[ensembl-dev] HER2 Exon 16 ID and Coordinates in GRC38

[Thomas Maurel]

Dear Pankaj,

> On 15 Jul 2015, at 22:36, Pankaj Agarwal <pankaj.agarwal.duke at gmail.com> wrote:
> 
> Hi,
> 
> 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.
> 
> 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.
It looks like the exon 16 of the ERBB2 gene has changed ID between Ensembl release 68 (http://jul2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:37752530-37922531;t=ENST00000269571 <http://jul2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:37752530-37922531;t=ENST00000269571>) and 69 (http://oct2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571 <http://oct2012.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571>). 
This Ensembl exon id is now “ENSE00003629888” in the Ensembl release 80 GRCh37.p13 assembly (http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571 <http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571>) and Ensembl release 81 GRCh38.p3 assembly (http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571 <http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141736;r=17:39615891-39785892;t=ENST00000269571>).
The Ensembl Gene ID has not changed and is still “ENSG00000141736” as you can see from the Ensembl Gene history page: http://ensembl.org/Homo_sapiens/Gene/Idhistory?db=core;g=ENSG00000141736;r=17:37844167-37886679 <http://ensembl.org/Homo_sapiens/Gene/Idhistory?db=core;g=ENSG00000141736;r=17:37844167-37886679>.
> 
> Additionally, is there a way to easily get the genome coordinates of a features if the Ensembl ID is known.
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 “Input external references ID list” dropdown of the Gene filter section and select the “Chromosome name”, Gene Start (bp) or Transcript Start(bp), Gene End (bp) or Transcript End(bp) and Strand attributes, For example: 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 <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>

For an Ensembl Exon ID, You can filter on it using the “Ensembl Exon ID” filter in the “Input external references ID list” 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: 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 <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>


Hope this helps,
Regards,
Thomas
> 
> Thank you,
> 
> - Pankaj
> 
> -- 
> Pankaj Agarwal
> Cancer Bioinformatician
> Data Analyst
> Dept. of Surgery
> Duke University
> 
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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