to F8. If I use the Genome Browser to search >> for F8, I find RefSeq: NM_000132.3 with the same CCDS number. However, >> the Start and End for this record are 154064070 and 154250998, >> respectively. Can anyone explain this discrepancy? I expected these >> values to match. This does not seem to be the 0 versus 1 offset >> discussed in the FAQ. >> >> >> >> >> >> Thank you, >> >> >> >> Kevin >> >> >> >> >> >> >> >> *Kevin Viel, PhD* >> >> Senior Research Statistician >> >> Patient Safety & Quality >> >> International College of Robotic Surgery >> >> Saint Joseph's Translational Research Institute >> >> >> >> *Saint Joseph**'s Hospital* >> >> 5671 Peachtree Dunwoody Road, NE, Suite 330 >> >> Atlanta, GA 30342 >> >> >> >> (678) 843-6076: Direct Phone >> >> (678) 843-6153: Facsimile >> >> (404) 558-1364: Mobile >> >> [email protected] <mailto:[email protected]> >> >> [email protected] <mailto:[email protected]> >> >> >> >> >> >> >> >> >> >> >> >> NOTICE: This e-mail message and all attachments transmitted with it may >> contain legally privileged and confidential information intended solely >> for the use of the addressee. In addition, this correspondence may >> contain private patient information protected under the federal privacy >> rule, 45 C.F.R. Parts 160 and 164, and applicable state law. >> Unauthorized use or disclosure of this information is strictly >> prohibited. If the reader of this message is not the intended recipient, >> you are hereby notified that any reading, dissemination, distribution, >> copying or other use of this message or its attachments is strictly >> prohibited. If you have received this message in error, please notify >> the sender immediately by return e-mail or at the telephone number above >> and delete the original message and all copies and backups thereof. >> Thank you >> >> >> >> >> >> Confidentiality Notice: >> This email, including any attachments is the >> property of Catholic Health East and is intended >> for the sole use of the intended recipient(s). >> It may contain information that is privileged and >> confidential. Any unauthorized review, use, >> disclosure, or distribution is prohibited. If you are >> not the intended recipient, please reply to the >> sender that you have received the message in >> error, then delete this message. >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
