Structural comparison of human and rat prostate-specific acid phosphatase (hPAP and rPAP) genes indicate that the exon number is different between these species. The hPAP gene contains 10 exons, whereas the rPAP gene was 11 exons. However, exons 2-9 of the genes are identical in size. The 5' regions of the two genes show 71% identity in the most homologous region +1 to +340. The 5' untranslated regions of the human and rat genes are 50 and 49 nucleotides long, respectively. An Alu sequence is present upstream from the proximal promoter of the hPAP gene. Five putative androgen response elements altogether were localized in both the human and rat gene, one of which is conserved in location and sequence between the two genes. Two of these elements in both genes, the conserved one in the proximal promoter region and another one in intron 1, were shown to bind androgen receptor efficiently in vitro.