TABLE 2.
Oligonucleotide primers used for RT-PCR
| Primer | Nucleotide sequence (5′ to 3′) | Polarity | Positionsa | Gene | RNA template(s) used in RT-PCR |
|---|---|---|---|---|---|
| 293 | AGCAACCTTGTGGTTGGTCTGT | + | 27805-27826 | 3′-NTR | All |
| 294 | CTTACATGGAGACACTCAACCA | − | 27920-27941 | 3′-NTR | All |
| 1344 | GAGAAAGAGCCAAGATGAATT | + | 27299-27319 | IGR N | All |
| 692 | GGATTAAGCATAGAATTCAT | − | 27313-27322 | N | P-MAR |
| 1383 | TAGCATTTGGATTAAGCATAGA | − | 27319-27340 | N | All |
| 1433 | AAGTTTGAGTAGCCACTTATC | + | 26773-26793 | IGRe M/HE | B6, B145, B150, B155, B156, B1314, P78 |
| 1345 | GAGACACTATCTTTAG | + | 27284-27299 | IGR N | P-MAR, P4, P9, P10 |
| 795 | GGATGACAGACACCACTCATC | − | 660-680b | HE | P-MAR |
| 1434 | CATCTTCTAAAGATAAGTGG | − | 26785-27804 | IGR M/HE | P4, P9, P10, B6, B145, P-MAR |
| 1435 | TCTTTGAAGATTGCCAAAA | + | 26061-26083 | IGR S/M | P4, P9, P10, B6, B145 |
| 1493 | AAGAATATTAAACTCAGCAT | − | 1-21c | HE | B150 |
| 1494 | AAGTTAGTCACTTTCTTTAGT | + | 26048-26068 | IGR S/M | B150, B155 |
| 1478 | GTGTTTAGTACTAGTTTAAGTT | + | 21259-21280 | ORF1b | P-MAR, B145 |
| 1542 | GCTGTACAGAGCATTTGGTCA | + | 853-873c | HE | B6, B145, B150 |
| 1543 | GCTGTTCAGAGTATTTGGTCA | + | 877-897b | HE | B6 |
| 1544 | GTGGTGAAAAATTCACACC | − | 289-307c | M | B150 |
| 1546 | GTGCTGCAAGGTGTTGCAGA | + | 26731-26750 | M | B150 |
| 1833 | CTAGGAAAATATGGATTATTA | − | 123-143d | HE | B155 |
a
Positions with respect to the Berne virus genome, unless indicated otherwise.
b
Position as counted from the iniation codon of the PToV Markelo HE gene.
c
Position as counted from the start codon of the BToV BRV HE gene.
d
Position as counted from the initiation codon of the B155 HE gene.
e
IGR, intergenic region.