Hi Dongcbuan, Open up the browser to the assembly that you are interested in. I am going to use the human hg19 assembly for this example. Below the image click "hide all" so that you can start with a clean slate.
Under the "Genes and Gene Prediction" section there is a track called "UCSC Genes". 1)In the drop down select "Full". 2) Click "refresh". The UCSC Genes track is now displayed in the browser. Under the section "Variation and Repeats" there are several polymorphism tracks. You will need to decide which ones to have displayed. 1)In this case, we'll set the drop down for "Common SNPs(132)" to "Full" and click "refresh". 2)Click on the the link "Common SNPs(132)" to get to the track control page for this track. a)Where it says "On details page, show function and coding differences relative to:" make sure that "UCSC Genes" is checked. b) Click "submit" at the top of the page. You now have common SNPs displayed along with UCSC Genes in the browser. This allows you to see which of exons have SNPs in them. You can click on a particular SNP in the browser image and this will take you to a details page. If you scroll down a little bit on the details page you will find information on "UCSC's predicted function relative to selected gene tracks:" which will help you identify which genes you might want to get DNA for. Hit the back button in your browser to return to the browser. Now you have a gene that you are interested in getting the DNA from. To do this use your mouse and right click on the gene of interest. Select "Get DNA for ..." Set the options you want and then click on "extended/case color options". This page has settings which will allow you to customize your sequence output. Click "submit" and your results will be displayed. I hope helps you get the information you are looking for. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Dongchuan Guo" <[email protected]> To: [email protected] Sent: Thursday, April 28, 2011 1:41:29 PM Subject: [Genome] Question of find DNA sequence To whom it may concern, I can find DNA sequence of a gene through UCSC genome browser. However, could you please let me know how to get DNA sequence of a gene that has been labeled with exons and known genomic polymorphisms. Thanks. Dongchuan Guo, PhD Assistant Professor Department of Internal Medicine The University of Texas Medical School at Houston Tel: 713-500-6849 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
