A full-length placental alkaline phosphatase (PLAP) cDNA was used to identify and clone the PLAP-like Nagao isozyme gene from human genomic libraries. The entire nucleotide sequence of the gene reveals the existence of 11 exons interrupted by 10 small introns (76-427 base pairs). Putative regulatory sequences have been identified in the promoter regions as well as dispersed in the introns. The deduced amino acid sequence of the Nagao isozyme indicates that the mature molecule is composed of 513 amino acids, of which 12 residues are different from the sequence of PLAP (98% homology). A sequence derived from exon III of the Nagao isozyme gene was used to synthesize a peptide (NH2-Lys-Leu-Gly-Pro-Glu-Thr-Phe-Leu-Ala-COOH) that contains two mutations with respect to the corresponding PLAP sequence. This peptide elicited rabbit polyclonal antibodies that reacted specifically with the seminoma Nagao isozyme but not with PLAP in electrophoretic transfer blots. These results indicate that the tumor, and possibly the normal testis, Nagao isozyme is encoded by a gene referred to as germ-cell alkaline phosphatase gene that differs from the PLAP gene expressed by syncitiotrophoblastic cells.