HLADB-2.28.0-January 2010 HLA-J Nucleotide Sequence Alignments Sequences Aligned: 15 January 2010 Steven G. E. Marsh, Anthony Nolan Research Institute. Nuc. Pos. 30 60 Prot. Pos. -20 -10 -1 1 J*01010101 ATG GGG TCA TGG CGC CCC GAA CCC TCC TCC TGC TGC TCT CGG GGA CCC TGG CCC TGG CCG AGA CCT GGG CGG | GCT J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- -.- --- --. --- --- --- --- --- --- --- | --- Nuc. Pos. 90 120 150 Prot. Pos. 10 20 J*01010101 CCC ACT CCA TGA GGT ATT TCA GCA CCG CCG TTT CCT GGC CGG GCC GCG GGG AGC CCA GCT TCA TTG CCG TGG GCT J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 180 210 Prot. Pos. 30 40 50 J*01010101 ACG TGG ACG ACA CGC AGT TCG TGC GGG TCG ACA GTG ACG CCG TGA GTC TGA GGA TGA AGA CGC GGG CGC GGT GGG J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --G --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --G --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. I 240 270 Prot. Pos. I 60 70 J*01010101 TGG AGC . AGG AGG GGC CGG AGT ATT GGG ACC TAC AGA CAC TGG GCG CCA AGG CCC AGG CAC AGA CTG ACC GAG J*01010102 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- C --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- . --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 300 330 360 Prot. Pos. 80 90 100 J*01010101 TGA ACC TGC GGA CCC TGC TCC GCT ACT ACA ACC AGA GCG AGG CGG | GGT ATC ACA TCC TCC AGG GAA TGT TTG GCT J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | C-- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | C-- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 390 420 Prot. Pos. 110 120 J*01010101 GCG ACC TGG GGC CCG ACG GGC GTC TCC TCC GCG GGT ATG AGC AGT ATG CCT ACG ACG GCA AGG ATT ACA TCG CCC J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 450 480 510 Prot. Pos. 130 140 150 J*01010101 TGA ACG AGG ACC TGC GCT CCT GGA CCG CCG CGG ATA CCG CGG CTC AGA TTA CCC AGC GCA AGT ATG AGG CGG CCA J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 540 570 Prot. Pos. 160 170 J*01010101 ATG TGG CTG AGC AAA GGA GAG CCT ACC TGG AGG GCA CCT GCA TGG AGT GGC TCC GCA GAC ACC TGG AGA ACG GGA J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 600 630 650 I 660 Prot. Pos. 180 190 I J*01010101 AGG AGA CGC TGC AGC GCG CGG | ACC CCC CCC AAG ACA CAC GTG ACC CAC CCC CC .. T CTC TGA ACA TGA GGC J*01010102 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- | --- --- --A .-- --- --- --- --- --- -A- -- TG - --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- | --- --- --A .-- --- --- --- --- --- -A- -- TG - --- --- --- --- --- J*0201 --- --- --- --- --- --- --- | --- --- --- --- --- --- --- --- --- --- -- .. - --- --- --- --- --- Nuc. Pos. 690 720 Prot. Pos. 200 210 220 J*01010101 ATA ACG AGG TCC TGG GTT CTG GGC TTC TAC CCT GCG GAG ATC ACA TTG ACC TGG CAG CGG GAT GGG GAG GAC CAG J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 750 780 810 Prot. Pos. 230 240 J*01010101 ACC CAG GAC ATG GAG CTC GTG GAG ACC AGG CCC ACA GGG GAT GGA ACC TTC CAG AAG TGG GCG GTT GTG GTA GTG J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 840 I 870 Prot. Pos. 250 260 I 270 J*01010101 CCT TCT GGA GAG GAA CAG AGA TAC ACA TGC CAT GTG CAG CAC AAG GGG . CTG CCC AAG CCC CTC ATC CTG AGA J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010107 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*01010108 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- . --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- C --- --- --- --- --- --- --- --- Nuc. Pos. 900 930 960 Prot. Pos. 280 290 J*01010101 TGG G | AG CCC TCT CCC CAG CCC ACC ATC CCC ATT GTG GGT ATC ATT GCT GGC CTG GTT CTC CTT GGA GCT GTG GTC J*01010102 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010103 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010104 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010105 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010106 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- J*01010107 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... J*01010108 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... J*0201 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- Nuc. Pos. 990 1020 Prot. Pos. 300 310 320 J*01010101 ACT GGA GCT GTG GTC ACT GCT GTG ATG TGG AGG AAG AAG AGC TCA G | AT AGA AAA GGA GGG AGC TAC TCT CAG GCT J*01010102 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010103 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010104 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010105 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010106 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010107 ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*01010108 ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- J*0201 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- --- --- --- --- --- --- --- --- Nuc. Pos. 1050 1080 Prot. Pos. 330 340 J*01010101 GCA A | GC AGC CAA AGT GCC CAG GGC TCT GAT GTG TCT CTC ACG GCT TGT AAA G | TG TGA J*01010102 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010103 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010104 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010105 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010106 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010107 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*01010108 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- --- J*0201 --- - | -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- - | -- ---