Comparison of intron 3 G runs and their sequence surroundings in HIV-1 subtypes. (A-B) Proviral DNA sequence surroundings of the HIV-1 consensus sequences A1 to AE of GI3-1 to GI3-4. Conserved sequences are represented by –, deviants by letters. Conserved G run motifs are highlighted by grey boxes. The ORF of vif and vpr including start and stop codons are indicated as declining boxes. The subtype sequences were analyzed with the RIP 3.0 software (http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html). (C) Molecular clones of pNL4-3 used in this study. Sequences of G runs GI3-1 and GI3-2 including surrounding nucleotides are depicted. Mutated sequences are represented by letters. Corresponding consensus sequences are indicated on the right. (D) The amino acid substitutions of the proviral clones used in this study. The sequence of G runs GI3-1 and GI3-2 including surrounding nucleotides is depicted. Substituted amino acids and their position in Vif Protein are shown in the table. Corresponding consensus sequences are indicated on the right.