Methods and compositions for the targeted integration of nucleotide sequences into a plant are provided. Particularly, the present invention is drawn to compositions comprising polynucleotide sequences having the following operably linked components: an intron, a nucleotide sequence of interest, and a terminator region, wherein the polynucleotide sequence comprises one or more recombination sites. The recombination sites are non-identical to one another and one of the recombination sites is contained within the intron.