Hi Dandan, Your description is exactly right for genes on the positive strand. So, the coordinates for UTRs for + strand genes are:
5'UTR: txStart to cdsStart 3'UTR: cdsEnd to txEnd For - strand genes, the logic is flipped. "Start" is still the lower number, so "start" refers to the 3' end and "end" refers to the 5' end: 5'UTR: cdsEnd to txEnd 3'UTR: txStart to cdsStart chr21 33104005 33104431 5' utr chr21 33073071 33073142 3' utr You should also be aware that the Genome Browser table coordinates are zero-based, half-open: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/23/12 12:42 AM, 海丹 严 wrote: > Dear sir, > > > I have tried to find the 5'UTR Exons and u3'UTR Exons of hg19 > descriptions in table browser when I choose output format of BED. But > I didn't find them. I think the start position of 5'UTR Exons is > txStart, the end position of 5'UTR Exons is cdsStart, the start > position of 3'UTR Exons is cdsEnd, the end position of 3'UTR Exons > is txEnd. I want to ensure what I think is right or not. > > > > dandan. _______________________________________________ Genome > maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
