Hi again, There was a typo in my first sentence. I meant to say:
The txStart and cdsStart coordinates in the UCSC Genome Browser tables always refer to the lowest-numbered coordinates (and cdsEnd and txEnd to the highest-numbered coordinates). -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/22/11 11:45 AM, Brooke Rhead wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
