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
