[BioMart Users] about 3'UTR retrieved from ensembl with biomart

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[BioMart Users] about 3'UTR retrieved from ensembl with biomart

Ligia Mateiu
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
[hidden email]

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Re: [BioMart Users] about 3'UTR retrieved from ensembl with biomart

Rhoda Kinsella
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.
 

You will see from the browser that there are a number of exons in the 3'UTR region.


I hope that helps, but if you have further questions, please contact [hidden email],
Regards
Rhoda



On 23 Nov 2012, at 09:22, Ligia Mateiu <[hidden email]> 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
[hidden email]
_______________________________________________
Users mailing list
[hidden email]
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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