Hi Gwen, I looked at NM_020407 (RHBG) in hg18 and hg19 (if you were you looking at a different assembly, please let me know) and the reading frame for exon10 is displaying as 0 in the browser. So, the table is correct by listing the exon frame as 0 for exon 10.
Here is a great explanation on exon frame from a previously answered question: https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group [email protected] wrote, On 04/14/10 05:10: > Hi, > > > > I encountered a incorrect exon frame in NM_020407 (RHBG). It is correct > in the Genome Browser, but when I get the data from hgTables I get > following information: > > > > #bin name chrom strand txStart txEnd cdsStart cdsEnd > exonCount exonStarts exonEnds id name2 > cdsStartStat cdsEndStat exonFrames > > 1764 NM_020407 chr1 + 154605626 154621633 > 154605664 154621261 10 > 154605626,154613715,154614404,154614666,154617761,154618220,154618482,15 > 4619162,154620941,154621192, > 154605851,154613902,154614555,154614814,154617928,154618358,154618616,15 > 4619284,154621016,154621633, 0 RHBG cmpl cmpl > 0,1,2,0,1,0,0,2,1,0, > > > > > > Exon 10 (colored in red) should have an exon frame of '1', but in the > output it says '0'. I'm using these data to translate the genes. Is > there a list of genes where people have encountered these problems > before or will there be an update where these kind of errors are fixed? > > > > > > Sincerely, > > Gwen Weustink > > Radboud University Nijmegen Medical Centre > > > > > Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het > handelsregister onder nummer 41055629. > The Radboud University Nijmegen Medical Centre is listed in the Commercial > Register of the Chamber of Commerce under file number 41055629. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
