Two ferret P. carinii gpA cDNA clones were identified that reacted identically with a panel of anti-gpA monoclonal antibodies, although their nucleotide sequences were 22% divergent. Each clone hybridized to a single mRNA species of 3,600 nucleotides only in P. carinii-infected lung mRNA, but RT-PCR analysis demonstrated that these cDNA clones were derived from two distinct gpA mRNA transcripts. Further PCR analysis demonstrated that the ferret P. carinii genome contains at least two gpA genes lying in tandem on a single chromosome separated by a 329-bp intergenic region. Based on the terminal gene sequences of this tandem repeat and the cDNA clones, a composite full-length ferret P. carinii gpA coding sequence was constructed. The intergenic region immediately downstream of the stop codon of the first gpA gene contains three putative polyadenylation signals, and constitutes the 3' untranslated region (UTR) of the gpA mRNA. Primer extension of the gpA mRNA resulted in products extending 74 and 244 nucleotides into the 5' UTR. However, the intergenic region lying greater than 25 nucleotides upstream of the first methionine of the second gpA gene was found to be absent from the 5' UTR.