APorcine teschovirus alignments
Accesssion No. | Domain II | [ --PK1a--] [III1][III2]
AB038528 192 UUGUCACCAGGUAUUGCACCAAUGGUGGCGACAGGGUACAGAAGAGCAAGUACUCCUGAC 251
AY392552 96 ...... 155
AY392550 67 ...... 126
AY392548 114 ...... 173
AY392540 98 ...... 157
AF231769 212 ...... 271
AF296100 112 ...... 171
AF296091 112 ...... 171
AY392547 111 ...... G...... 170
AY392542 116 ...... 175
AY392541 110 ...... 169
AF296117 112 ...... 171
AF296092 112 ...... 171
AF296089 112 ...... 171
AF296095 112 ...... 171
AF296119 112 ...... 171
AF296113 113 ...... 171
AY392555 102 ...... C...... 161
AY392553 114 ...... 173
AY392539 114 ...... 173
AF296111 113 ...... G...... 171
AF296090 113 ...... 171
AY392554 66 ...... G...... 125
AY392532 106 ...... G...... 165
AJ011380 212 ...... G...... 271
AF296118 112 ...... C...... C...... 171
AF296112 112 ...... G...... 171
AF296107 112 ...... G...... 171
AF296088 112 ...... G...... 171
AF296093 112 ...... 171
AF296096 212 ...... 271
AY392549 114 ...... 173
AY392546 113 ...... 172
AY392536 105 ...... A...... 164
AY392534 138 ...... G...... 197
AF296115 111 ...... 170
AF296104 212 ...... G...... 271
AF296103 212 ...... G...... 271
AF296102 112 ...... G....C...... 171
AF296087 112 ...... G...... 171
AF296094 112 ...... 171
AF231768 116 ...... 175
AY392537 124 ...... G...... 183
AY392535 67 ...... 126
AF296108 112 ...... G...... 171
DQ355222 1 ...... 39
AY392551 98 ...... G...... C...... 157
AF231767 212 ...... 271
AF296109 113 ...... A...C.....U...... 172
AY392533 124 ...... UC...... 183
[-----IIIa------] [------IIIb------]
AB038528 252 UGGGUAAUGGGACUGCAUUGCAUAUCCCUAGGCACCUAUUGAGAUUUCUCUGGGGCCCAC 311
AY392552 156 ...... 215
AY392550 127 ...... 186
AY392548 174 ...... 233
AY392540 158 ...... 217
AF231769 272 ...... 331
AF296100 172 ...... 231
AF296091 172 ...... 231
AY392547 171 ...... 230
AY392542 176 ....C...... 235
AY392541 170 ....C...... 229
AF296117 172 ....C...... 231
AF296092 172 ....C...... 231
AF296089 172 ...... 231
AF296095 172 ...... 231
AF296119 172 ...... 231
AF296113 172 ....A...... 231
AY392555 162 ....C...... 221
AY392553 174 ...... 233
AY392539 174 ...... 233
AF296111 172 ....C...... 231
AF296090 172 ....C...... G...... 231
AY392554 126 ...... 185
AY392532 166 ....C...... G...... 225
AJ011380 272 ....C...... 331
AF296118 172 ....C...... 231
AF296112 172 ...... 231
AF296107 172 ...... 231
AF296088 172 ....C...... 231
AF296093 172 ...... 231
AF296096 272 ....C...... G...... 331
AY392549 174 ....C...... G...... 233
AY392546 173 ....C...... C...... C...... 232
AY392536 165 ....C...... 224
AY392534 198 ....C...... 257
AF296115 171 ....C...... 230
AF296104 272 ....C...... G...... 331
AF296103 272 ....C...... G...... 331
AF296102 172 ....C...... 231
AF296087 172 C...C...... 231
AF296094 172 ....C...... G...... 231
AF231768 176 ....C...... 235
AY392537 184 ....C...... 243
AY392535 127 ....C...... G...... C...... 186
AF296108 172 ....C...... A...... 231
DQ355222 40 ...... 99
AY392551 158 ....C...... C...... 217
AF231767 272 ....C...... G...... C...... 331
AF296109 173 ....C...... G...... U...... 232
AY392533 184 ....C...... U...... 243
[III2][--- IIId------] [III1] [---IIIe---] [PK2a
AB038528 312 CAGCGUGGAGUUCCUGUAUGGGAAUGCAGGACUGGACUUGUGCUGCCUGACAGGGUCGCG 371
AY392552 216 ...... 275
AY392550 187 ...... 246
AY392548 234 ...... 293
AY392540 218 ...... 277
AF231769 332 ...... 391
AF296100 232 ...... 291
AF296091 232 ...... 291
AY392547 231 ...... 290
AY392542 236 ...... 295
AY392541 230 ...... 289
AF296117 232 ...... 291
AF296092 232 ...... 291
AF296089 232 ...... 291
AF296095 232 ...... C...... 291
AF296119 232 ...... C...... 291
AF296113 232 ...... 291
AY392555 222 ...... 281
AY392553 234 ...... 293
AY392539 234 ...... C.... 293
AF296111 232 ...... 291
AF296090 232 ...... 291
AY392554 186 ...... 245
AY392532 226 ...... 285
AJ011380 332 ....A...... 391
AF296118 232 ...... 291
AF296112 232 ....A...... 291
AF296107 232 ....A...... 291
AF296088 232 ...... 291
AF296093 232 ....A...... 291
AF296096 332 ....A...... 391
AY392549 234 ...... 293
AY392546 233 ....A...... 292
AY392536 225 ....A...... 284
AY392534 258 ...... A...... 317
AF296115 231 ....A...... 290
AF296104 332 ...... 391
AF296103 332 ...... 391
AF296102 232 ....A...... 291
AF296087 232 .G...... 291
AF296094 232 ...... A...... 291
AF231768 236 ...... A...... 295
AY392537 244 ...... 303
AY392535 187 ...... 246
AF296108 232 ....A...... 291
DQ355222 100 ...... 159
AY392551 218 ....A...... 277
AF231767 332 ...... A...... U...... 391
AF296109 233 ...... 292
AY392533 244 ....A...... 303
AF296114 1 ...... 41
AF296106 1 ...... 41
AF296101 1 ...... 41
AF296099 1 ...... 41
AF296105 1 ...... 41
AF296098 1 ...... C...... 41
AF296121 1 ...... 41
AF296116 1 ...... 41
AF296110 1 ...... 41
AF296120 1 ...... 41
PK2a-] [---PK1b---] [-PK2b-]
AB038528 372 GCUGGCCGUCUGUACUUUGUAUAGUCAGUUGAAACUCACCAUG 414
AY392552 276 ...... 318
AY392550 247 ...... 289
AY392548 294 ...... 336
AY392540 278 ...... 320
AF231769 392 ...... 434
AF296100 292 ...... 334
AF296091 292 ...... 334
AY392547 291 ...... 333
AY392542 296 ...... 338
AY392541 290 ...... 332
AF296117 292 ...... 334
AF296092 292 ...... 334
AF296089 292 ...... 330
AF296095 292 ...... 334
AF296119 292 ...... 334
AF296113 292 ...... 334
AY392555 282 ...... 324
AY392553 294 ...... U.... 332
AY392539 294 ...... 332
AF296111 292 ...... 334
AF296090 292 ...... 334
AY392554 246 ...... U.... 284
AY392532 286 ...... 328
AJ011380 392 ...... 434
AF296118 292 ...... 334
AF296112 292 ...... U...... 334
AF296107 292 ...... G...... 334
AF296088 292 ...... 330
AF296093 292 ...... UG...... 334
AF296096 392 ...... 434
AY392549 294 ...... U.... 332
AY392546 293 ...... 335
AY392536 285 ...... G...... 327
AY392534 318 ...... U...... 360
AF296115 291 ...... G...... 329
AF296104 392 ...... G...... 434
AF296103 392 ...... G...... 434
AF296102 292 ...... 334
AF296087 292 ...... 334
AF296094 292 ...... 330
AF231768 296 ...... 328
AY392537 304 ...... G...... U.... 342
AY392535 247 ...... U.U...... 289
AF296108 292 ...... 330
DQ355222 160 ...... 202
AY392551 278 ...... UG...... 320
AF231767 392 ...... C...... A...... 434
AF296109 293 ...... 331
AY392533 304 ...... 337
AF296114 42 ...... 84
AF296106 42 ...... 84
AF296101 42 ...... 84
AF296099 42 ...... 84
AF296105 42 ...... 80
AF296098 42 ...... 84
AF296121 42 ...... UG...... 84
AF296116 42 ...... U.U...... 84
AF296110 42 ...... U.... 80
AF296120 42 ...... 75
BDuck hepatitis virus type 1 alignments
Accesssion No. | ------Domain II ------|
DQ249299 361 GUCUAUGCCUUGGGCUAAUGGUCUUCGUUGUGAAACGGAUUACCGGUAGUAGCAUCUUAG 420
DQ219396 364 ...... U...... 423
DQ226541 364 ...... 423
DQ249300 338 ...... 397
DQ249301 346 ...... 405
EF093502 301 ...... A...... 360
DQ864514 363 ...... C...... 422
DQ886445 328 ...... 387
Domain II | [ --PK1a--] [III1] [--III2--] [--IIIa
DQ249299 421 ACUACCAAGGUUGUAGGUGAGUGUGUGGUCUAGAGUAGGCACACAUCUGUCCAGGCACAU 480
DQ219396 424 ...... 483
DQ226541 424 ...... 483
DQ249300 398 ...... 457
DQ249301 406 ...... 465
EF093502 361 ...... U...... 420
DQ864514 423 ...... U...... 482
DQ886445 388 ...... C...... U...... 447
----IIIa------] [----IIIb----] [--III2--] [------IIId
DQ249299 481 GCACAUUGUUGCGAUUGCUCCAGACUAGUUCCUGAGGGACAGAUGUUGUGGGGGGCUUGG 540
DQ219396 484 ...... 543
DQ226541 484 .U...... A...... 543
DQ249300 458 ...... A...... A...... 517
DQ249301 466 ...... 525
EF093502 421 ...... C.. 480
DQ864514 483 ...... C.. 542
DQ886445 448 ...... U...... C.. 507
IIId------] [III1] [---IIIe---] [-PK2a-] [---PK1b---]
DQ249299 541 GAAAACCCCCUUAACCUACAUUGCCUGAUAGGGUCGCGGCUGGUCGAGUCCCACACACUA 600
DQ219396 544 ...... C...... 603
DQ226541 544 ...... C...... 603
DQ249300 518 ...... C...... 577
DQ249301 526 ...... C.A...... U...... A...... 585
EF093502 481 ...... C...... 540
DQ864514 543 ...... C...... 602
DQ886445 508 ...... C...C...... 567
[-PK2b-]
DQ249299 601 UAAUACCAGUAGACUUUCAUGCAAUG 626
DQ219396 604 ...... 629
DQ226541 604 ...... 629
DQ249300 578 ...... 603
DQ249301 586 ...... 611
EF093502 541 ...... A.... 566
DQ864514 603 ...... A.... 628
DQ886445 568 ...... A.... 593
CPorcine enterovirus 8/Porcine enterovirus A alignments
Accesssion No. |------DOMAIN II ------| [PK1a-
AF406813 168 UGUCGAUAGCCAUGUUAGCGACGCGCUUCGGCGUGCUCCUUUGGUGAUUCGGCGACUGGU 227
AY392543 143 ...... U...... 202
AY392545 130 ...... U...... 189
AY392544 134 ...... U...... 193
AY392538 110 ...... C..U...... 169
AY392556 55 ...... U...... 114
PK1a-] [III1] [---III2--] [------IIIa------] [III3]
AF406813 228 UACAGGAGAGUAGACAGUGAGCUAUGGGCAAACCCCUACAGUAUUACUUAGGGG-AAUGUGC 288
AY392543 203 ...... G...... G...... 264
AY392545 190 ...... U...... A...... 251
AY392544 194 ...... G...... G...... 255
AY392538 170 ...... U...... G...... 231
AY392556 115 ...... G...... G....G.....C.....G...... 176
AM261005 2 ...... G...... 52
AM261004 2 ...... G...... 52
AM261003 2 ...... G...... 52
AM260999 2 ...... G...... 52
AM260997 2 ...... G...... G...... 52
AM261008 2 ...... A...... U...... G...... A...... 52
AM261007 2 ...... G...... 52
AM261006 2 ...... G...... 52
AM261002 5 ...... G...... C.....G...... 52
AM261000 5 ...... U...G...... C.....G...... 52
AM260996 1 ...... U..G...... C..A...... 52
AM261001 5 ...... G...... C.....G...... 52
AM260998 10 ...... U...... A...... 52
AM260995 5 ...... G...... C.....G...... 52
[------IIIb------] [III3] [-III2-
AF406813 289 AAUUGAGACUUGACGAGCGUCUCUUU-GAGAUGUGGCGCAUGCUCUUGGCAUUACCAUAG 347
AY392543 265 ...... G.A-...... 323
AY392545 252 ...... A...... -...... 310
AY392544 256 ...... G.A-...... 314
AY392538 232 ...... U.....CA-...... 290
AY392556 177 ...... CA-....C...... 235
AM261005 53 ...... C-...... 111
AM261004 53 ...... C-...... 111
AM261003 53 ...... C-...... 111
AM260999 53 ...... -...... 111
AM260997 53 ...... -...... 111
AM261008 53 ...... -...... 111
AM261007 53 ...... C-...... 111
AM261006 53 ...... C-...... 111
AM261002 53 ...... A-...... G. 111
AM261000 53 ...... A-...... 111
AM260996 53 ...... A....G.A-...... 111
AM261001 53 ...... G...... A-...... 111
AM260998 53 ...... U.G...... 112
AM260995 53 ...... CA-....C...... 111
--III2] [------IIId------] [III1] [---IIIe---] [-PK2a-]
Query 181 UGAGCUUCCAGGUUGGGAAACCUGGACUGGGUCUAUACUGCCUGAUAGGGUCGCGGCUGGC 241
AF406813 348 ...... 408
AY392543 324 ...... A...... 384
AY392545 311 ...... A...... 371
AY392544 315 ...... A...... 375
AY392538 291 ...... A...... 351
AY392556 236 ...... C...C...A...... 296
AM261005 112 ...... G.... 150
AM261004 112 ...... G.... 150
AM261003 112 ...... G.... 150
AM260999 112 .A...... G.... 150
AM260997 112 ...... G.... 150
AM261008 112 ...... G.... 150
AM261007 112 ...... C....C...... G.... 150
AM261006 112 ...... C....C...... G.... 150
AM261002 112 ...... C...... 150
AM261000 112 ...... C...... 150
AM260996 112 ...... 150
AM261001 112 ...... G...... C...... 150
AM260998 113 ...... G.... 151
AM260995 112 ...... G...... C...... 150
[---PK1a---] [-PK2b-]
Query 242 CGCCUGUAACUAGUAUAGUCAGUUGAAAACCCCCCAUG 279
AF406813 409 ...... 446
AY392543 385 ...... C...... 422
AY392545 372 ...... C.... 404
AY392544 376 ...... C..... 409
AY392538 352 ...... C...... 389
AY392556 297 ...... C...... 334
DSimian picornavirus alignments
Accesssion No. [------
AY064717 301 GGCAAUUGUGGUAAGUGAUGUUAGUCAUUGGCAGUUGAAACCUGCCCAAAACAUCCUAGG 360
AY064719 301 ...... G...... 360
AY064715 302 ...... U.G...G...... 361
AY064708 320 ...... UG...... U..G..G...... 379
AY064720 308 ...... CU....A..CAG.....U...... GGA...A.GU...... 367
AY064718 307 ...... CU....A..CAG.....U...... GGA...A.GU...... 366
AY064716 306 ...... CU....A..CAG.....U...... GGA...A.GU...... 365
------Domain II------
AY064717 361 UCUACGCUGUGCGGGCCGAAGUAAGUCUGGGAACAACAGGGAGUAUGCUGUUUUCUGCUU 420
AY064719 361 ...... U..... 420
AY064715 362 ...... A...... G...... U..... 421
AY064708 380 ...... CU.A....U...... CA...... 439
AY064720 368 ...... A..U...... UCU.....A..A.....UCU.A. 427
AY064718 367 ...... A..U...... UCU.....A..A.....UCU.A. 426
AY064716 366 ...... A..U...... UCU.....G..A.....UCU.A. 425
------] [---PK1a---] [III1] [--III2--] [-----IIIa-
AY064717 421 UCACCCAACACGACCGUACACGAAAGAGCUAGAGGCAUCUGGAGGCAAAGGGAAAAGAAU 480
AY064719 421 ...... G. 480
AY064715 422 ...... 481
AY064708 440 ...... CU.U.G...... CU. 499
AY064720 428 .AG...... C.U..UG...... CU.U.G...... U.....C.. 487
AY064718 427 .AG...... C.U..UG...... CU.U.G...... U.....C.. 486
AY064716 426 .AG...... C.U..UG...... CU.U.G...... U.....C.. 485
---IIIa--] [III3] [------IIIb------]
Query 481 UUCUUAGCCCGAAUGUUCAUUUGAGUCCUUGACGAAUGCGUCCCUUCUGUCCCGAAGGUG 540
AY064717 481 ...... 540
AY064719 481 ...... A...... C...... G.... 540
AY064715 482 .....C...... G...... C...... G.... 541
AY064708 500 .G...... G...... C.... 559
AY064720 488 .G.....A...... A.G-..A...... G...UGU.ACAG...... CUGAUG. 506
AY064718 487 .G.....A...... A.G-..A...... G...UGU.ACAG...... CUGAUG. 505
AY064716 486 .G.....A...... A.G-..A...... G...UGU.ACAG...... CUGAUG. 504
[III3] [---III2--] [------IIId-----
Query 541 AGGCGUAUGGCGCAUGCUCAUGGCAUUACUCCAAGGUGUAUCUAGAGGGGGGGGGGCCCC 600
AY064717 541 ...... 600
AY064719 541 ...... -...... 599
AY064715 542 ...... -...... 600
AY064708 560 ...... C.A.U...... GUGA....-.....U.. 618
AY064720 549 CA.-...... U...... C.AU.U...... U...... -...... 603
AY064718 548 CA.-...... U...... C.AU.U...... U...... -...... 602
AY064716 547 CA.-...... U...... C.AU.U...... U...... -...... 601
IIId] [III1] [---IIIe---] [-PK2a-] {---PK1b---]
AY064717 601 CUCUACUUAGUCUAGUGCUACCUGACAGGGCCGCGGCUGGUCGUUUGUGUAUGGUAUA 658
AY064719 600 ...... 657
AY064715 601 ...... 658
AY064708 619 UCAC...... 676
AY064720 604 ..A...... CG....G...... 661
AY064718 603 ..A...... CG....G...... 660
AY064716 602 ..A...... CG....G...... 659
[-PK2b-]
AY064717 659 ACCAGUAGUAAUCCCCCAUG 678
AY064719 658 ...... 677
AY064715 659 ...... 678
AY064708 677 ...... 696
AY064720 662 ...... 681
AY064718 661 ...... 680
AY064716 660 ...... 679
EAvian encephalomyelitis virus type 1 alignments
Accesssion No. | ------Domain II ------|
AJ225173 201 AUCCCUUUGCGUUUCACAGAACCAUCCUAACCAUGGGUGUAGUAUGGGAAUCGUGUAUGG 260
AY517471 200 ...... 259
AY275539 201 ...... 260
| [--PK1--] III1[---III2--] [------IIIa-----
AJ225173 261 GGAUGAUUAGGAUCUCUCGUAGAGGGAUAGGUGUGCCAUUCAAAUCCAGGGAGUACUCUG 320
AY517471 260 ..G...... U...... 319
AY275539 261 ...... 320
IIIa-] [III3][---IIIb1----][------IIIb2------][III3]
AJ225173 321 GCUCUGACAUUGGGACAUUUGAUGUAACCGGACCUGGUUCAGUAUCCGGGUUGUCCUGUA 380
AY517471 320 ...... 379
AY275539 321 .....A...... C...... A...... 380
[----IIIc--] [---III2--] [------IIId------]III1
AJ225173 381 UUGUUACGGUGUAUCCGUCUUGGCACACUGAAAGGGUAUUUUUGGGUAAUCCUUUCCUAC 440
AY517471 380 ...... A...... C...... C...... 439
AY275539 381 ...... U...... C.C...... 440
[---IIIe---] PK2a [--PK1b-] [PK2b]
AJ225173 441 UGCCUGAUAGGGUGGCGUGCCCGGCCACGAGAGAUUAAGGGUAGCAAUUUAAACAUG 497
AY517471 440 ...... C...... 496
AY275539 441 .AU...... 497
Aligned sequences of (A) porcine teschovirus isolates, (B) duck hepatitis virus type 1, (C) porcine entervirus 8/porcine entervirus A, (D) simian picornaviruses and (E) avian encephalomyocarditis virus type 1, labeled to show Genbank accession numbers and annotated to show predicted structural elements and nucleotide differences relative to the designated type sequence. Compensatory substitutions are shaded light blue, disruptive substitutions are shaded yellow, structurally silent single substitutions are shaded grey and substitutions in unpaired elements are bold without shading. A few italicized PEV8 residues were excluded from further consideration because sequenced fragments lacked 5’-terminal sequences that form helix III1, so that it is incomplete and it is impossible to determine whether sequence differences correspond to e.g. compensatory mutations.