We propose a realistic flipped SU(5) model derived from a five-dimensional orbifold SO(10) model. The Standard Model (SM) fermion masses and mixings are explained by combining the traditional Froggatt-Nielsen mechanism with the five-dimensional wave function profiles of the SM fermions. Employing tree-level spontaneous R-symmetry breaking in the hidden sector and extra(ordinary) gauge mediation, we obtain realistic supersymmetry breaking soft mass terms with non-vanishing gaugino masses. Including the messenger fields at the intermediate scale and Kaluza-Klein states at the compactification scale, we study gauge coupling unification. We show that the SO(10) unified gauge coupling is very strong and the unification scale can be much higher than the compactification scale. We briefly discuss proton decay as well. A? 2010 SISSA.