Hi Ligia If you take a look at this transcript in the Ensembl browser, you will see that this transcript is thought to undergo nonsense mediated decay. This is a process which detects nonsense mutations and prevents the expression of truncated or erroneous proteins. http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000124782;r=6:7107830-7252213;t=ENST00000492574
You will see from the browser that there are a number of exons in the 3'UTR region. http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000124782;r=6:7107830-7252213;t=ENST00000492574 I hope that helps, but if you have further questions, please contact [email protected], Regards Rhoda On 23 Nov 2012, at 09:22, Ligia Mateiu <[email protected]> wrote: > Dear Madame/Sir, > For my research, I needed the 3'UTRs for the Affy U133Plus2 platform and they > were nicely available in Ensembl and I could retrieve them with Biomart. I > realized that for approx 15% of the transcripts the 3'UTR seems fragmented. > Below there is an example. I do not understand the meaning. I would greatly > appreciate an answer. > > INPUT script: > ... > $query->setDataset("hsapiens_gene_ensembl"); > $query->addFilter("with_affy_hg_u133_plus_2", ["Only"]); > $query->addFilter("chromosome_name",["6"]); > > $query->addAttribute("3utr"); > $query->addAttribute("ensembl_gene_id"); > $query->addAttribute("ensembl_transcript_id"); > $query->addAttribute("chromosome_name"); > $query->addAttribute("3_utr_start"); > $query->addAttribute("3_utr_end"); > $query->addAttribute("strand"); > ... > > OUTPUT: > ... > >ENSG00000124782|ENST00000492574|6|7211806;7248744;7229230;7189392;7211037;7226700;7187667;7246657;7182334|7211942;7252209;7232140;7189555;7211181;7226889;7187756;7247454;7183552|1|7176442|7252209 > > > Thank you for your time, > Ligia Mateiu > > > -- > Ligia Mateiu, MD Ph.D. > > Laboratory of Reproductive Genomics > O&N I Herestraat 49 - bus 602 > 3000 Leuven > [email protected] > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD
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