Table 1.
Primers for RT-PCR amplification, SHAPE and RLM-RACE.
| ELVd-specific primers (and polaritya) | Sequence (5′→ 3′) | Positionsb | Use |
|---|---|---|---|
| RF-1024 (c) | TATGGGGAGAGGTCGTC | 333–317 | SHAPE (+) and 5′-RACE (RT) |
| RF-701 (c) | AGAGGTCGTCCTCTATCTCTCCTGGAAGG | 326–298 | 5′-RACE (+) (PCR) |
| RF-1070 (c) | GAGCAATCCTTTTGAGGTACACCC | 294–271 | 5′-RACE (+) (nested PCR) |
| RF-975 (h) | GGGTGGGTGTACCTCTTTTGGATTGCT | 267–293 | SHAPE (−) and 5′-RACE (RT) |
| RF-1071 (h) | CCTTCCAGGAGAGATAGAGGACGACCTCT | 298–326 | 5′-RACE (−) (PCR) |
| RF-1313 (h) | GGGTGGTGTGTGCCACCCCT | 1–20 | 5′-RACE (−) (nested PCR) |
| RF-1331 (h) | GACGGTGGGTTCGTCGACACC | 198–218 | SHAPE (−) |
| RF-676 (h) | CCTTWAAWCGTTCCTCCAAG | 86–105 | RT-PCR (−) (Progeny) |
| RF-677 (c) | WCGAATCCTCCGAATTTA | 85–68 | PCR (+) (Progeny) |
| RF-1299 (h) | GAGGACGACCTCTCCCCATA | 314–333 | RT-PCR (−) (Progeny) |
| RF-1298 (c) | TATCTCTCCTGGAAGRCCGG | 313–294 | PCR (+) (Progeny) |
| Adaptors and adaptor-specific primers | Sequence (5′→ 3′) | Positions | Use |
| Adaptor A | CGACUGGAGCACGAGGACACUGACAUGGACUGAAGGAGUAGAAA | ||
| RF-553 (h) | TGGAGCACGAGGACACTGACATG | 5–27 | 5′-RACE (+) (PCR) |
| RF-554 (h) | GACACTGACATGGACTGAAGGAGTAG | 16–41 | 5′-RACE (+) (nested PCR) |
| Adaptor B | CUCAAAAGUUUCGCCGUAUCUCAACGGCUCAUCAGUGGGCUUAGCCCAGACUUUUGAGAGAAGUGGCG | ||
| RF-37 (h) | CGGCCTCATCAGTGGGCTTAG | 25–44 | 5′-RACE (−) (PCR) |
| RF-1086 (h) | CCCAGACTTTTGAGAGAAG | 45–63 | 5′-RACE (−) (nested PCR) |
a
h, homologous; c, complementary
b
Numbering refers to plus polarity