Question: extracting 5'UTR of each gene
1
gravatar for ashkan
2.7 years ago by
ashkan110
ashkan110 wrote:

I have RNA-seq data and aligned them. I am looking for a way to get only 5'UTR of each gene and look for a motif. do you guys know how to get the 5'UTR?

rna-seq • 1.8k views
ADD COMMENTlink modified 2.7 years ago by Ron970 • written 2.7 years ago by ashkan110
4

Provided your genome is available - Ensembl (BioMart) or UCSC (Table Browser). Tools to use are in respective brackets.

ADD REPLYlink written 2.7 years ago by genomax70k
1

retrieval of upstream non-coding sequences

ADD REPLYlink written 2.7 years ago by F3.4k

Which organism are you working with ?

A simple solution would be to download homer and then install the genome of your interest, which comes with the annotations like exons, introns, 3'UTR, 5'UTR etc. With a simple grep, you could extract all the 5'UTRs and you could use homer for motif analysis.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by geek_y9.8k

As @genomax2 suggested, you can easily get the required sequences from Ensembl. Follow the turorial here.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Persistent LABS740
1
gravatar for swbarnes2
2.7 years ago by
swbarnes26.2k
United States
swbarnes26.2k wrote:

A gtf file for your genome should contain coordinates for 5' UTR sequences. Ensembl has a bunch.

ADD COMMENTlink written 2.7 years ago by swbarnes26.2k
0
gravatar for Ron
2.7 years ago by
Ron970
United States
Ron970 wrote:

This has been answered here:

How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?

Genomic Positions Of 3'Utrs Of Refseq-Genes

ADD COMMENTlink written 2.7 years ago by Ron970
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1630 users visited in the last hour