Hello Simanta, I'm having trouble with the link you sent but it looks like you were viewing this gene on mouse (mm9) from the UCSC genes track:
uc008ufs.2 (aka Faah) Probably the clearest way to see the coordinates you are asking about is to use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to view the main table housing the data behind the UCSC genes track. Once in the Table Browser select: clade: Mammal genome: Mouse assembly: mm9 group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene if you click the "describe table schema" button you'll see a description of the columns of this table (including txStart/End and cdsStart/End). To obtain these coordinates for a specific gene, click on "paste list" beside "identifiers (names/accessions)" and paste in your gene id (in this case uc008ufs.2). You can also paste in a list of genes. if you then choose: output format: all fields from selected table and click "get output" it will return a list of transcription and coding start and end sites as well as the other info in the knownGene table. If you want to restrict the output to only the coordinates choose "output format: selected fields from primary and related tables". Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 6/13/12 3:34 PM, sim path wrote: > Hi All > > I am trying to find the location of transcription start site of a gene in > the genome, I mean the genomic base number of the starting base. how to do > that. like in the link below what is the base position number in genome of > the starting base in that sequence, that is the "T" ...how to find that? > > link: > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=277869181&g=htcDnaNearGene&i=uc008ufs.2&c=chr4&l=115669260&r=115690507&o=knownGene&hgSeq.promoter=on&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit > > Thanks in advance ! > Simanta Pathak > UT Southwestern Med Center > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
