How to find sequences of the 3' and 5' regions of a non-coding RNA

Question

[Amlan]

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?

Answer 1

[Sukhi Singh]

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).

1. 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

[Amlan]

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

[Sukhi Singh]

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