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 I´d 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.
-
-
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
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment