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Hello,<br>
<br>
I'm using BIomart to access Ensembl. I'm interested in UTR regions,
so I'm using the following query:<br>
mart = useDataset("mmusculus_gene_ensembl", mart =
useMart("ensembl"))<br>
utrInfos <- getBM(attributes=c('ensembl_gene_id',
'ensembl_transcript_id',
'5_utr_start','5_utr_end','3_utr_end','3_utr_start','start_position','end_position','transcript_start','transcript_end'),
filters=c('ensembl_gene_id'),
values=c('ENSMUSG00000018733'),mart=mart);<br>
<br>
However the result of this query seems to have a weired structure as
it contains 4 rows for each transcript, from which two contain
different 5' utr boundaries.<br>
In contrast, what I would expect is a single row for each transcript
with 5' AND 3' utr information (if available). <br>
I've tried the same query for other genes, but the the results
always have a similar structure.<br>
<br>
The same happens if I run my query through the webinterface. Here's
the URL for the above mentioned example:<br>
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<pre><a class="moz-txt-link-freetext" href="http://www.ensembl.org/biomart/martview/f20886e0142055da2a2b0a9de30d5ca8/f20886e0142055da2a2b0a9de30d5ca8/f20886e0142055da2a2b0a9de30d5ca8?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.structure.ensembl_gene_id">http://www.ensembl.org/biomart/martview/f20886e0142055da2a2b0a9de30d5ca8/f20886e0142055da2a2b0a9de30d5ca8/f20886e0142055da2a2b0a9de30d5ca8?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.structure.ensembl_gene_id</a>|mmusculus_gene_ensembl.default.structure.ensembl_transcript_id|mmusculus_gene_ensembl.default.structure.5_utr_start|mmusculus_gene_ensembl.default.structure.5_utr_end|mmusculus_gene_ensembl.default.structure.3_utr_end|mmusculus_gene_ensembl.default.structure.3_utr_start|mmusculus_gene_ensembl.default.structure.start_position|mmusculus_gene_ensembl.default.structure.end_position|mmusculus_gene_ensembl.default.structure.transcript_start|mmusculus_gene_ensembl
.default.structure.transcript_end&FILTERS=mmusculus_gene_ensembl.default.filters.ensembl_gene_id."ENSMUSG00000018733"&VISIBLEPANEL=resultspanel</pre>
</span>Do you have any ideas what the problem with my query could
be?<br>
<br>
Best,<br>
Holger Brandl<br>
<pre class="moz-signature" cols="80">--
Dr. Holger Brandl
Bioinformatics Service
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden, Germany
Tel.: +49/351/210-2738
Fax: +49 351 210 2000
www: <a class="moz-txt-link-freetext" href="http://www.mpi-cbg.de">http://www.mpi-cbg.de</a>
</pre>
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