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Are there different efficacies for shRNA that target the 3'UTR of a gene vs. the CDS?
While none of the shRNA are individually validated, we have anecdotal evidence to suggest that the loaded RISC seems to target as well in the 3’ UTR (although not the 5’ UTR) as in the CDS and therefore there’s no particular known reason to prefer targeting the 3'UTR or the CDS. It is simply a matter of predicting the best target sequence for each gene.