Hi Hersh, Have you taken a look at our conservation/alignment tracks? The Conservation track on hg19 aligns 46 species. You might also look at TransMap and maybe Other RefSeq.
For your second question, the example you cite, 'A8MVU8', seems to be a protein ID (not a gene name). You'll probably have to make a key for yourself, since the sequence output will only show the UCSC Gene Names - as you saw. So, in the table browser, select "output format: selected fields from primary and related tables". On the subsequent page, check only 'name' and 'proteinID' boxes and then get output. You'll now have a list of what proteinID matches to which UCSC gene name in the sequence output you got. And just in case -- if you want to get the common gene name (gene symbol) in your key too, use the instructions above, but in addition to selecting 'name' and 'proteinID', also select "geneSymbol" from the hg19.kgXref table. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 1/7/12 8:16 AM, Hersh wrote: > Hi All, > > I have a list of genes which are common in few species. I want to extract > genomic sequence for all the genes in these organisms and do multiple > alignment to see conserved regions for same gene across the genome. Is > there anyway to do this is one go? > > I know I can extract DNA seq via table browser and uploading list of genes > in identifiers names/accessions. However there is a problem with this. I > have a gene list in format like 'A8MVU8' but whenever I upload this list > and choose refgene or UCSC genes output doesn't give same gene name. Output > format shows gene name is ucsc or refgene format. This is causing some > confusion. I am not sure whether gene seqs are in same order as genelist > uploaded in the table browser. Is there any better way of doing this? > > KIF18A > Regards > Hersh > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
