Determine long non-coding RNA from a list

Question

[bigjay2578]

Dumb question with probably an easy answer. I have a list of genes ~800 long. Is there a resource I can use that can tell me which of these is a long non-coding RNA?

Answer 1

[WouterDeCoster]

I would use Ensembl biomaRt to get you the gene biotype.

Answer 2

[h.mon]

It is not a dumb question, though it needs some work to be a well-written question. Anyway, if you google for long non coding rna annotation you will get a long list of resources. For example, my top three hits are: FEELnc, lnc-GFP, ncFANs.

lnc-GFP is a method for annotating known lncRNAs, so probably not helpful to you, but the paper has this good description of why your question isn't dumb (it is a bit old and the situation has improved):

First, our knowledge on lncRNAs is limited; even the functional elements in the primary sequence of non-coding genes, if exist, remain unknown (16). Second, the poor sequence conservation of lncRNAs (17) makes it difficult to infer putative functions for lncRNAs by genomic comparison. Third, the lack of collateral information, such as molecular interaction data and expression profiles, also hampers the functional annotation of lncRNAs. Fourth, to examine the functions of lncRNAs based on their secondary-structure information is still infeasible because of the little associations between functions and secondary-structure for lncRNAs (18).