Hi Hanna! Another Genome Browser user replied to your question, but I'm not sure it went to you directly. The answer is here:
https://lists.soe.ucsc.edu/pipermail/genome/2012-June/029446.html Stephane is right: there are still multiple locations for DUX4 on hg19. When you type a name into the "gene" box, the browser takes you to a single location, even if there are multiple locations available (this is in part to make it easier to navigate to genes that have multiple transcripts with the same name in nearly the same position). Also, only the UCSC Genes and RefSeq Genes tracks are searched when you use the "gene" box (see http://genome.ucsc.edu/goldenPath/help/geneSearchBox.html for more information). However, when you type a name into the "position/search" box, all matches in all tracks are displayed. If there are multiple matches, you will be taken to a page that allows you to select one. Our mailing list software strips attachments, so I'm not sure which gene tracks you were looking at. In this case, where there are mappings to multiple chromosomes, it would likely be helpful to turn on a few different gene tracks (UCSC Genes, RefSeq Genes, and GENCODE, for instance) to see if they agree about the placement of DUX4. Some sets are more curated than others; you can read about each set by clicking on a single gene and scrolling down, or by clicking the blue track name under the main Genome Browser graphic. I hope this helps explain what you are seeing in the Genome Browser. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 6/7/12 11:47 AM, Cheung, Hannah wrote: > Hi, > > I am trying to search for the genome location of DUX4. I realize > that there is a family of DUX4 genes, but I have also noticed that on hg18, DUX4 is mapped to chromosomes 10 or 4, while in hg19, it is mapped to chromosome 18. What is the reason for this? What is the correct location for the gene? > > (Please see enclosed screen captures). > > Thanks, > Hannah Cheung, PhD > Postdoctoral Associate, Plon Lab > President of Baylor College of Medicine Postdoctoral Association > 1102 Bates Ave > Rm.1200.18 > Texas Children's Hospital > Houston, TX 77030 > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
