<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Beat<div>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.</div><div>Regards</div><div>Rhoda</div><div><br><div><div>On 19 May 2012, at 15:55, Beat Wolf wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="font-family: 'DejaVu Sans'; font-size: 9pt; font-weight: 400; font-style: normal; "><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">Hi,</div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">i'm a computer scientist and not a biologist, so perhaps i missed something about the DMD gene changing recently.</div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">I have an automated unit test for my application that uses biomart. It happens to test the DMD-001 transcript of the DMD gene.</div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">I<span style="color: rgb(31, 28, 27); ">n the 66 version of enembl, the UTR3 coordinates of the exon number 79 where:</span></div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><table border="0" cellspacing="2" cellpadding="0" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; "><tbody><tr><td><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-size: medium; color: rgb(31, 28, 27); ">31137345</span></div></td><td><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-size: medium; color: rgb(31, 28, 27); ">to 31140035</span></div></td></tr></tbody></table><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="color: rgb(31, 28, 27); ">which was correct. Now with the version 67 of ensembl, the UTR3 region in the same exon is:</span></div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><table border="0" cellspacing="2" cellpadding="0" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; "><tbody><tr><td><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-size: medium; color: rgb(31, 28, 27); ">31137345 to</span></div></td><td><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-size: medium; color: rgb(31, 28, 27); ">31137344</span></div></td></tr></tbody></table><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">Which can not be correct, because that means that UTR3 has a length of 1. The other numbers don't match up either.</div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">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.</div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">Greetings</div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">Beat Wolf</div><p style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">On Thursday 10 May 2012 10:58:58 Thomas Maurel wrote:<br></div><p style="white-space: pre-wrap; margin-top: 12px; margin-bottom: 12px; margin-left: 40px; margin-right: 40px; text-indent: 0px; "><span style="background-color: rgb(0, 0, 0); ">The latest Ensembl update (e!67) has been released : </span><a href="http://www.ensembl.org/"><span style="text-decoration: underline; color: rgb(0, 87, 174); background-color: rgb(0, 0, 0); ">http://www.ensembl.org/</span></a><br><br><span style="background-color: rgb(0, 0, 0); ">Here are some highlights:</span><br><br><span style="background-color: rgb(0, 0, 0); ">Human: The patches for the human genome assembly have been updated to GRCh37.p7, </span><span style="background-color: rgb(0, 0, 0); ">Human somatic variants from COSMIC have been updated to release 58 and we now provide the 1000 genomes phase 1 genotype data.</span></p><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 40px; margin-right: 40px; text-indent: 0px; "><br>New species: Nile tilapia (Oreochromis niloticus).<br><br>New genomes: The assemblies for Pig and Squirrel have been updated.</div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 40px; margin-right: 40px; text-indent: 0px; "><br>A complete list of the changes in release 67 can be found at <a href="http://www.ensembl.org/info/website/news.html"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.org/info/website/news.html</span></a><br><br>For the latest news on the ensembl project visit our blog at <a href="http://www.ensembl.info/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/</span></a><br></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="background-color: rgb(0, 0, 0); "><br></span></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; ">The release blog post can be viewed here : <a href="http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/</span></a></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="background-color: rgb(0, 0, 0); ">Best regards,</span></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="background-color: rgb(0, 0, 0); ">Thomas Maurel</span></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(0, 0, 0); ">--</span></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(0, 0, 0); ">Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge - CB10 1SD - UK</span></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; text-indent: 0px; "><br><br></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></span></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Ensembl Production Project Leader,</div></div><div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span></div></span> </div><br></div></body></html>