Required for protein transport between the Golgi and the endoplasmic reticulum. May contribute to tethering of coatomer-coated retrograde transport vesicles to the ER membrane through interaction with and stabilization of the SNARE complex. Component of a peripheral membrane protein complex consisting of DSL1, SEC39/DSL3 and TIP20. Bound to a SNARE complex consisting of UFE1, USE1, SEC20 and SEC22 or YKT6 through direct interaction of TIP20 with SEC20. Interacts with TIP20 and DSL1. Cells with a reduced level of SEC39 show a defect in post-translational processing of PRC1/CPY. Belongs to the SEC39 family.