Hello, Tom. I would like to start by mentioning that the RefSeq Genes track is regularly updated while the UCSC Genes track is not. If you look at the track controls for any individual track (by either clicking the gray bar at the left of the graphical display or by clicking the track name in the track list below the graphical display), you will see "Data last updated" near the top of the page so you will know how current the data is. The UCSC Genes data was last updated 08-Oct-2009 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene) while the RefSeq Genes track was last updated 12-Dec-2011 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene). The UCSC Genes track is in the process of being updated and the updated track should be released soon.
>From the URL you provided, your search clearly shows that there are genes in the UCSC Genes track at the same position as the genes in the RefSeq Genes track, but they do not share the same RefSeq ID. The B9D1 genes in the UCSC Genes track have RefSeq ID NM_015681 which does correspond with one of the items in the RefSeq Genes track at that location. The other B9D1 genes in the RefSeq Genes track have RefSeq ID NM_001243473. If you follow the link to NCBI, you will find that this RefSeq ID (as well as NM_001178007, NM_182896.2 and NM_001199397) was added to NCBI fairly recently and as such, is not included in our UCSC Genes track yet. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Tommaso Mazza Sent: Tuesday, December 13, 2011 1:33 AM To: [email protected]; [email protected] Subject: [Genome] Missing NM genes in knowngene table Hi, I'm using the Table Browser function to get a BED file out of my NM_ list. 4 of my NMs are unknown to the "knowngene" table. NM_001243473 NM_001178007 NM_182896.2 NM_001199397 even if they actually exist in *UCSC RefSeq Genes* (look at: http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2F hgTracks&clade=mammal&org=Human&db=hg19&position=B9D1&hgt.suggest=&hgt.sugge stTrack=knownGene&Submit=submit&hgsid=228079873&hgt.newJQuery=1&pix=1403). Why and how to do when this recurs? Thanks Tom -- Tommaso Mazza, Ph.D. Bioinformatics unit Casa Sollievo della Sofferenza - Mendel Viale Regina Margherita 261 00198 Roma IT Tel: +39 06 44160526 Fax: +39 06 44160538 E-mail: [email protected] Web page: http://www.css-mendel.it/ Personal web: http://www.tommasomazza.eu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
