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The renormalization of conductances in a Y junction of spinless Luttinger-liquid wires additionally coupled to acoustic longitudinal phonons is investigated in fermionic representation. This system corresponds to geometry of a tunneling experiment and exhibits the interplay between the Coulomb repulsion and the attractive retarded interaction mediated by phonons. The retardation effects related to the propagation of phonons through the junction with arbitrary transmission and reflection amplitudes are taken into account. The appearing logarithmic corrections to conductances of the junction are treated in a renormalization group approach, and scaling exponents are calculated up to infinite order in the interaction after RPA-type summation. The fixed points and corresponding scaling exponents are considered in various non-equilibrium regimes. We show that the boundary exponent and the bulk anomalous dimension of fermion operator are characterized by two different Luttinger parameters, referring to the main wire, thanks to non-local character of phonon-mediated interaction. In the limiting case of the junction of only two wires, the scaling exponents found by our method are in exact correspondence with previous bosonization analysis.