Polynucleotides, vectors, vector systems, cells, and methods for expressing AAV Rep proteins are provided. In certain aspects, these polynucleotides, vectors, vector systems, cells, and methods may be used to produce higher levels of small Rep transcripts as compared to large Rep transcripts. In certain aspects, these polynucleotides, vector systems, cells, and methods may be used to produce higher levels of small Rep proteins as compared to large Rep proteins. In certain aspects, these polynucleotides, vectors, vector systems, cells, and methods may be used to produce recombinant AAV (rAAV). Increased expression of small Rep as compared to large Rep is useful in many aspects, such as, increasing total virions and increasing packaged virions during the production of rAAV.