Figure 3
From: Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
Mean (blue) synonymous substitution rates observed across gag, pol , vif and vpr genes. Mean dS was calculated over sliding windows of three codons. Horizontal lines mark the most stringent (red) and less stringent (purple) significance thresholds. (a) dS across the gag gene. 'sl4'; the fourth stem loop of the encapsidation signal, 'INS1'; a motif within the first inhibitory sequence region, 'INS2'; a motif within the second inhibitory sequence region. (b) dS across the pol gene. 'crs'; start of the cis-repressive sequence, horizontal dotted line is the nuclease hypersensitive region and sites 'B', 'G', 'C' and 'D' are confirmed transcription factor binding sites known as site-B, GC-box, site-C and site-D respectively. 'p1'and 'p2'; conserved sites within nuclease hypersensitive region. "ese"; exonic splicing enhancer. (c) dS across the vif gene. (d) dS across the vpr gene. 'ssa3'; 3' splice acceptor site A3, 'rnase'; RNae-V1 cleavage site.