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Beta-amyloid (Abeta) is formed by sequential cleaving of the amyloid precursor protein by two proteolytic enzymes, beta- and gamma-secretases. Beta-secretase (BACE) is a type I transmembrane aspartic proteinase that is highly expressed in the mammalian brain. Four alternative splice variants of BACE are currently known and each encodes for a protein isoform with a different enzymatic activity. In Alzheimer's disease (AD) patients, the enzymatic activity and protein levels of BACE are increased in the neocortex, suggesting their differential expression may have a role in Abeta plaque formation. We have determined the differential expression of BACE mRNA and its splice variants in eight regions of the rat and two of the human brain. In humans, the frontal cortex which shows Abeta deposition in AD, expressed three-fold more BACE than the cerebellum and four fold more than the rats' frontal cortex both of which do not form Abeta plaques. The highest BACE levels of rats were found in the frontal cortex and less in other areas. Although most human and rat brain regions expressed all four BACE variants, the human cerebellum did not express the I-457 BACE variant. Human and rat frontal cortex expressed high levels of the I-501 and I-457 variants, but I-432 was highly expressed only in the rat. Species-specific differences were evident between human and rat brain areas, suggesting that BACE transcript variants may have different evolutionary conservation. Differential expression of BACE variants may explain the broad spectrum of phenotypic abnormalities and possible pathogenetic mechanisms underlying Alzheimer's disease.