We have identified cDNAs encoding three isoforms (a1, a2, and a3) of the 100-kDa a subunit of the mouse vacuolar proton-translocating ATPase (V-ATPase). The predicted protein sequences of the three isoforms are 838, 856, and 834 amino acids, respectively, and they display approximately 50% identity between isoforms. Northern blot analysis demonstrated that all three isoforms are expressed in most tissues examined. However, the a1 isoform is expressed most heavily in brain and heart, a2 in liver and kidney, and a3 in liver, lung, heart, brain, spleen, and kidney. We also identified multiple alternatively spliced variants for each isoform. Reverse transcriptase-mediated polymerase chain reaction revealed that one splicing variant of the a1 isoform (a1-I) was expressed only in brain, whereas two other variants (a1-II and a1-III) were expressed in tissues other than brain. These alternatively spliced forms differ in the presence or absence of 6 -7 amino acid residues near the amino and carboxyl termini of the proteins encoded. The a3 isoform is also encoded by three alternatively spliced variants, two of which are predicted to encode a protein that is truncated near the border of the aminoand carboxyl-terminal domains of the a subunit and therefore lacks the integral transmembrane-spanning helices thought to participate in proton translocation. Expression of each isoform (with the exception of a1-I) was detectable at all developmental stages investigated, with a1-I absent only in day 7 embryos. The results obtained suggest that isoforms of the 100-kDa a subunit may contribute to tissue-specific functions of the V-ATPase.The vacuolar (H ϩ )-ATPases (or V-ATPases) 1 function as ATPdependent proton pumps to acidify intracellular compartments in eukaryotic cells. V-ATPases are present in a variety of intracellular compartments, including clathrin-coated vesicles, endosomes, lysosomes, Golgi-derived vesicles, chromaffin granules, synaptic vesicles, and the central vacuoles of yeast, Neurospora, and plants (1-9). Vacuolar acidification is essential for such processes as receptor-mediated endocytosis, intracellular targeting, protein processing and degradation, and coupled transport. V-ATPases have also been identified in the plasma membrane of certain specialized cells, where they function in processes such as renal acidification (7), cytoplasmic neutralization (10), bone resorption (11), tumor metastasis (12), and coupled transport of K ϩ (13). These plasma membrane functions of the V-ATPase require that cells be able to target VATPases to the cell surface, but the mechanisms involved in this selective targeting are not understood.The V-ATPases of animals, plants, and fungi are structurally very similar and are composed of two functional domains (1-9). The V 1 domain is a peripheral complex (molecular mass, 600 -650 kDa) composed of eight different subunits ranging in molecular mass from 70 to 14 kDa (subunits A-H) that is responsible for ATP hydrolysis. The V 0 domain is a 260-kDa integral complex composed of five subun...