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
