Ca2؉ channel  subunits (Ca v s) are essential for regulating the surface expression and gating of high voltage-activated Ca 2؉ channels through their interaction with Ca 2؉ channel ␣ 1 subunits. In efforts to uncover new interacting partners and new functions for Ca v , we identified a new splicing isoform of Pax6, a transcription factor crucial for the development of the eye, nose, brain, and pancreas. Pax6 contains two DNA binding domains (paired domain and homeodomain), a glycine-rich linker connecting these two domains and a C-terminal proline-, serine-, and threonine-rich transactivation domain. The protein sequence and function of Pax6 are highly conserved from invertebrate to human. The newly isolated isoform, named Pax6(S), retains the paired domain, linker, and homeodomain of Pax6, but its C terminus is composed of a truncated classic proline, serine, and threonine domain and a unique S tail. Pax6(S) shows a similar level of transcriptional activity in vitro as does Pax6, but only in primates is the protein sequence highly conserved. Its spatial-temporal expression profiles are also different from those of Pax6. These divergences suggest a noncanonical role of Pax6(S) during development. The interaction between Pax6(S) and Ca v  is mainly endowed by the S tail. Co-expression of Pax6(S) with a Ca 2؉ channel complex containing the  3 subunit in Xenopus oocytes does not affect channel properties. Conversely, however,  3 is able to suppress the transcriptional activity of Pax6(S). Furthermore, in the presence of Pax6(S),  3 is translocated from the cytoplasm to the nucleus. These results suggest that full-length Ca v  may act directly as a transcription regulator independent of its role in regulating Ca 2؉ channel activity.4 is a cytosolic auxiliary protein of multimeric high voltage-activated (HVA) Ca 2ϩ channel complexes, which include L-, N-, P/Q-, and R-type Ca 2ϩ channels. It plays an essential role in chaperoning the channel complex to the plasma membrane and normalizing its gating properties (1-4). Crystal structures of Ca v  in complex with its high affinity binding site in the principal poreforming ␣ 1 subunit (Ca v ␣ 1 ) show that much of the exposed surface of Ca v  is unoccupied and is available to engage in interactions with other regions of Ca v ␣ 1 or with other proteins (5-7). Indeed, an increasing number of proteins has been shown to directly interact with Ca v , including the Rem/Rad/Gem/Kir (RGK) family of small monomeric GTPases (8, 9), RIM1 (10), ryanodine receptors (11), Ahnak (12, 13), bestrophin-1 (14), and dynamin (15). Many of these proteins have been reported to regulate the activity of HVA Ca 2ϩ channels. To search for other potential Ca v -interacting proteins, we carried out yeast two-hybrid screens using the  3 subunit as bait. Among the candidate target proteins we isolated, one was related to Pax6.Pax6 is a transcription factor that belongs to the paired box (Pax) family (16 -25). It is widely expressed in the eye, nose, pancreas, and the central nervous system ...