Hi Ivan, Thank you for reporting this issue. We have added this issue to our list of things to do. If you have further questions, please contact the mailing list: [email protected].
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Ivan Adzhubey <[email protected]> Date: Thu, Aug 18, 2011 at 3:14 PM Subject: [Genome] Human mitochondrial (chrM) genes use standard genetic code? To: [email protected] Hi, I have noticed that CDSes for transcripts on hg19/chrM are sometimes translated in Genome Browser using standard genetic code, while the correct vertebrate mitochondrial code variant is used in other places. Specifically, Genome Browser web GUI correctly uses mitochondrial code for chrM transcripts, e.g.: http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrM:14762-15888&hgsid=207890589&db=hg19 While following this gene (uc004coy.2) link in the GUI and then clicking on "Protein (186 aa)" link under "Sequence and Links to Tools and Databases" on the gene description page: http://genome.ucsc.edu/cgi-bin/hgGene?hgsid=207890589&hgg_do_getProteinSeq=1&hgg_gene=uc004coy.2 ...displays incorrect protein sequence obtained using the standard code. Also, accessing protein sequence for uc004coy.2 transcript via knownGenePep table in the Table Browser outputs the same incorrect standard code-derived sequence. Moreover, it looks like human mitochondria-encoded genes annotated on chrM were actually predicted using the standard code. When translated using vertebrate mitochondrial code instead, these reading frames display numerous in-frame termination codons, making the CDS annotations look rather dubious. Is this a known issue and if so, are there any plans for a fix? --Ivan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
