Hello, The txStart and cdsStart coordinates in the UCSC Genome Browser tables always refer to the lowest-numbered coordinate (and txStart and cdsStart to the highest-numbered coordinate). This greatly simplifies the arithmetic that is done to display the genes. You can think of start number as "the beginning of the gene in the display" and the end number as "the end of the gene in the display."
If the negative strand is specified, txStart and cdsStart are actually referring to the end of transcription and the end of the coding region when reading the sequence 5' to 3'. You should also be aware of the coordinate system used in the Genome Browser: 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 11/16/11 6:17 AM, Ma, Yiyi wrote: > Hi UCSC Genome Professionals, I have a question with regard to strand > issue of table of RefSeq Genes. Did you consider the strand > difference and do the coordinates in the table is only on forward > strand without any consideration of the strand issue? > > I saw some genes with negative strand but their txStart and cdsStart > coornidates are still smaller than txEnd and cdsEnd. According to my > understanding, those genes on negative strand should have smaller > txEnd than txStart. For example, when txStart is (-3) to txEnd (-1) > and the coordinates in your table should be txStart is 3 and txEnd is > 1. > > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
