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Table 1 Target regions within Conserved Domain RT_rtv

From: An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

Region No. Residue Position
(wild type)
Residue
(wild type)
Function annotation HXB2 coordinates Mutation in RT2 and prevalence3 Evaluated Region in MA4
1 24, 25 W,P DBS 2619-2622 - 2610 - 2630
2 60 V - 2727 I(14) 2700 - 2760
  61 F AS 2730 -  
  62 A - 2733 V(14)  
  64 K - 2736 R(1.9)  
  65 K dBS 2742 R(2.1)  
  67 D - 2748 N(38), G(2.5)  
3 72 R dBS 2763 - 2750 -2800
  74-76, 78, 81 L,V,D,R,N DBS-AS 2769-2790 -  
4 89 E DBS-AS 2814 - 2800 - 2840
  90 V - 2828 I(3.3)  
  91,92,94 Q,L,I DBS-AS 2820-2829 -  
5 100-103 L,K,K,K NNBS 2847-2856 - 2835 - 2870
6 110-115 D,V,G,D,A,Y dBS-AS 2877-2892 - 2865 - 2905
7 151 Q dBS-AS 3000 M(3.4) 2985-3020
  152,154,157 G,K,P DBS-AS 3003-3018 -  
8 178 I - 3081 M(7.5), L(6.4) 3070-3130
  179 V NNBS 3084 I(7.9), D(1.3)  
  181 Y - 3090 C(14)  
  183 Y NNBS-DBS-AS 3096 -  
  184 M variable 3099 V(50), I(1.4)  
  185 D dBS-AS 3102 -  
  186 D AS 3105 -  
  188 Y NNBS 3111 L(3.5)  
  190 G NNBS 3117 -  
9 227 F NNBS 3228 L(1.6) 3210-3255
  228 L - 3231 H(12), R(4.2)  
  230 M DBS-AS 3237 L(1.8)  
  231 G DBS-AS 3240 -  
  1. 1Positions according to the HXB2 reference genome numbering system (coordinate map)
  2. 2RT drug resistance mutations prevalence was calculated from 17,167 sequences exposed to either of these drug types (HIV Drug Resistance Database)
  3. 3Mutation prevalence (percent) data are available at the HIV Drug Resistance Database
  4. 4MSA: multiple alignment
  5. In bold, residues directly involved in enzyme activity
  6. DBS, DNA binding site
  7. dBS, dNTP binding site
  8. NNBS, non-nucleoside reverse transcriptase inhibitor binding site
  9. AS, active site