  We study the connection between quark and lepton mass matrices in a
supersymmetric SO(10) GUT model in six dimensions, compactified on an orbifold.
The physical quarks and leptons are mixtures of brane and bulk states. This
leads to a characteristic pattern of mass matrices and high-energy CP violating
phases. The hierarchy of up and down quark masses determines the CKM matrix and
most charged lepton and neutrino masses and mixings. The small hierarchy of
neutrino masses is a consequence of the mismatch of the up and down quark mass
hierarchies. The effective CP violating phases in the quark sector, neutrino
oscillations and leptogenesis are unrelated. In the neutrino sector we can
accomodate naturally $\sin \theta_{23} \sim 1$, $\sin \theta_{13} \lesssim 0.1$
and $m_1 \lesssim m_2 \sim \sqrt{\Delta m^2_\text{sol}} < m_3 \sim \sqrt{\Delta
m^2_\text{atm}}$.
