Suggestions for experimental or in silico validation related to ncRNA or protein - (Mar/15/2012 )

Suggestions for experimental or in silico validation related to ncRNA or protein encoding?

We have a problem investigating a newly identified RNA. UCSC genome browser at least, shows no protein-coding gene in the specific region. ORF analysis proposes several short peptides encoded by the short transcript but with no similarities blasting the predicted amino acid sequence against all known proteins.

How can we proceed (experimentally or in silico) in order to check whether our transcript of interest is non-coding or coding for a yet unknown protein.

Glad to hear from you!

Make antibodies that detect the peptides.