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Table 4 Properties of 22 CTL epitopes that frequently co-occur together in the reference HIV-1 genomes (per the 62-all sequence set).

From: Discovery of novel targets for multi-epitope vaccines: Screening of HIV-1 genomes using association rule mining

Gene Protein Non overlapping genomic regions Amino acid sequence HLA allele * Amino acid Coordinates Number of "unique" association rules each epitope is involved Number of association rules each region is involved
      Start End   
Gag p24 1 SPRTLNAWV B*0702 16 24 2 2
   2 SEGATPQDL# B*4001 44 52 127 72
   3 GHQAAMQML# B*1510, B*3901 61 69 214 110
   4 KRWIILGLNK## B*2705 131 140 7 95
    GLNKIVRMY B*1501 137 145 195  
    VRMYSPVSI Cw18 142 150 1  
Pol RT 5 IETVPVKL B*4001 5 12 9 9
   6 KLVDFRELNK A*0301 73 82 188 100
   7 GIPHPAGLK A*0301 93 101 124 73
   8 TVLDVGDAY### B*3501 107 115 38 31
   9 NETPGIRYQY B18 137 146 14 9
    IRYQYNVL B*1401 142 149 11  
   10 LVGKLNWASQIY B*1501 260 271 112 51
    KLNWASQIY A*3002 263 271 114  
  RT-RNase 11 IVTDSQYAL Cw*0802 495 503 149 69
    VTDSQYALGI B*1503 496 505 153  
  RT-Integrase 12 LFLDGIDKA B81 560 8 121 68
  Integrase 13 KTAVQMAVF B*5701 173 181 52 39
    AVFIHNFKRK A*0301, A*1101 179 188 15  
    FKRKGGIGGY B*1503 185 194 4  
   14 VPRRKAKII B42 260 268 2 2
Nef   15 FLKEKGGL### B*0801 90 97 52 34
  1. These epitopes are harbored by 15 different protein-coding genomic regions. For each epitope and genomic region the number of "unique" association rules (as defined in Table 2) is shown, as well as the corresponding HLA alleles that recognize that particular CTL epitope.
  2. * HLA alleles as defined in the HIV Molecular Immunology Database, Los Alamos National Laboratory.
  3. #, ## and ### designate potentially promiscuous CTL epitopes that are: (#) recognized by alternative HLA alleles, (##) potentially embedded, or (###) shared between allele pairs (per [59]).