Semaphorins/collapsins (semaphorins) comprise a large family of proteins implicated in axonal guidance during development. We cloned a novel member (semaZ) of the semaphorin gene family from a rat brain cDNA library. Sema Z was thought to be an integral membrane glycoprotein of 887 amino acids including a sema domain composed of 532 amino acids. The amino acid sequence of Sema Z showed 28-35% identity with other semaphorins in its sema domain, including 15 conserved cysteine residues. The cytoplasmic domain of Sema Z was found to be rich in prolines. Our phylogenetic analysis based on the amino acid sequence of the sema domains and the location of conserved N-glycosylation sites suggested that the sema domain of Sema Z belongs to a new class, class VI. We detected the semaZ mRNA in the first branchial arch of embryonic day 11 (E11) rat embryo, and subsequently in the myotomes and the dorsal root ganglia in developing somites from E11.5 through E13.5, but not in the brain. However, at E15, 18, 21 and P0, semaZ was highly expressed in the brain. Sema Z might play a role in both peripheral and central nervous system development.