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?
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
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.