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The 5'-end of the bovine adrenodoxin gene contains unique structural characteristics. Exons 1 and 2 appear to encode different presequences for this mitochondrial precursor protein. However, exon 1 contains a stop codon (TAA) in place of amino acid 15. Thus, while two species of bovine adrenodoxin mRNA arise from a single gene, only the abundant mRNA species (90%) is translated into the adrenodoxin precursor which contains the presequence encoded by exon 2. The minor mRNA species (10%) contains the sequence encoded by exon 1 and cannot be translated into an adrenodoxin precursor. Presumably the sequence within exon 2 is removed from this minor mRNA species by alternative splicing. Furthermore, the initiation of transcription of the major adrenodoxin mRNA (exon 2) lies within intron 1 of this unusual gene, while that for the other mRNA (exon 1) lies in the 5'-flanking region. Thus, the adrenodoxin gene is the first example of a gene encoding a mitochondrial protein which falls into the category of genes having alternate promoters utilizing a pattern of alternative splicing.