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Old 01-10-2017, 10:49 AM   #1
Marcos Lancia
Location: Argentina

Join Date: Apr 2015
Posts: 31
Question Looking for 3'-UTR and 5'-UTR sequences

Hi everyone! I have a question, I hope you can help me out. I have a list of genes that IŽd like to obtain their 5'-UTR and 3'-UTR sequences. I work with Medicago truncatula, and I have RNA-SEQ data to work with. Any idea?? Thanks so much.
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Old 01-11-2017, 12:50 AM   #2
Senior Member
Location: Vienna

Join Date: Oct 2011
Posts: 121

Hi Marcos,

It seems that your plant is a model species and well annotated. You could download the gene annotation and extract the 5' and 3' UTR from the gff3 file.
In order to incorporate the RNA-Seq data, you need to align the reads to the Medicago truncatula annotation and intersect the alignment with the genes' 5' and 3' UTR boundaries.

Michael.Ante is offline   Reply With Quote

3'-utr, 5'-utr

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