Hi, Sorry for disturbing.
When I download the UCSC gene 'knownGene' table. I am confused by the 'txstart' and 'txend' items. In the description, 'txstart' means 'Transcription start position'. I think for genes who are on 'minus' strand, the 'transcription start site' may have upper numbered coordinates than 'end site'. So for minus-strand genes 'txend's are Transcription start sites(TSS) and for plus-strand genes 'txStart's are Transcription start sites(TSS). Is that right? Example from UCSC gene: #name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID uc001aaa.2 chr1 + 1115 4121 1115 1115 3 1115,2475,3083, 2090,2584,4121, uc001aaa.2 uc009vip.1 chr1 + 1115 4272 1115 1115 2 1115,2475, 2090,4272, uc009vip.1 uc009vis.1 chr1 - 4268 6628 4268 4268 4 4268,4832,5658,6469, 4692,4901,5805,6628, uc009vis.1 uc001aag.1 chr1 - 5658 7231 5658 5658 4 5658,6469,6738,7095, 5810,6628,6918,7231, uc001aag.1 uc009vjc.1 chr1 - 6720 7614 6720 6720 2 6720,7095, 6918,7614, uc009vjc.1 Thank you very much and happy new year! Hongyan Hongyan Wang Postdoctoral Fellow The Methodist Hospital Research Institute Office: 713-441-2820 [email protected] Methodist. Leading Medicine. Recognized by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE magazine's "100 Best Companies to Work For" list six years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
