<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div apple-content-edited="true" class="">Hi Luke,</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">I think there are a few things going on here to explain that will hopefully resolve your issue.</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">Firstly the annotation for CHD2 against GRCh38 was from a re-annotation of the genome. That gene was not simply lifted over from the previous assembly but was a fresh call (supported by NM_001271.3 as detailed for the longest transcript from [1]). The line "This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates" is created by lifting over the coordinates from GRCh38 to GRCh37. It is not saying you can find the same gene in GRCh37 at this position. That's why we have the additional link to ENSG00000173575 in GRCh37 to ensure we can send you to the correct locus.</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">Does that help?</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">All the best,</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">Andy</div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">1 - <a href="http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000173575;r=15:92900189-93028005;t=ENST00000394196" class="">http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000173575;r=15:92900189-93028005;t=ENST00000394196</a></div><div apple-content-edited="true" class=""><br class=""></div><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">------------<br class="">Andrew Yates - Genomics Technology Infrastructure Team Leader<br class="">The European Bioinformatics Institute (EMBL-EBI)<br class="">Wellcome Genome Campus<br class="">Hinxton, Cambridge<br class="">CB10 1SD, United Kingdom<br class="">Tel: +44-(0)1223-492538<br class="">Fax: +44-(0)1223-494468<br class="">Skype: andy.yates.ebi</div><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><a href="http://www.ebi.ac.uk/" class="">http://www.ebi.ac.uk/</a><br class="">http://www.ensembl.org/</div></div></div></div></div>
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<br class=""><div style=""><blockquote type="cite" class=""><div class="">On 22 Apr 2016, at 09:55, Luke Goodsell <<a href="mailto:Luke.Goodsell@ogt.com" class="">Luke.Goodsell@ogt.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Are misconversions by the Assembly Converter being fixed?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On the GRCh38 EnsEMBL browser page for CHD2 (<a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575" style="color: purple; text-decoration: underline;" class="">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575</a>), it states “This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates.” However, the GRCh37 page (<a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575</a>) shows the co-ordinates as “Chromosome 15: 93,426,526-93,571,237”.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">These co-ordinates are the same as the “Assembly Converter” conversion, from which I assume the browser takes its data.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Kind regards,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Luke<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><p style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Verdana; font-size: 10pt; color: rgb(102, 102, 102);" class=""><b class="">Disclaimer</b></p><p style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Verdana; font-size: 8pt; color: rgb(102, 102, 102);" class="">The information contained in this communication from the sender is confidential. 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