Hi there, If you're looking for this information for ALL coding regions in the human genome, then you're best off downloading a slew of files from the Download site (http://hgdownload.cse.ucsc.edu/downloads.html), including some known gene set (UCSC Genes, Ensembl, RefSeq, etc), and doing a big slew of informatics to obtain the portion of your downloaded data that overlaps with some gene in the gene set.
On the other hand, if a large set of coding regions would get you started on some proof-of-concept work, then you could obtain your data more easily with the table browser. There is a user's guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. Briefly, what I'd do is (1) pick a gene set (e.g. UCSC Genes, Ensembl, RefSeq,...) and select the corresponding track in the table browser, (2) pick a chromosome such as chr22 (small as chromosomes go, but perfectly large for proof of concept work), and then use the table browser Filter button together with the gene track to select the coding regions on chr22, and (3) select custom track in the output format slider to make yourself a custom track of these coding regions. Then, for example, to get the mRNA that overlap the coding regions on this chromosome, select the mRNA track on the table browser, and then use the intersect button to intersect the mRNA track with your custom track. Or, for the conservation, do the same trick with the conservation track to select the conservation of each of the bases overlapping your custom track. I hope this helps you get started. Cheers, Melissa > -------- Original Message -------- > Subject: [Genome] UCSC information > Date: Tue, 22 Jun 2010 18:34:23 -0400 > From: Tychele <[email protected]> > To: [email protected] > > Hi, > > I am looking for some data from the genome browser. The information I > am looking for is specific to all coding regions of the human genome. > I would like to collect the following information: > > Gene Name > mRNA > Amino Acid Position > Amino Acid Residue > Conservation > Codon > Codon Position 1 Conservation > Codon Position 2 Conservation > Codon Position Conservation 3 > List gene name > Accession Number of mRNA > position of the amino acid in the protein > One letter code for amino acid > list the species it's conserved in > The codon for example CCC > list the species the first base of the codon is conserved in > list the species the second base of the codon is conserved in > list the species the third base of the codon is conserved in > > Is there somewhere I can download this information from the genome > browser or do you have a suggestion on how to most efficiently find > this information? Your response is appreciated. > > Sincerely, > > Tychele Turner > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
