A Drosophila melanogaster gene (dvha) encoding a vacuolar ATPase subunit A has been isolated and characterized, The gene encodes a protein which is 607 amino acids long, The deduced amino acid sequence of the cloned gene is 86.5 and 82.1% identical to those of Manduca sexta and bovine vacuolar ATPase subunit A, respectively, Analysis of a genomic clone revealed that there are three coding exons, RNA blot analysis detected two transcripts; a 2.9 Mb transcript present in both adult heads and bodies; a 0.5 kb transcript present predominantly in adult heads.