A variety of secreted and membrane proteins play key roles in the formation of neuronal circuits in the central nervous system. Using the signal sequence trap method, we isolated and characterized a novel gene, Btcl1 (brain-specific transmembrane protein containing two CUB and an LDLa domains). BTCL1 has significant homology with neuropilin-1 and -2 in their CUB domains. Domain structure of BTCL1 indicates that BTCL1 belongs to a new class of brain-specific CUB domain-containing protein. On Northern blot analysis, Btcl1 mRNA was observed as a single transcript of 3.7 kb specifically in the brain. In situ hybridization analysis revealed that Btcl1 mRNA was highly expressed in the hippocampal CA3 region, olfactory bulb, and neocortex in the adult brain. Expression pattern of mRNA and structural similarity with neuropilin suggest that BTCL1 plays a role in the development and/or maintenance of neuronal circuitry.