TABLE 1.
Primary sequence and secondary structure elements analysis of the JEV’s UTRs.
| UTR |
5′UTR
|
3′UTR
|
|||||||||
| Genotypes | I | II | III | IV | V | I | II | III | IV | V | |
| Primary sequence | Length (nt) | 96 | 95 | 95 | 95 | 95 | 565–571 | 570 | 557–583 | 584 | 586–591 |
| Similarity | 90.7–100% (μ = 98.31%) |
— | 95.9–100% (μ = 99.36%) |
— | 99–100% (μ = 99.34%) |
95.5–100% (μ = 98.71%) |
— | 88.6–100% (μ = 97.83%) |
— | 94.9–100% (μ = 96.6%) |
|
| Nucleotide composition | A = 32.38% | A = 31.58% | A = 31.58% | A = 29.47% | A = 32.63% | A = 28.12% | A = 29.3% | A = 29.17% | A = 29.28% | A = 30.72% | |
| G = 24.00% | G = 24.21% | G = 24.20% | G = 24.21% | G = 24.21% | G = 29.65% | G = 28.95% | G = 29.03% | G = 28.42% | G = 28.51% | ||
| T = 31.14% | T = 32.63% | T = 32.66% | T = 33.68% | T = 31.93% | T = 18.32% | T = 18.25% | T = 18.51% | T = 18.15% | T = 18.83% | ||
| C = 12.50% | C = 11.58% | C = 11.57% | C = 12.63% | C = 11.23% | C = 23.92% | C = 23.51% | C = 23.42% | C = 24.14% | C = 21.95% | ||
| A > T > G > C | T > A > G > C | T > A > G > C | T > A > G > C | A > T > G > C | G > A > C > T | A > G > C > T | A > G > C > T | A > G > C > T | A > G > C > T | ||
| Repeat sequences (number) | 5 | 4 | 4 | 3 | 4 | 5 | 4 | 5 | 5 | 4 | |
|
| |||||||||||
| Secondary structure (Location and length) | SLA | 5–71 (67 nt) |
5–71 (67 nt) |
5–71 (67 nt) |
11–73 (63 nt) |
5–71 (67 nt) |
na | na | na | na | na |
| SLB | 73–109 (37 nt) |
73–108 (36 nt) |
73–108 (36 nt) |
85–95 (11 nt) |
73–108 (36 nt) |
na | na | na | na | na | |
| 5′UAR| | 79–103 (13 nt) |
79–102 (14 nt) |
79–102 (15 nt) |
79–102 (13 nt) |
79–102 (12 nt) |
na | na | na | na | na | |
| UFS| | | 73–109 (12 nt) |
73–108 (12 nt) |
73–108 (12 nt) |
— | 73–108 (12 nt) |
na | na | na | na | na | |
| cHP | 116–135 (20 nt) |
115–134 (20 nt) |
115–134 (20 nt) |
115–134 (20 nt) |
115–134 (20 nt) |
na | na | na | na | na | |
| 5′DAR | 109–113 (5 nt) |
108–112 (5 nt) |
108–112 (5 nt) |
108–112 (5 nt) |
108–112 (5 nt) |
na | na | na | na | na | |
| 5′cCS | 137–147 (11 nt) |
136–146 (11 nt) |
136–146 (11 nt) |
136–146 (11 nt) |
136–146 (11 nt) |
na | na | na | na | na | |
| Domain1 | VVR | na | na | na | na | na | 1–48 (48 nt) |
1–49 (49 nt) |
1–62 (62 nt) |
1–62 (62 nt) |
1–74 (74 nt) |
| xrRNA1 | na | na | na | na | na | 54–128 (75 nt) |
55–129 (75 nt) |
68–142 (75 nt) |
68–142 (75 nt) |
80–154 (75 nt) |
|
| 3′vrSL | na | na | na | na | na | 136–208 (73 nt) |
137–209 (73nt) |
150–222 (73 nt) |
150–222 (73 nt) |
162–234 (73 nt) |
|
| xrRNA2 | na | na | na | na | na | 123–278 (67 nt) |
214–280 (67 nt) |
227–293 (67 nt) |
228–293 (66 nt) |
238–302 (65 nt) |
|
| PK1| | na | na | na | na | na | 83–87 107–111 (3 nt) | 84–88 108–112 (3 nt) | 97–101 121–125 (3 nt) | 97–101 121–125 (3 nt) | 109–113 133–137 (3 nt) | |
| PK2 | na | na | na | na | na | 240–242 261–263 (3 nt) | 241–243 262–264 (3 nt) | 254–256 275–277 (3nt) | 254–256 275–277 (3 nt) | 263–265 284–286 (3 nt) | |
| 3′vrCS1 | na | na | na | na | na | 154–179 (26 nt) | 155–180 (26 nt) | 168–193 (26 nt) | 168–193 (26 nt) | 180–205 (26 nt) | |
| Domain2 | DB1 | na | na | na | na | na | 300–370 (71 nt) | 301–371 (71 nt) | 314–384 (71 nt) | 314–384 (71 nt) | 323–393 (71 nt) |
| DB2 | na | na | na | na | na | 381–448 (68 nt) | 382–449 (68 nt) | 395–462 (68 nt) | 395–462 (68 nt) | 402–469 (68 nt) | |
| PK3 | na | na | na | na | na | 322–328 449–455 (7 nt) | 323–329 450–456 (7 nt) | 336–342 463–469 (7 nt) | 336–342 463–469 (7 nt) | 345–351 450–456 (7 nt) | |
| PK4 | na | na | na | na | na | 403–407 459–463 (5 nt) | 404–408 459–463 (5 nt) | 417–421 472–475 (5 nt) | 417–421 472–476 (5 nt) | 424–428 480–484 (5 nt) | |
|
| |||||||||||
| 3′dbRCS | na | na | na | na | na | 341–367 419–445 (27 nt) | 342–368 420–446 (27 nt) | 355–381 433–459 (27 nt) | 355–381 433–459 (27 nt) | 364–390 440–466 (27 nt) | |
| 3′dbCS2 | na | na | na | na | na | 381–391 (11 nt) | 382–392 (11 nt) | 395–405 (11 nt) | 395–405 (11 nt) | 402–412 (11 nt) | |
| 3′dbsHP | na | na | na | na | na | 450–464 (15nt) | 451–464 (14 nt) | 464–477 (14 nt) | 464–477 (14 nt) | 471–485 (15 nt) | |
| 3′cCS | na | na | na | na | na | 460–470 (11 nt) | 460–470 (11 nt) | 473–483 (11 nt) | 473–483 (11 nt) | 481–491 (11 nt) | |
| 3′sHP | na | na | na | na | na | 473–489 (17 nt) | 473–489 (17 nt) | 486–502 (17 nt) | 486–502 (17 nt) | 494–510 (17 nt) | |
| 3′DAR | na | na | na | na | na | 473–478 (5 nt) | 473–478 (5 nt) | 486–491 (5 nt) | 486–491 (5 nt) | 494–498 (5 nt) | |
| 3′UAR| | na | na | na | na | na | 481–504 (13 nt) | 481–504 (14 nt) | 495–417 (15 nt) | 495–417 (13 nt) | 502–525 (12 nt) | |
| 3′SL | na | na | na | na | na | 490–573 (84 nt) | 490–573 (84 nt) | 503–586 (84 nt) | 503–586 (85 nt) | 511–594 (84 nt) | |
| : Non-contiguous nucleic acid sequence; | | : non-contiguous complementary nucleic acid sequence; NA: Not available. The results of nucleotide similarity and base composition were all within genotypes. SLA, stem loop A; SLB, stem loop B; UFS, 5′-UAR-flanking stem; 5′UAR, 5′ upstream AUG region; 5′DAR, 5′ downstream AUG region; cHP, capsid-coding region hairpin; 5′cCS, 5′cyclization sequence; VR, variable region; xrRNA, the exoribonuclease XRN1 resistant RNA; PK, pseudoknot; 3′vrCS1, the 3′UTR variable region conserved sequences 1; 3′dbRCS, the 3′UTR dumbbell structure repeated conserved sequences; 3′dbCS2, the 3′UTR dumbbell structure conserved sequences 2; 3′dbsHP, the 3′UTR DB region small hairpin; 3′cCS, 3′cyclization sequence; 3′DAR, 3′ downstream AUG region; 3′UAR, 3′upstream AUG region upstream AUG region; 3′sHP, the 3′UTR short hairpin; 3′SL, the 3′UTR stem loop.