Table 1.
Oligonucleotide primers used for the cDNA amplification and sequencing of JEV/Bo/Aichi/1/2010
| Primer | Sequence (5'-3') | Position | Purpose | References |
|---|---|---|---|---|
| JF1 |
TTACTCAGCGCAAGTAGGAGCGTCTCAAG |
1440-1468 |
RT-PCR (E region) |
Yeh et al. (2010) |
| JF2 |
TTACTCAGCGCAAGTTGGGGCGTC |
1440-1463 |
|
|
| JR1 |
ATGCCGTGCTTGAGGGGGACG |
1675-1655 |
|
|
| JR2 |
CAYGCTGTGCTCGAAGGGGACG |
1675-1654 |
|
|
| JE955f |
TGYTGGTCGCTCCGGCTTA |
956-974 |
RT-PCR (E region) |
Nerome et al. (2007) |
| JE2536r |
AAGATGCCACTTCCACAYCTC |
2537-2517 |
|
|
| JE10141f |
TGGATTGAAGAAAATGAATGGATG |
10141-10164 |
RT-PCR (3'UTR) |
Nerome et al. (2007) |
| JE10965r |
AGATCCTGTGTTCTTCCTCTC |
10965-10945 |
|
|
| JEV9-2193F |
ATCTGTGTGAACTTCTTGGC |
9-28 |
RT-PCR and sequencing |
Katayama et al. (2013) |
| JEV9-2193R |
TTTACCCAGCGTGCTTCCAGC |
2193-2173 |
|
|
| JEV1850-3845F |
TGGACAAACTGGCTCTGAAGGG |
1850-1871 |
|
|
| JEV1850-3845R |
TTCTCTTGGTTCGTCCATCTCG |
3845-3824 |
|
|
| JEV3655-5606F |
CTACTTGTGCTGATGCTTGG |
3655-3674 |
|
|
| JEV3655-5606R |
ATTGGGGCATTTGAGTC |
5606-5590 |
|
|
| JEV5409-7958F |
CCATAGACTAATGTCACCAAAC |
5409-5430 |
|
|
| JEV5409-7958R |
AGAGTTGCTGCGTAGTAG |
7958-7941 |
|
|
| JEV7543-9421F |
GACAATGGAGCCAGTGC |
7543-7559 |
|
|
| JEV7543-9421R |
CCTTGACCACTTTGTGCCTG |
9421-9402 |
|
|
| JEV9234-10965F |
CATTCTCCGTGACATAGCAGG |
9234-9254 |
|
|
| JEV9234-10965R |
AGATCCTGTGTTCTTCCTCACC |
10965-10944 |
|
|
| JEV1108R |
GGACATCTAGTGTTGGTTTG |
1108-1089 |
5'RACE and sequencing |
Katayama et al. (2013) |
| JEV1030R |
CTCCACTGGCTCCTTCTATG |
1030-1011 |
|
|
| JEV157R |
ATCCGCGTTTCAGCATATTGATGG |
157-134 |
|
|
| JEV9568F |
GTCATCGGACCACAACACTTG |
9568-9588 |
3'RACE and sequencing |
Katayama et al. (2013) |
| JEV10757F |
CCGTGGAAACAACATTATGC |
10757-10776 |
|
|
| JEV3305R |
TCAAGGACAATGCCGTTCTC |
3305-3286 |
Sequencing |
Katayama et al. (2013) |
| JEV5124R |
CTCTTGACGGTCGCCTTGC |
5124-5106 |
|
|
| JEV7367R |
TCCACGACGGCATTCTTCATTAT |
7367-7345 |
|
|
| JEV7819F |
AACATAGTGGGAGGACATC |
7819-7837 |
|
|
| JEV8993R |
GCATTGACCATCTCCCAGAAC |
8993-8973 |
|
|
| JEV10306R |
CCCTCACTTGGTTTATTGCCG |
10306-10286 |
|
|
| JEV970R |
CTGGAGCGACCAATAGCAAG |
970-951 |
Sequencing |
This study |
| JEV2240F |
GTGACACAGCCTGGGACTTC |
2240-2259 |
|
|
| JEV3906F |
AGTCCACGGAATCCTGAATG |
3906-3925 |
|
|
| JEV6041F |
CCACCAGTGAAGATGACAGCAAC |
6041-6063 |
|
|
| JEV7539R |
CAAGGTGAGTGTGGCTGCCGTC |
7539-7518 |
|
|
| JEV8090F |
AGCCTAGTGACACCCTGTTC |
8090-8109 |
|
|
| JEV9249R | TATGTCACGGAGGATGTATC | 9249-9230 |