Figure 2

Result from a run of the chimpanzee genome (panTro2). The chimpanzee version of the human HERVFc1 retroviral sequence [3] is shown. The components LTR (5 LT & 3 LT), primer binding site (PBS), gag (internal structural proteins; motifs named CA and NC), pro (protease, motifs named PR), pol (pol gene, motifs named RT, RH and IN), env (envelope gene, motifs named SU and TM), and polypurine tract (PPT) are shown. Figures above each motif denote its score (0–100). The following features are also predicted: Red bars denote stop codons, blue bars start codons. Triple lines denote putative protein encoding sequences. Green bars denote putative asparagine glycosylation sites, "/" splice donor, "\ " splice acceptor, "S" "Slippery" sequence (possible frameshift sites), and "8" pseudoknot sequences (which are also possible frameshift sites).