Two variant cDNAs, mosaic seine protease large-form (MSPL) and transmembrane protease serine 13 (TMPRSS13), have been identified from a human lung cDNA library by polymerase chain reaction. The deduced amino acid sequences of these proteins show a type II transmembrane protein structure with a unique and long cytoplasmic tail containing tandem repeat phosphorylation motifs of protein kinases, a transmembrane domain, and a trypsin-like serine protease domain at the extracellular C-terminal side. These proteins have an identical serine protease sequence except for the C-terminal ends, and the consensus protease domain exhibits 42, 39 and 43% sequence identity with those of plasma kallikrein, hepsin and transmembrane protease serine 2 (TMPRSS2), respectively. Although both genes are widely expressed in various tissues, they are predominantly expressed in human lung, placenta, pancreas and prostate. TMPRSS13 is expressed higher than MSPL in thymus, spleen and peripheral blood lymphocytes, particularly in CD8+ cells and CD19+ cells. Enzymatic properties of the recombinant soluble MSPL and TMPRSS13 show that these enzymes preferentially recognize the sites consisting of paired basic amino acid residues, and are strongly inhibited by aprotinin, benzamidine and Bowman-Birk trypsin inhibitor, but poorly inhibited by alpha 1-antitrypsin and leupeptin. These properties raise the possibility that MSPL and TMPRSS13 play roles in the proteolytic processing of prohormones, precursors of growth factors, and also play roles in the pathogenicity of many viruses and bacteria in vivo.