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]
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