Hello, The Table browser can provide this information. http://genome.ucsc.edu/cgi-bin/hgTables Help links are in the top paragraph.
Basic query path would be: 1) Set the clade, genome, assembly, group=Gene and Gene Predictions, track=RefSeq Genes. 2) The default table has the genomic coordinates of the RefSeq sequence alignments. Click on "describe table schema" to view example data. 3) To limit output based on RefSeq Transcript IDs, paste or upload the IDs into the identifiers filter 4) Configure output format to be complete table or only selected fields 5) Name file and download as gzip Some help to interpret the file format and coordinate systems: http://genome.ucsc.edu/FAQ/FAQformat#format9 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Jennifer Jackson UCSC Genome Bioinformatics Group Anna Kosubek wrote: > Hello, > > is there a fast way to get the scaffold-number (and strand) that describes > the position of the stop-codon / start of the 3´UTR of a X. tropicalis > gene by using a RefSeq Transcript ID e.g. NM_001078970? > I need the scaffold-numbers for 3´UTR of about 2000 tropicalis genes, in > order to analyse micro array data (Affimetrix) for motifs in the 3´UTR, so > is there also a possibility to enter a list of RefSeq Transcript IDs and > receive a list of the according scaffold-position? > > Thanks a lot > > Ania > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
