<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Holger<div>When you query the UTR information from mart, what you are actually getting is one result row per exon. Therefore if you add the exon_id to your attributes you will see that the results make more sense as you get a unique row per exon in each transcript. I hope that makes sense, but please get back to me if you have further questions.</div><div>Regards</div><div>Rhoda</div><div><br></div><div><br></div><div><br><div><div>On 14 Mar 2011, at 14:42, Holger Brandl wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> 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> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"> <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> </div> _______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>http://lists.ensembl.org/mailman/listinfo/dev<br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Ensembl Bioinformatician,</div></div><div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span> </div><br></div></body></html>