AMP deaminase (AMPD) is a central enzyme in eucaryotic energy metabolism, and tissue-specific as well as stage-specific isoforms are found in many vertebrates. This study demonstrates the AMPDI gene product in rat is alternatively spliced. The second exon, a 12-base miniexon, was found to be excluded or included in a tissue-specific and stage-specific pattern. This AMP deaminase (AMP aminohydrolase; EC 3.5.4.6) (AMPD) activity has been found in all eucaryotic cells examined thus far, but it is not present in procaryotes, which suggests that this enzyme catalyzes a reaction that is important for energy metabolism in the specialized environment of the eucaryotic cell. Tissue-specific and stage-specific isoforms of AMPD have been reported in many vertebrates (14,22,23). In human and rats, two functional AMPD genes have been identified (16a). AMPDJ is expressed at high levels in skeletal muscle; AMPD2 is expressed in many nonmuscle tissues of the adult animal as well as in embryonic muscle, cardiac muscle, and smooth muscle. Two clinical phenotypes of inherited AMPD deficiency have been described in humans. Homozygous deficiency of AMPD activity restricted to erythrocytes has been estimated to have a frequency of -0.03% in Japanese, Chinese, and Koreans (21). Deficiency of AMPD restricted to skeletal muscle is a common cause of inherited metabolic myopathy in the United States and Europe (30), and the latter phenotype is presumably a consequence of mutations in the AMPDJ gene.Alternative splicing is used in many tissues, including skeletal muscle, to generate protein diversity (2). Prior studies suggest that more than one transcript may be produced from the AMPDJ gene in rat skeletal muscle. RNase mapping experiments performed with an AMPDI probe demonstrated the presence of two transcripts that have identical or closely related 5' and 3' termini, but the internal sequences of these transcripts diverge at one or more points (29). The study described here demonstrates that two mRNAs are produced from the rat AMPDJ gene and that the only difference between these two transcripts is the inclusion or exclusion of exon 2, a 12-base miniexon. The relative abundance of these two AMPD1 transcripts is regulated by tissue-specific and stage-specific signals. This pattern of alternative splicing exhibited by rat AMPDJ has been referred to as cassette splicing. It has been assumed in this type of splicing, the variably retained exon is removed as a part of a larger intron that contains the exon as well as both of the flanking introns (2). The study presented here demonstrates that this is not the only mechanism for cassette splicing. In the case of AMPDI, a novel pathway for alternative splicing has been identified. This pathway requires the formation of an RNA intermediate that generates a functional, alternative 5' splice donor site at the point where exon 1 is ligated to exon 2. The analogous RNA intermediate of the human AMPDI transcript generates a potential 5' splice donor site at the boundary of exon 1 and exon 2 that i...