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Background  The foamy viral genome encodes four central purine-rich elements localized in the integrase-coding region of  pol . Previously, we have shown that the first two of these RNA elements (A and B) are required for protease dimerization and activation. The D element functions as internal polypurine tract during reverse transcription. Peters et al., described the third element (C) as essential for  gag  expression suggesting that it might serve as an RNA export element for the unspliced genomic transcript.    Results  Here, we analysed  env  splicing and demonstrate that the described C element composed of three GAA repeats known to bind SR proteins regulates  env  splicing, thus balancing the amount of  gag / pol  mRNAs. Deletion of the C element effectively promotes a splice site switch from a newly identified  env  splice acceptor to the intrinsically strong downstream localised  env  3′ splice acceptor permitting complete splicing of almost all LTR derived transcripts. We provide evidence that repression of this  env  splice acceptor is a prerequisite for  gag  expression. This repression is achieved by the C element, resulting in impaired branch point recognition and SF1/mBBP binding. Separating the branch point from the overlapping purine-rich C element, by insertion of only 20 nucleotides, liberated repression and fully restored splicing to the intrinsically strong  env  3′ splice site. This indicated that the  cis -acting element might repress splicing by blocking the recognition of essential splice site signals.    Conclusions  The foamy viral purine-rich C element regulates splicing by suppressing the branch point recognition of the strongest  env  splice acceptor. It is essential for the formation of unspliced  gag  and singly spliced  pol  transcripts.    Electronic supplementary material  The online version of this article (doi:10.1186/s12977-017-0337-6) contains supplementary material, which is available to authorized users.

A purine-rich element in foamy virus pol regulates env splicing and gag/pol expression