LIMP II is a glycoprotein expressed in the membrane of lysosomes and secretory granules with lysosomal properties. Sequence analysis of a CNBr-cleaved peptide allowed the synthesis of a 47-mer oligonucleotide that was used to screen a rat liver cDNA library in lambda gt11. This resulted in isolation of a 2-kilobase cDNA containing 1,434 bases encoding the entire protein. The deduced amino acid sequence indicates that LIMP II consists of 478 amino acid residues. The segment spanning residues 4-6 to 26 constitute an uncleavable signal peptide. LIMP II possesses a hydrophobic amino acid segment near the carboxyl end, that together with the uncleaved signal peptide may anchor the protein to the membrane through two distant segments. The major portion of the protein resides on the luminal side and displays 11 potential N-glycosylation sites and 5 cysteine residues. Two short cytoplasmic tails, 2-4 and 20-21 amino acids long, correspond to the NH2- and COOH-terminal ends of the protein, respectively. Transfection of COS cells with the cDNA of LIMP II resulted in expression of the protein and its transport to lysosomes. Comparison of the entire sequence to various data bases of known proteins revealed extensive homology between LIMP II and the cell surface protein CD36 involved in cell adhesion. No significant homology was detected with the two families of lysosomal membrane proteins A and B, recently described.