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The predicted sequence of human gastric cathepsin E (CTSE) was determined by analysis of cDNA clones isolated from a library constructed with poly(A+) RNA from a gastric adenocarcinoma cell line. The CTSE cDNA clones were identified using a set of complementary 18-base oligonucleotide probes specific for a 6-residue sequence surrounding the first active site of all previously characterized human aspartic proteinases. Sequence analysis of CTSE cDNA clones revealed a 1188-base pair open reading frame that exhibited 59% sequence identity with human pepsinogen A. The predicted CTSE amino acid sequence includes a 379-residue proenzyme (Mr= 40,883) and a 17-residue signal peptide. The predicted CTSE amino acid composition was consistent with that of purified material from gastric mucosa and gastric adenocarcinoma cell lines. Additional evidence for the identification of the CTSE cDNA clones was obtained by analysis of poly(A+) RNA isolated from CTSE-producing and -nonproducing gastric adenocarcinoma cell subclones. Three RNA transcripts (3.6, 2.6, and 2.1 kilobases) were identified in poly(A+) RNA isolated from a gastric adenocarcinoma cell line that produced CTSE that were absent from nonproducing subclones. CTSE contains 7 cysteine residues, of which 6 were localized by comparative maximal alignment analysis with pepsinogen A to conserved residues that form intrachain disulfide bonds. The seventh cysteine residue of CTSE is located within the activation peptide region of the proenzyme. We suspect that this residue forms an interchain disulfide bond and thereby determines the dimerization of CTSE proenzyme molecules that is observed under native conditions. The CTSE gene was localized to human chromosome 1 by concurrent cytogenetic and cDNA probe analyses of a panel of human × mouse somatic cell hybrids.