Hi Sheila, The table browser is a great place to start.
In the Table browser, start with the UCSC Genes track and perform a join with the kgAlias table. Select output type = selected fields. The field "kgAlias.alias" will have the alternate names we know about. You can also download coordinates and the other data types you mention with similar joining methods to the other linked tables. Genes are grouped by having the same coding region. UTR regions may differ. Please be aware that not all genes will be in our data track. We exclude genes that have not been mapped to the reference assembly or that fail other quality checks. Please see this track's description page for details about how we create this non-redundant data set. An alternate recommended reference for this data is the Human Genome Nomenclature Committee's downloads. You may find genes here that we have excluded. http://www.genenames.org/data/gdlw_index.html Table browser help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Please let us know if we can help with more customized query details, Jennifer Jackson UCSC Genome Bioinformatics Group On Fri, Jan 30, 2009 at 10:17 AM, Sheila Reynolds <[email protected]> wrote: > Hi, > > I've been trying to figure out how to get this from the Table browser but > have not been successful so far. Basically, what I'd like to get is a text > file with one row for every human gene that anyone has ever identified, with > all of the various names that this gene has had in any database known to the > UCSC browser. (If this same file could also be made to include the > chromosome, txStart, and all of the exon positions as well that would be > even better.) > > thanks ! > > Sheila > > > For example, this is the information that is listed in part of the page at > > http://genome.ucsc.edu/cgi-bin/hgGene?db=hg18&hgg_gene=uc004dkf.1&hgg_chrom=chrX&hgg_start=48317779&hgg_end=48321748 > > * [image: > -]<http://genome.ucsc.edu/cgi-bin/hgGene?hgsid=120834283&hgg_section_synonym_close=1#synonym> > Other > Names for This Gene * > *Alternate Gene Symbols:* NM_006743, NP_006734, P98179, RBM3_HUMAN, RNPL, > uc004dke.1 > *UCSC ID:* uc004dkf.1 > *RefSeq Accession: * > NM_006743<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=120834283&g=refGene&i=NM_006743&c=chrX&o=48317779&l=48317779&r=48321748&db=hg18> > *Protein: P98179 <http://www.expasy.org/cgi-bin/niceprot.pl?P98179>* (aka > RBM3_HUMAN) > *CCDS:* > CCDS14301.1<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=120834283&g=ccdsGene&i=CCDS14301.1&c=chrX&o=48317779&l=48317779&r=48321748&db=hg18> > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
