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 |