IRBIT is an inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R)-binding protein that inhibits the activation of IP(3)R by competing with IP(3) for the common binding site on IP(3)R. In this study, we characterize an IRBIT homologue, termed Long-IRBIT. Long-IRBIT is highly homologous to IRBIT ( approximately 88%) and heteromerizes with IRBIT. In spite of complete conservation of critical amino acids required for the interaction with IP(3)R and comparable phosphorylations on critical four Ser residues for IP(3)R-binding, Long-IRBIT retains little ability to interact with IP(3)R. Deletion mutagenesis analysis revealed that this low affinity to IP(3)R is attributable to an inhibitory effect of the Long-IRBIT specific N-terminal appendage (LISN domain). Immunohistochemical analysis revealed the distinct distribution of Long-IRBIT and IRBIT in mouse cerebellar cortex, that is, Long-IRBIT is mainly expressed in interneurons such as basket cells, while IRBIT is mainly expressed in glial cells. Furthermore, Long-IRBIT, but not IRBIT, underwent phosphorylation during neuronal differentiation in neuroblastoma cells and this phosphorylation was dependent on the LISN domain. These results suggest that Long-IRBIT has a different function from IRBIT.