Hello, You can use the Table browser to obtain this information. http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
General query path for human: 1) navigate to target assembly, then select track "UCSC Genes" 2) set region=genome and paste in the identifier "SMPD1" 3) select output format "selected fields from primary and related tables" and name output file for download 4) submit query, then on the next form, scroll down and add in the tables kgTargetAli and knownCanonical, submit, then pick the fields to include in the output. As an example using hg19, relevant fields would include: hg19.knownGene.name hg19.kgTargetAli.qSize hg19.kgTargetAli.qStart hg19.kgTargetAli.qEnd hg19.kgTargetAli.blockCount hg19.kgTargetAli.blockSizes hg19.kgTargetAli.qStarts hg19.kgXref.geneSymbol hg19.knownCanonical.transcript Use the "describe table schema" tool to see the table field data definitions. For some, additional definations are in this FAQ (example: kgTargetAli is "PSL" format in the FAQ). http://genome.ucsc.edu/FAQ/FAQformat.html There can be multiple transcripts representing any gene. As a general rule, the longest transcript is selected as the canonical. Because your focus is on a single gene, examining all transcripts and picking which to use is probably worth examining. For context, pull up the gene in the Assembly browser window (type the gene name into the gene search box) and review the overall gene structure there. I found that using the track UCSC Genes in hg19, the gene SMPD1 has five transcripts and "uc001mcw.2" is the canonical. I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support On 7/13/10 2:29 AM, [email protected] wrote: > i want to information for the in P475T and L351R/fsR600 exons correct > position in the smpd1 gene total sequence. niemann pick disease ----smpd1 > gene > > what is the 1. P475 T > 2.L351R/fsR600 these two are take from patients (may be > chromosomes are mutations), i want to correct position in the smpd1 gene > exon in the total sequence of smpd1. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
