The force and torque on a Janus sphere moving in a rarefied gas with a thermal gradient are calculated. The regime of large Knudsen number is considered, with the momenta of impinging gas molecules either obtained from a Chapman-Enskog distribution or from a binary Maxwellian distribution between two opposing parallel plates at different temperature. The reflection properties at the surface of the Janus particle are characterized by accommodation coefficients having constant but dissimilar values on each hemisphere. It is shown that the Janus particle preferentially orients such that the hemisphere with a larger accommodation coefficient points towards the lower temperature. The thermophoretic velocity of the particle is computed, and the influence of the thermophoretic motion on the magnitude of the torque responsible for the particle orientation is studied. The analytical calculations are supported by Direct Simulation Monte Carlo results, extending the scope of the study towards smaller Knudsen numbers. The results shed light on the efficiency of oriented deposition of nanoparticles from the gas phase onto a cold surface.