Can shRNAmir hairpins be subcloned in the pLKO.1 (TRC shRNA) vector?

Not directly because the cloning sites are not the same. The shRNAmir hairpins are cloned into the shRNAmir vectors in between the XhoI (5') and EcoRI (3') sites. The TRC shRNA hairpins are cloned in between the EcoRI (3') and AgeI (5') sites in the pLKO. 1 vector.