All inbred strains of mice carry the Ren-1 structural gene, which encodes the renin-1 isozyme, the classical renin activity found in kidneys. In addition, some strains carry a second renin structural gene, Ren-2, which encodes the predominantly expressed SMG rennin isozyme, renin-2. Ren-1 and Ren-2 exhibit markedly different patterns of tissue- specific expression. In an effort to understand the molecular basis for this differential expression, a detailed analysis of the transcripts originating from these loci was undertaken. S1 analysis of SMG and kidney RNA populations indicated that the majority of transcripts initiate at one major site on Ren-1 and Ren-2. Interestingly a minor fraction of transcripts in the SMG initiate at two upstream sites. These transcripts encode an upstream ORF which is in frame with that of the renin precursor. The precise tissue-specificities of Ren-1 and Ren-2 were also examined: in the kidney, SMG, and also in several extrarenal tissues, since there is increasing evidence of renin expression in a number of extrarenal sites. To distinguish between the two highly homologous transcripts, an assay was developed exploiting established base sequence differences between Ren-1 and Ren-2 mRNA's by extension of a primer downstream of such a base difference in the presence of the appropriate ddNTP. Using this assay, Ren-1 and Ren-2 were found to be equally well expressed in the kidney, whereas in the SMG only Ren-2 is efficiently expressed. Interestingly in the other extrarenal tissues examined, testis, liver and heart, it is the Ren-1 allele that is preferentially expressed. The assay was also able to demonstrate the similarity in response of Ren-l/Ren-2 to certain physiological stimuli, such as sodium depletion. Thus, this study of the regulation of mouse renin gene expression has demonstrated further striking differences in the tissue-specific expression of Ren-l/Ren-2, and added to the increasingly compelling evidence of extrarenal renin gene expression.