Cell-cell interactions are primarily mediated by secreted and transmembrane proteins which play essential roles in the neuronal circuit formation. However, molecular mechanisms underlying neuronal circuit formation, which is mediated by the cell-cell interactions, remain largely elusive. We isolated and characterized a novel gene, Btcl2 (brain-specific transmembrane protein containing CUB [complement subcomponent C1r/C1s, sea urchin protein Uegf, and BMP-1] and LDLa [low-density lipoprotein receptor domain class A] domains 2), using the signal sequence trap (SST) method. The extracellular domain of BTCL2 contains two CUB domains and an LDLa domain. BTCL2 and BTCL1 have similar domain structures, sharing 51% overall identity. The CUB1, CUB2, and LDLa domains of these two proteins share 63%, 72%, and 84% identity, respectively. The CUB domains of BTCL1 and BTCL2 share significant identity with those of neuropilins. Btcl2 mRNA was detected as a single 6-kb transcript in Northern blot analysis. In situ hybridization (ISH) analysis revealed that both Btcl1 and Btcl2 mRNAs were observed restrictively in brain throughout embryonic and postnatal stages. Btcl1 and Btcl2 mRNAs were expressed uniquely in the pontine nucleus and subplate, which are required for establishing the neuronal circuit formation. These results will aid in resolving the mechanisms underlying neuronal circuit formations (e.g., pontocerebellar and thalamocortical axon guidance) and permit more precise studies aimed at understanding the role of BTCL1 and BTCL2 in the central nervous system.