Table 1.
Pairing of PvmiR399 isoforms a, b and e with the predicted binding sites of the 5′ UTR of the PvPHO2 target gene from BAT477 and DOR364 genotypes. The sequence of the predicted binding sites is shown in Figure 3. Watson-Crick base pairing is indicated by “I”; G:U base pairing by “:”; and “-” indicates a mismatch. Each miRNA:mRNA alignment score is shown in parenthesis: mismatch penalty = 1, G:U pair penalty = 0.5 [25]. Differences between BAT477 and DOR364 in binding site 1 are highlighted in red.
| miRNA | PvmiR399 binding site PHO2 5′ UTR region | BAT477 miRNA:mRNA pairing (score) | DOR364 miRNA:mRNA pairing (score) |
|---|---|---|---|
| PvmiR399a | 1 | I-IIIIII-IIIIIIIIIIII (2.0) | I-IIIII--IIII-IIIIIII (4.0) |
| PvmiR399b | 1 | I-IIIIIIIIIIIIIIIIIII (1.0) | I-IIIII-:IIII-IIIIIII (3.5) |
| PvmiR399e | 1 | IIIIIIII-IIIIIIIIIIII (1.0) | IIIIIII--IIII-IIIIIII (3.0) |
| PvmiR399a | 2 | IIIII-IIIIII-IIII--II (4.0) | IIIII-IIIIII-IIII--II (4.0) |
| PvmiR399b | 2 | IIIIII---III-IIII--II (6.0) | IIIIII---III-IIII--II (6.0) |
| PvmiR399e | 2 | I-III-IIIIII-IIII--II (5.0) | I-III-IIIIII-IIII--II (5.0) |
| PvmiR399a | 3 | I-IIIIIIIIIIIIIIIIIII (1.0) | I-IIIIIIIIIIIIIIIIIII (1.0) |
| PvmiR399b | 3 | I-IIIIIIIII-IIIIIIIII (2.0) | I-IIIIIIIII-IIIIIIIII (2.0) |
| P-miR399e | 3 | IIIIIIIIIIIIIIIIIIIII (0.0) | IIIIIIIIIIIIIIIIIIIII (0.0) |
| PvmiR399a | 4 | I--II:IIIIIIIIIIIIII: (3.0) | I--II:IIIIIIIIIIIIII: (3.0) |
| PvmiR399b | 4 | I--II:II-IIIIIIIIIII: (4.0) | I--II:II-IIIIIIIIIII: (4.0) |
| PvmiR399e | 4 | I--II:IIIIIIIIIIIIII: (3.0) | I--II:IIIIIIIIIIIIII: (3.0) |
| PvmiR399a | 5 | I--IIIIIIIIIIIIIII-II (3.0) | I--IIIIIIIIIIIIIII-II (3.0) |
| PvmiR399b | 5 | I--IIIII-IIIIIIIII-II (4.0) | I--IIIII-IIIIIIIII-II (4.0) |
| PvmiR399e | 5 | I--IIIIIIIIIIIIIII-II (3.0) | I--IIIIIIIIIIIIIII-II (3.0) |