Hi Hao, The names you list are isoforms of the same gene. In the genome browser you can see that though they have the same transcription start and end, they are different from each other in the number and location of their exons. If you are looking for the canonical set of genes, I suggest using the knownCanonical table here: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/6/10 11:01 AM, [email protected] wrote: > Dear Colleague, > > > > I downloaded the UCSC known Gene file from here > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz > > How should I interpret the similar entries with similar gene start positions? > > name chrom strand txStart txEnd > uc009vit.1 chr1 - 4268 9622 > uc009viu.1 chr1 - 4268 9622 > uc001aae.2 chr1 - 4268 9622 > uc009viv.1 chr1 - 4269 19221 > > Are these corresponding to the same genes or different genes? > > Thanks, > Hao Zheng > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
