In mice, the three Pcdh gene clusters each contain 14–22 homologous “variable” exons arrayed in tandem. Each variable exon is transcribed from its own promoter, and encodes the entire extracellular domain, a transmembrane domain, and a short intracellular domain of the corresponding Pcdh protein. In Pcdha and Pcdhg clusters (but not Pcdhb cluster), these variable exons are followed by a set of three “constant” exons, which are joined to each variable exon via cis-splicing to encode a common distal intracellular domain (Tasic et al., 2002; Wang et al., 2002a). An interesting feature of the genomic organization of the Pcdh gene clusters is that the last two variable exons in the Pcdha cluster, as well as the last three variable exons in the Pcdhg cluster, are more similar to each other than to other variable exons within their respective cluster (Wu et al., 2001). These 5 Pcdh genes (Pcdhac1, Pcdhac2, Pcdhgc3, Pcdhgc4, and Pcdhgc5) are designated C-type genes, to be distinguished from A-type and B-type genes of the Pcdhg cluster. The C-type isoforms bear several unique features among all Pcdhs: 1)
