A novel cDNA encoding the nonselective type of endothelin (ET) receptor was isolated from a rat brain cDNA library. The cloned cDNA encoded a 442-amino acid protein with seven putative transmembrane domains. Nucleotide sequence analysis showed that the rat brain cDNA differed from the cloned rat lung nonselective ET receptor (ETB) cDNA by three extra nucleotides in its coding regions, which prcxluced an encoded protein with four amino acid substitutions. In addition, both the 5' and 3' noncoding sequences of the rat brain cDNA were divergent from those of rat lung cDNA. Expression of the rat brain cDNA in COS-1 cells demonstrated that the encoded receptor displayed equal affinity toward the three ET isopeptides. However, Southern blot analysis indicated a single-copy gene for the rat ETB receptor. Further genomic cloning and sequence analysis demonstrated that rat brain cDNA encoded the authentic protein sequences of the rat ETB receptor. Moreover, the 5' noncoding sequences in rat brain cDNA that were divergent from those in rat lung cDNA were encoded by a distinct region, an upstream exon, in the rat ETb genome. All the findings suggest that rat brain cDNA represents an alternative transcript of the rat ETB gene. Preliminary Northern blot analysis indicated that the expression of this ETB cDNA sequence might be not only in the brain but also in other tissues, whereas its expression might be somehow tissue-spe-cifically regulated.