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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hello,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I'm
using BioMart to fetch all protein coding portions of all exons of all
transcripts of my favourite gene (Ensembl Genes 67, Homo sapiens genes
GRCh37.p7). In the past, 'Genomic coding start' and 'Genomic coding end' would
give me all exon coordinates minus UTRs. However, now it seems to return the
UTR coordinates as well. Perhaps this is related to the UTR issue reported by
Beat below?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thank
you.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Simon.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Rhoda
Kinsella<br>
<b>Sent:</b> Tuesday, May 22, 2012 3:38 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Ensembl release 67 is out!<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Beat<o:p></o:p></p>
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<p class=MsoNormal>We are currently looking into why this has occurred but it
is certainly a bug in our mart databases. I will respond as soon as we have a
fix in place. Thank you for reporting this and apologies for any inconvenience.<o:p></o:p></p>
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<p class=MsoNormal>Regards<o:p></o:p></p>
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<p class=MsoNormal>Rhoda<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On 19 May 2012, at 15:55, Beat Wolf wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>Hi,<o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>i'm a computer scientist and not a biologist, so perhaps i missed
something about the DMD gene changing recently.<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>I have an automated unit test for my application that uses
biomart. It happens to test the DMD-001 transcript of the DMD gene.<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>I</span><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:#1F1C1B'>n the 66 version of enembl, the UTR3 coordinates of the exon
number 79 where:</span><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'><o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137345</span><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>to 31140035</span><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:#1F1C1B'>which was correct. Now with the version 67 of ensembl, the UTR3
region in the same exon is:</span><span style='font-size:9.0pt;font-family:
"DejaVu Sans","serif";color:black'><o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137345 to</span><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137344</span><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>Which can not be correct, because that means that UTR3 has a
length of 1. The other numbers don't match up either.<o:p></o:p></span></p>
</div>
<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>Did the DMD gene change? Is the information stored differently in
ensembl? What values do i need to reconstruct the true UTR3 region? Or is this
a bug in the new ensembl version. If yes, how many other genes are affected?
Currently i will stay on the 66 version thanks to the archives, but i have some
connection issues with it, it seems to be much less stable than the 67 version.<o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>Greetings<o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"DejaVu Sans","serif";
color:black'>Beat Wolf<o:p></o:p></span></p>
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<p style='margin:0in;margin-bottom:.0001pt;white-space:pre-wrap'><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:black'> </span><span
style='font-size:9.0pt;font-family:"DejaVu Sans","serif";color:#1F497D'><o:p></o:p></span></p>
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