Hi Yohan, It would be extremely difficult to add a column to this table at this point. It is one of several defined formats used in the Genome Browser (see http://genome.ucsc.edu/FAQ/FAQformat.html, "GenePred table format").
However, you might be interested in looking at the kgTxInfo table. It contains all of the information displayed under the "Gene Model Information" heading on the UCSC Genes details pages, which includes classification of each gene as "coding, noncoding, antisense or nearCoding." A detailed description of the kgTxInfo fields is here: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_txInfoDescription=1 I hope this is helpful. -- Brooke Rhead UCSC Genome Bioinformatics Group On 08/09/11 06:07, Lee, Yohan (NIH/NIMH) [C] wrote: > Dear Vanessa and Brooke, > > Thank you so much for your assistance and clarification, I completely > understand it now. > Both of you were so complete in your answers! Thank you! > > I am wondering if it would be worthwhile to place in the schema a column which delineates which exons are non coding v coding. I am thinking this will become more relevant as the number of non coding biologically relevant RNAs are being revealed so rapidly in the literature. > > Thanks, > Yohan > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Tuesday, August 09, 2011 12:20 AM > To: Lee, Yohan (NIH/NIMH) [C] > Cc: [email protected] > Subject: Re: [Genome] hg18; ucsc genes, refseq genes; > chr2:1,731,486-1,832,226 exon count v coding exon count > > Hello Yohan, > > You are correct; the coordinates that Vanessa referenced are for > uc002qxd.2 on hg19. You are also correct that the corresponding > exonEnds are 2001119,2057895,2176760,2288275,2335045. (The exonStarts > were accidentally pasted twice!) Sorry for the confusion. > > It sounds like your understanding is correct, but if you have any > further questions, please feel free to write back to [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 08/08/11 06:48, Lee, Yohan (NIH/NIMH) [C] wrote: >> Hi Vanessa, >> >> Thank you for such a detailed response, I think I understand now. >> Just for clarification's sake I have a few confirmation questions. >> >> 1) I wanted to confirm that you were referencing hg19 for the gene >> b/c I found the coordinates you mentioned for the hg19 version of this gene > and not the hg18 version that I was referencing. >> 2) You wrote: >> The remaining 5 exons that are non-coding >> begin after the cdsEnd (1983549) which have the exonStarts: >> 2000962,2057749,2176643,2288175,2334738 and their corresponding >> exonEnds: 2000962,2057749,2176643,2288175,2334738. >> >> Did you mean the corresponding exonEnds to be >> 2001119 for exonStart 2000962 >> 2057895 for exonStart 2057749 >> 2176760 for exonStart 2176643 >> 2288275 for exonStart 2288175 >> 2335045 for exonStart 2334738 >> The reason I ask is b/c your exonStarts and exonEnds are identical. >> Are they supposed to be identical b/c they are non-coding? >> >> Thanks, >> Yohan >> >> -----Original Message----- >> From: Vanessa Kirkup Swing [mailto:[email protected]] >> Sent: Saturday, August 06, 2011 11:29 PM >> To: Lee, Yohan (NIH/NIMH) [C] >> Cc: [email protected] >> Subject: Re: [Genome] hg18; ucsc genes, refseq genes; >> chr2:1,731,486-1,832,226 exon count v coding exon count >> >> Hi Yohan, >> >> That is a very good question. In the browser, the non-coding exons are >> displayed in shorter blocks and coding exons are represented as taller >> blocks. In some cases where there is a UTR and a coding region the >> exon will be display as a mixture (short and tall). This means that >> the non-coding and coding regions are located in the the exon and are >> counted as a coding exon. >> >> In this case the 5 non-coding exons are at the end which can be seen >> in this session (the first one is a taller block which means it is >> coding): >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=hg19_5_coding_redmine%234832 >> >> >> In the table browser, determining the locations of the non-coding >> blocks is a bit trickier. For uc002qxd.1 you need to first look at the >> cdsStart, and exonStarts. In this case the cdsStart (1795638) is after >> the first exonStarts (1792886). This means that that the first exon is >> a mixture non-coding and coding because of the UTR. In this case, the >> exon is counted as coding. The remaining 5 exons that are non-coding >> begin after the cdsEnd (1983549) which have the exonStarts: >> 2000962,2057749,2176643,2288175,2334738 and their corresponding >> exonEnds: 2000962,2057749,2176643,2288175,2334738. >> >> I hope this helps clarify coding and non-coding exons. If you have >> further questions, please contact the mailing list: >> [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: Lee, Yohan (NIH/NIMH) [C] <[email protected]> >> Date: Thu, Aug 4, 2011 at 8:36 AM >> Subject: [Genome] hg18; ucsc genes, refseq genes; >> chr2:1,731,486-1,832,226 exon count v coding exon count >> To: "[email protected]" <[email protected]> >> >> >> Hi, >> >> I am looking at the UCSC track for uc002qxd.1, and it shows exon >> count: 25, and coding exon count: 20. >> When I look at track Refseq and link, mRNA/Genomic alignments, there >> is no obvious way to determine which are the coding and non coding >> exons. I also downloaded the table browser for this section and cannot >> tell which of the 5/25 exons are not the coding ones. >> Please help. >> >> Thanks, >> Yohan >> _______________________________________________ >> 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
