Hello Wensheng, All genes are transcribed from the 5'->3' end of a genomic strand. Alignments are also generated in this mannor, so that the most 5' exon is first and the most 3' exon is last.
However, how the data is stored in the database should also be understood. Coordinates are always stored smallest->largest based on the positive strand. That means for genes that align to the negative strand, the txStart is actually the end of the alignment and the txEnd is actually the start of the alignment. This is also true for all other coordintes (cdsStart/end, exons, etc.). In addition, the coordinate system is "zero-based, half-open". It is important to understand if you are using the data in the tables or flat files. An explaination is here: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Zhang Wensheng" <[email protected]> wrote: > From: "Zhang Wensheng" <[email protected]> > To: [email protected] > Sent: Friday, February 5, 2010 9:10:07 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] table "refGene" > > Hello, > > I have a question about the table "refGene" in the group "genes and > gene prediction track". Are the positions (txStart, txEnd, and > others) counted from the 5 prime end of the genome for the positive > strand and counted from the 3 prime for the minus strand? > > > Thank you very much > > > Wensheng > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
