A cDNA clone encoding a neural-specific putative protein-tyrosine-phosphatase (protein-tyrosine-phosphate phosphohydrolase, EC 3.1.3.48) has been isolated from a rat striatal cDNA library. The deduced amino acid sequence predicts a protein of approximately 369 amino acids with a strong homology to other members of the family of protein-tyrosine-phosphatases. In vitro translation produces a protein with an apparent molecular mass of 46 kDa. A potential attachment mechanism to the cytoplasmic membrane is suggested by a myristoylation amino acid-consensus sequence at the N terminus of the protein. RNA analyses of various regions of rat brain reveal a 3-kilobase (kb) and a 4.4-kb mRNA. The 3-kb mRNA is highly enriched within the striatum relative to other brain areas and has been termed a "striatum enriched phosphatase" (STEP). In contrast, the 4.4-kb message is most abundant in the cerebral cortex and rare in the striatum. These two messages appear to be alternatively processed RNA transcripts of a single gene.