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

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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
Michael.Ante
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Location: Vienna

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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.

Cheers,
Michael
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