Dear Mr/Ms/Miss, I am a postdoc in van Nimwegen's group from the Biozentrum (Basel). I am using the human gene annotations that are provided by the UCSC web site. In particularly, I am using the file refGene.txt that can be downloaded here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ I am a bit confused regarding how to interpret the frames of the exons. I have checked several cases (exons in the positive strand) in the UCSC genome browser and, surprisingly, I found that if the frame of the exon is 0 then the codon starts in the second base. If the frame is 1 then the codon starts in the first base. And finally, if the frame is 2 then, as expected, the codon starts in the third base. Is this normal? Am I doing something wrong? Any indication of how to interpret the frames or where to find a detailed description of the file refGene.txt would be very helpful. Thank you very much in advance for your time and your help. Best regards, Nacho Molina. _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
