Hello, Varun. The UCSC Genes track is a set of tables in the hg19 database. The main table is called knownGene and contains information about each of the UCSC gene identifiers (i.e., uc003axi.2). If you physically want the entire table, you can download knownGene.txt.gz from our download server at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ or from our FTP server at ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/.
If you want to cross reference the UCSC gene name with the gene symbol, there is a companion table to knownGene called kgXref which matches the UCSC gene name to a number of other identifiers such as RefSeq ID, UniProt ID, gene symbol, etc. This table can also be downloaded via the links provided above, but the easiest way to perform such a cross reference would be to use the Table Browser. Please see this previously-answered mailing list question for instructions on how to do so: https://lists.soe.ucsc.edu/pipermail/genome/2012-April/028884.html. 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 varun gupta Sent: Wednesday, May 16, 2012 1:17 PM To: [email protected] Subject: [Genome] ucsc genes Hi So i am interested in finding all the ucsc genes in UCSC known gene database. It would also be nice if you could tell me where is this database(not like going on to tables and selecting known genes etc). Moreover after finding all the ucsc genes what is the best way i can convert these ucsc gene names into common gene names like for uc003axi.2 it is RPL3 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
