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Whey acidic protein (WAP) is a major milk protein found in mouse and rat. Cloned WAP cDNAs from both species have been sequenced and the respective protein sequences have been deduced. Mouse and rat WAP (134 and 137 amino acids respectively) are acidic, cysteine rich proteins which contain a N-terminal signal peptide of 19 amino acids. Most of the cysteines are located in two clusters containing six cysteine residues each, arranged in an identical pattern. Comparison of the mouse and rat WAPs show that the signal peptide and the first cysteine domain are conserved to a greater extent than the rest of the protein. This result is reflected in the nucleotide sequence homology, where the regions coding for the signal peptide and cysteine domain I are the only regions where the rate of replacement substitution is lower than the rate of silent substitution. The 3' non-coding regions show a 91% conservation which is half the substitution rate for the coding region. This low rate of sequence divergence in the 3' non-translated region of the mRNA may indicate a functional importance for this region.