Hi Michael, On mm9, if you enter the id, uc009fcc.1, in the box labeled "position/search" on top of the browser page and click "jump," you'll see AF365932 in the UCSC Genes track. Click on the item to see its details. You will see in the top-most light blue bar that it says, "Mouse Gene AF365932 (uc009fcc.1) Description and Page Index," indicating that the item you saw in the genome browser labeled as AF365932 is in fact uc009fcc.1.
Also, when I look at the gene in the browser, I do see the rendering in the browser does show 7 exons, however, they are all non-coding exons (notice they are half height and in the detail page of this gene it states, "Coding Exon Count: 0"). Additionally, if you would rather see the UCSC Gene ID as the label for UCSC Gene items in the browser, you can configure that from the UCSC Gene track controls page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=knownGene Where you see "Label" deselect "gene symbol" and select "UCSC Known Gene ID". If you click submit, you should see the same gene with the UCSC ID label instead of the gene name. I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Michael Muratet wrote, On 10/15/2010 3:55 PM: > Dear Colleagues > > I have come across a mouse gene in the browser that's a bit confusing. > I used the knownGene list for annotation in an RNA-seq analysis and > saw differential expression in uc009fcc.1. I used bigBams to load the > reads into the browser for further examination and went to the > uc009fcc locus on chr7. uc009fcc does not show up but AF365932 does. > AF365932 is indeed the cross-ref value in kgXref. But uc099fcc is > listed with 7 exons and AF365932 appears to have only one according to > its Genbank record and the way it's rendered. The Refseq and Ensembl > genes at that locus look like they are much better matches. Is there a > control I have missed that would show uc009fcc? > > Thanks > > Mike > > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > [email protected] > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
