Table 3 Regions of the HIV-1 sequence which should be considered for exclusion in positive selection analysis studies.
From: Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
Gene | dS Variance | Overlapping regions | Highly conserved (most stringent cutoff) | Other sites conserved at 0.05 significance |
|---|---|---|---|---|
gag | 2.1 | 2086 – 2295 (gag/pol) | 793 – 807 | 821–823 |
|  |  |  | 898 – 903 | 1036–1038 |
|  |  |  | 985 – 996 | 1810–1812 |
|  |  |  | 1309 – 1314 | 1831–1833 |
|  |  |  |  | 1969 – 1974 |
|  |  |  |  | 2002–2004 |
|  |  |  |  | 2023 – 2025 |
pol | 1.8 | 5041 – 5097 (pol/vif) | 4092 – 4094 | 2490–2495 |
|  |  |  | 4764 – 4790 | 2850 – 2858 |
|  |  |  | 4864 – 4866 | 3252 – 3257 |
|  |  |  | 4926 – 4937 | 3304 – 3312 |
|  |  |  |  | 3867 – 3881 |
|  |  |  |  | 3966 – 3971 |
vif | 2.7 | 5560 – 5619 (vif/vpr) | - | - |
vpr | 3.9 | 5833 – 5850 (vpr/tat) | 5769 – 5777 | - |
|  |  |  | 5794 – 5805 |  |
tat | 2.9 | 5968 – 6060 (tat/rev) | 5855 – 5863 | - |
|  |  |  | 5957 – 5968 |  |
vpu | 1.4 | 6223 – 6312 (vpu/env) | 6101 – 6106 | - |
|  |  |  | 6143 – 6151 |  |
|  |  |  | 6167 – 6178 |  |
env | 3. 2 | 8380 – 8796 (env/rev) | 7656 – 7667 | 7077 – 7082 |
|  |  |  | 7834 – 7842 | 7125 – 7130 |
|  |  |  | 8349 – 8354 | 7629 – 7634 |
|  |  |  | 8376 – 8378 |  |
nef | 3.6 |  | 9067 – 9086 | 8869 – 8874 |
|  |  | - | 9087 – 9093 (nef/LTR) | 8887 – 8892 9121 – 9126 |
|  |  |  | 9183 – 9192 (nef/LTR) | 9235 – 9237 |
|  |  |  | 9391 – 9399 (nef/LTR) |  |