Hello, The Table browser can extract this data.
The general query path would be: 1) go to http://genome.ucsc.edu/cgi-bin/hgTables 2) set clade/genome/assembly for the Rat assembly 3) choose a track to base the exon data on from the group "Genes and Gene Prediction Tracks". RefSeq Genes in an example. You could use the mRna track from the group "mRna and EST tracks", but the exon-type data would be called "blocks" (meaning alignment blocks) and the confidence in the data would be lower, since the Genbank mRna sequences are not curated the way that the RefSeq sequences are and the BLAT alignment method is slightly less sensitive (there could be missing terminal exons, or gaps causing an exon to be split into two blocks, etc.). 4) set region=genome or limit to a particular position 5) filter by identifiers in the track #3 above, if desired 6) choose output as sequence (fasta) or BED or Custom track, submit 7) on following pages choose "exons" (or blocks) 8) name and download data or leave in browser (for Custom track) Some more help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#OutputFormats http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/FAQ/FAQformat Please let us know if you need further assistance, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Li Zhihui" <[email protected]> wrote: > From: "Li Zhihui" <[email protected]> > To: [email protected] > Sent: Thursday, January 21, 2010 1:34:35 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Rat Exon sequence > > Hi all, > > I am trying to get the exon sequence of Rat, is there any good > location to get that out? > > Regards > Sol > > _________________________________________________________________ > Windows 7: Find the right PC for you. Learn more. > http://windows.microsoft.com/shop > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
