Protocadherins (Pcdhs) are members of the rapidly growing cadherin superfamily and are thought to be involved in cell-cell recognition in the central nervous system. Using human BH-Pcdh cDNA, we retrieved a homologous gene from the database. The new gene (Pcdh-X, HGMW-approved symbol PCDH11) was present on a genomic clone of human chromosome X (clone bWXD306), between two sequence tagged sites, sWXD1362 and 221. Pcdh-X therefore maps to the XY homology region in Xq21.3. The open reading frame consists of 1021 amino acids (aa) including seven cadherin repeats (EC1-7) in the extracellular domain. The Pcdh-X gene consists of at least three exons; the first exon encodes the 5'-untranslated region, EC1, and half of EC2, the second exon encodes the remainder of the Pcdh-Xa, and the third exon encodes the cytoplasmic tail of Pcdh-Xb and its 3'-untranslated region. The second exon has an alternative splice site that is used to produce two isoforms with different cytoplasmic tails of 10 (Pcdh-Xa) or 14 amino acids (Pcdh-Xb). Northern blot analysis revealed an approximately 6.0-kb transcript expressed in human and mouse fetal brain.