Structure of a plant Ty1- copia retrotransposon, which contains two long terminal repeat (LTR) elements at either end (red boxes) surrounded by short inverted repeats (black arrows). The LTRs contain elements U3, R and U5 for transcription initiation and termination. The primer binding site (PBS) and polypurine tract (PPT) are priming sites for reverse transcription (solid black lines). The PBS also matches a limited set of tRNAs. The universal 5’TG end and the CA 3’ terminus adjacent to the PBS are shown as small black boxes. The internal domain consists of gag and pol regions. The gag region encodes capsid-like proteins (CP) and has a nucleic acid binding moiety (NA). The pol region encodes protease (PR), integrase (INT), reverse transcriptase (RT) and RNase-H.