Figure 4

Mean (blue) synonymous substitution rates observed across tat, vpu , env and nef genes. (a) dS across the tat gene. 'ess2'; exonic splicing silencer ESS2, 'ssa4b'; 3' splice acceptor site A4b. (b) dS across the vpu gene. 'n2', 'n3' and 'n4'; novel conserved sites. (c) dS across the env gene. "n1" is the novel conserved site. The black dotted horizontal lines indicate poorly aligned regions that were excluded from the analysis. "rre"; rev-responsive element, *; the 9 nucleotides (5' GACGGUACA 3') which bind to the Rev protein with highest affinity, "ss"; splice site region for the tat and rev 3' exons. (d) dS across the nef gene. "G-A"; G-to-A hypermutations (see Additional file 1), 'var'; highly variable region, 'ppt'; poly-purine tract, "c"; PPT integrase attachment site, 'nre'; start of the negative repressive sequence, 'ets'; Ets-1 transcription factor binding site.