I am knocking down a gene using RNAi. When I blasted the 500 odd base-pairs that I use for knockdown, it turns out that there is a 29BP match to another gene. I was wondering if such a construct could result in an off-target effect.
If I recall correctly, dicer processing dsRNA into ~25 nt fragments, so it is possible that you could have off target effects. It’s more likely that an observable phenotype comes from the knock-down of your gene of interest, but to rule out the off-target effect you should validate using a mutant.