Hi, I am looking at the downloaded tRNAs.txt file for hg19, and there is 1 base difference associated with End position on chromosome (but not Start position) for tRNA entries.
One example is chr1.tRNA136-AsnGTT, for which the tRNAs.txt file (downloaded yesterday, with a time stamp of 2012-2-13) showed the following record: 713 chr1 16847079 16847153 chr1.tRNA136-AsnGTT 1000 - Asn GTT No canonical tRNA introns</BLOCKQUOTE> 77.65 http://gtrnadb.ucsc.edu/Hsapi19/ http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.ht ml#Homo_sapiens_chr1.trna136-AsnGTT So considering the 0-based position information in annotation files, I was expecting that this gene will map to chr1:16847080-16847154. However, on genome browser, this gene (chr1.tRNA136-AsnGTT) is shown as chr1:16847080-16847153 <http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=262084701&db=hg19&position=chr1%3A16847080-16847153>, which is different for 1 base at the End position. I did notice that the tRNA track on genome browser display shows 2012-02-02 as the updated date. Is this the reason for this discrepancy, or there is something I misunderstood from the tRNAs.txt file? Thank you, Jun _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
