Question: How to find sequences of the 3' and 5' regions of a non-coding RNA
0
gravatar for Amlan
3.7 years ago by
Amlan20
United States
Amlan20 wrote:

Hello all,

I have spent a good amount of time on this but could not find a way to separate the 3' and 5' regions of a non coding RNA. http://www.ncbi.nlm.nih.gov/ has the whole ncRNA sequences. UCSC table browser apparently has only the mRNA transcripts. But how would I get the exact range of chromosomal positions for the 3' and the 5' regions of an ncRNA?

sequence • 927 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Amlan20
1
gravatar for Sukhdeep Singh
3.7 years ago by
Sukhdeep Singh9.7k
Netherlands
Sukhdeep Singh9.7k wrote:

Your link is incomplete, I dont know which study you are referring to exactly but still!

Your steps could be:
1) Pulling the sequences downs (whole ncRNA), mapping them to respective genome, read filtering etc and obtain a final mapped dataset (Tophat/Bowtie can do that).

2) Generate a reference ncRNA 5'/3' regions and check which fragments map to them. This will give you your answer.

You could also pull down ncRNA reference fasta (I dont know where exactly from), generate 5'/3' list, index them using Bowtie and map your whole dataset to that refence. So, essentially you would have a BAM file which you could convert to fasta/BED, depending on what you want and gives you your answer. 

UCSC Table Browser should have the references you wanted or try biomart martview.

HTH

ADD COMMENTlink written 3.7 years ago by Sukhdeep Singh9.7k

Thanks a lot Sukhdeep. But "Generate a reference ncRNA 5'/3' regions" is actually my question. I don't know how to generate those 5'/3' regions of a ncRNA. I can get the whole ncRNA sequence from this ENSEMBL link. But I can't separate the 5' and 3' regions from those whole ncRNA sequences. UCSC table browser or Biomart neither have those 3' and 5' regions separately for ncRNA

ADD REPLYlink written 3.7 years ago by Amlan20

Essentially the start and end coordinates of the ncRNAs that you will pull down will represent their 5'/3' positions. You can code them to have a symmetrical locus (eg +/-500b) .
Check these posts on how to fetch sequences.

ncRNA mouse file from UCSC or other source
How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads

Cheers

ADD REPLYlink written 3.7 years ago by Sukhdeep Singh9.7k
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: 1136 users visited in the last hour