Which part of lncRNAs is more suitable to design primers for?

14 March 2024 1 3K Report

Hi, It seems lncRNAs have not exon parts on NCBI gene bank file, so if I want to design primers to detect for example MALAT1 by qRT-PCR (syber-green) in cell culture extract, which section is better to amplify?

Another problem is BLASTing the primers, because the results are almost zero! why?

Frederic Lepretre

Hi Ghasem

yes you're right this gene has only one exon (almost for the highest expressed transcript of this gene (see pict)) and in qPCR it could be noising. to avoid RNA degradation and loss of copies of the entire gene, primer design must be done at the most 3' of the gene with respect to the RTq-PCR primer design rules.

all the best

fred

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