Hi Melissa, It looks like all the genes in the list you provided do exist in hg19 RefSeq Genes, except three. I looked these up genes up in NCBI and the records have been removed due to insufficient support for the transcript. NM_203407 (http://www.ncbi.nlm.nih.gov/nuccore/NM_203407.1?report=genbank) NM_173357 (http://www.ncbi.nlm.nih.gov/nuccore/NM_173357.2?report=genbank) NM_014221 (http://www.ncbi.nlm.nih.gov/nuccore/NM_014221.3?report=genbank)
If I understand what you are trying to do correctly, then yes you can get the alignments 'en masse' via our Table Browser. Click on "Tables" on the blue bar on the top of the main page and make the following selections: clade: Mammal genome: Human assembly: Feb. 2009 (GRCh37/hg19) group: Genes and Gene Prediction Tracks track: RefSeq Genes table: refGene region: genome (or if you only want to search chromosome X, select "position" & enter: chrX) identifiers (name/accessions): click 'paste list' or 'upload list' and provide your accessions or select your file to upload; click submit output format: CDS FASTA alignment from multiple alignment output file: if you would rather have the results saved to a file instead of displaying in the browser window, enter the name you would like the output file to have, otherwise, leave blank file type returned: plain text Click "get output". Select the formatting options you prefer and the organisms for which you'd like alignments; click "get output." Your results will be a list of the alignments at the locations of the genes in your list. For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form. It provides brief descriptions of the Table Browser controls. You can also see the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. I hope this is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/19/11 3:00 PM, Melissa A. Wilson Sayres wrote: > Hi there, > > I am working with the human X chromosome, and attempting to extract > alignments across several mammals using data from UCSC and tools in Galaxy. > > My problem is when I try to download to coordinates of the coding exons, > several genes show up, but all of the genes in the attached list give me > this error message: > > # No results returned from query. > > > However, when I click through the UCSC website, using the interactive RefSeq > Gene page, and follow the link for "CDS_FASTA_alignment" I can view the > mammalian alignment I want. > > Do you know why the server isn't giving me the coordinates? And, is there an > alternative way (perhaps through the UCSC server that I can extract the > alignments *en masse*, instead of one-by-one? > > Thank-you, > Melissa > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
