Error retriving complete transcripts from ENSEMBL

We are using the latest production release of Jalview. A student did the following:

Having found a variant they wanted to visualise in exon ENSE00003533602 in the BRCA1 gene ENSG00000012048 transcript BRCA1-001 ENST00000357654

retrieved the genomic sequence from ENSEMBL using the Fetch Sequences option. The transcript was retrieved but was missing the desired exon.

The exon is clearly included in the ENSEMBL website (both Gr38 and Gr37)

Any ideas as to why this exon is not seen? It is very large (3426 aa), and trying to directly retrieve it with the Fetch Sequences also fails.

…d

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee

Hello David,

The short answer is that exon ENSE00003533602 does not appear in the GFF exon features for the gene retrieved by Jalview:

http://rest.ensembl.org/overlap/id/ENSG00000012048?content-type=text/x-gff3&feature=exon

Why that is different from a view on the Ensembl web site will need a bit of further investigation.

Thanks,

Mungo

···

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 21 March 2017 15:25:38
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Error retriving complete transcripts from ENSEMBL

We are using the latest production release of Jalview. A student did the following:

Having found a variant they wanted to visualise in exon ENSE00003533602 in the BRCA1 gene ENSG00000012048 transcript BRCA1-001 ENST00000357654

retrieved the genomic sequence from ENSEMBL using the Fetch Sequences option. The transcript was retrieved but was missing the desired exon.

The exon is clearly included in the ENSEMBL website (both Gr38 and Gr37)

Any ideas as to why this exon is not seen? It is very large (3426 aa), and trying to directly retrieve it with the Fetch Sequences also fails.

…d

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee

I think there is a typo for ENSE00003522602 which does seem to appear as an exon feature in Jalview?

Mungo

···

Email signature

University of Dundee shield logo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017


From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 21 March 2017 15:25:38
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Error retriving complete transcripts from ENSEMBL

We are using the latest production release of Jalview. A student did the following:

Having found a variant they wanted to visualise in exon ENSE00003533602 in the BRCA1 gene ENSG00000012048 transcript BRCA1-001 ENST00000357654

retrieved the genomic sequence from ENSEMBL using the Fetch Sequences option. The transcript was retrieved but was missing the desired exon.

The exon is clearly included in the ENSEMBL website (both Gr38 and Gr37)

Any ideas as to why this exon is not seen? It is very large (3426 aa), and trying to directly retrieve it with the Fetch Sequences also fails.

…d

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee