Hi Yuan, Per your screenshot, the number 1189290 is refering to the base (A) listed directly below it, not the one to the right of it. So, the starting T is indeed located at 1189292 (i.e. and the fourth base in the sequence, A, is showing at 1189295).
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 11/27/11 8:06 PM, Yuan Jian wrote: > thanks, > please input position chr1:1,189,287-1,189,302 > I attached the figure. you can see it starts 1198291 instead of 1189292. > Yu > > > ________________________________ > From: Brooke Rhead<[email protected]> > To: Yuan Jian<[email protected]> > Cc: UCSC<[email protected]> > Sent: Monday, 28 November 2011 10:57 AM > Subject: Re: [Genome] bug? > > Hi, > > On the GRCh37/hg19 assembly, the graphic for UBE2J2 in the RefSeq Genes track > appears to be correctly displayed, starting at base 1189292. It is a little > confusing when you are zoomed in very closely, because the box that denotes > the gene begins at the tick mark that is labeled 1189291. However, the box > is drawn only to the right of the tick mark, and it is not meant to indicate > that the gene covers 1189291. > > In case that was confusing: base 1189291 is an "A", and it is not included > in the gene. Base 1189292 is a "T", and it is included in the gene. > > I hope this helps explain what you are seeing! If you have further > questions, please contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/25/11 7:42 PM, Yuan Jian wrote: >> Hi >> gene UBE2J2 starts at 1189292, but in genome browser it starts at 1189291 (I >> found it when zooming in). >> >> BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END >> QUERY START END TOTAL >> ----------------------------------------------------------------------------------------------------- >> browser | 2389 100.0% 1 - 1189292 1209234 >> NM_194458 1 2389 2396 >> _______________________________________________ >> 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
