<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="">Dear Pankaj,<div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On 15 Jul 2015, at 22:36, Pankaj Agarwal <<a href="mailto:pankaj.agarwal.duke@gmail.com" class="">pankaj.agarwal.duke@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi,</div><div class=""><br class=""></div><div class="">I am working on a project where I need information on exon 16 of the HER2 (ERBB2) gene. I am using GRCh38 for my analysis. From a paper I found the Ensembl ID for this exon as ENSE00001121079. When I searched on Ensembl through BioMart, it does not show up.</div><div class=""><br class=""></div><div class="">I was wondering if the IDs for genes, exons have changed in the latest version of the genome (v 38). The ID that I have is from a paper that was published before v38 was release.</div></div></div></blockquote>It looks like the exon 16 of the ERBB2 gene has changed ID between Ensembl release 68 (<a href="http://jul2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:37752530-37922531;t=ENST00000269571" class="">http://jul2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:37752530-37922531;t=ENST00000269571</a>) and 69 (<a href="http://oct2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571" class="">http://oct2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571</a>). </div><span class=""><span class=""><div>This Ensembl exon id is now “ENSE00003629888” in the Ensembl release 80 GRCh37.p13 assembly (<a href="http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571" class="">http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571</a>) and Ensembl release 81 GRCh38.p3 assembly (<a href="http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571" class="">http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571</a>).</div><div>The Ensembl Gene ID has not changed and is still “<font color="#000000" class="">ENSG00000141736” as you can see from the Ensembl Gene history page: </font><a href="http://ensembl.org/Homo_sapiens/Gene/Idhistory?db=core;g=ENSG00000141736;r=17:37844167-37886679" class="">http://ensembl.org/Homo_sapiens/Gene/Idhistory?db=core;g=ENSG00000141736;r=17:37844167-37886679</a>.</div></span></span><div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><div class="">Additionally, is there a way to easily get the genome coordinates of a features if the Ensembl ID is known.</div></div></div></blockquote>Yes, this is possible using BioMart. For an Ensembl Gene or Transcript ID, You can use the “Ensembl Gene ID” or “Ensembl Transcript ID” filter in the <span style="widows: 1;" class="">“</span><span style="widows: 1;" class="">Input external references ID list</span><span style="widows: 1;" class="">” dropdown of the Gene filter section</span> and select the “Chromosome name”, Gene Start (bp) or Transcript Start(bp), Gene End (bp) or Transcript End(bp) and Strand attributes, For example: <a href="http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id%7Chsapiens_gene_ensembl.default.feature_page.chromosome_name%7Chsapiens_gene_ensembl.default.feature_page.start_position%7Chsapiens_gene_ensembl.default.feature_page.end_position%7Chsapiens_gene_ensembl.default.feature_page.strand&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id.%22ENSG00000141736%22&VISIBLEPANEL=resultspanel" class="">http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.chromosome_name|hsapiens_gene_ensembl.default.feature_page.start_position|hsapiens_gene_ensembl.default.feature_page.end_position|hsapiens_gene_ensembl.default.feature_page.strand&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000141736"&VISIBLEPANEL=resultspanel</a></div><div class=""><br class=""></div><div style="widows: 1;" class="">For an Ensembl Exon ID, You can filter on it using the “Ensembl Exon ID” filter in the “<span style="widows: 1;" class="">Input external references ID list</span>” dropdown of the Gene filter section. Then select the “Ensembl Exon ID”, “Exon Chr Start (bp)” and “Exon Chr End (bp) attributes from the structure attribute page. For example: <a href="http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.structure.ensembl_gene_id%7Chsapiens_gene_ensembl.default.structure.ensembl_transcript_id%7Chsapiens_gene_ensembl.default.structure.ensembl_exon_id%7Chsapiens_gene_ensembl.default.structure.exon_chrom_start%7Chsapiens_gene_ensembl.default.structure.exon_chrom_end%7Chsapiens_gene_ensembl.default.structure.rank&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_exon_id.%22ENSE00003629888%22&VISIBLEPANEL=resultspanel" class="">http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.structure.ensembl_gene_id|hsapiens_gene_ensembl.default.structure.ensembl_transcript_id|hsapiens_gene_ensembl.default.structure.ensembl_exon_id|hsapiens_gene_ensembl.default.structure.exon_chrom_start|hsapiens_gene_ensembl.default.structure.exon_chrom_end|hsapiens_gene_ensembl.default.structure.rank&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_exon_id."ENSE00003629888"&VISIBLEPANEL=resultspanel</a></div><div class=""><br class=""></div><div style="widows: 1;" class=""><br class=""></div><div style="widows: 1;" class="">Hope this helps,</div><div style="widows: 1;" class="">Regards,</div><div style="widows: 1;" class="">Thomas</div><div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><div class="">Thank you,<br class=""></div><div class=""><br class=""></div><div class="">- Pankaj<br clear="all" class=""><br class="">-- <br class=""></div><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">Pankaj Agarwal<br class=""></div><div class="">Cancer Bioinformatician</div><div class="">Data Analyst</div><div class="">Dept. of Surgery</div><div class="">Duke University</div><div class=""><br class=""></div></div></div></div></div></div></div>
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<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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