Table 4.
Putative target genes of novel miRNAs identified using psRNATarget and TAPIR programs
| Novel miRNA | Target Acc. | Tool used | Score | mfe | Start | Seed gap | Seed mismatch | Seed gu | Gap | Mismatch | gu | E | UPE | Inhibition | Annotation | e-value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Stv_1 |
BG523199 |
psRNA/TAPIR |
2.5 |
0.7 |
55 |
0 |
0 |
1 |
0 |
1 |
1 |
2 |
9.668 |
Cleavage |
AT1G55490 [Arabidopsis thaliana] |
4e-71 |
| Stv_2 |
BG525025 |
psRNA/TAPIR |
0 |
1 |
418 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10.485 |
Cleavage |
Phosphoglycerate kinase [Arabidopsis thaliana] |
8e-101 |
| Stv_7 |
BG526734 |
psRNA/TAPIR |
3.5 |
0.78 |
463 |
0 |
1 |
0 |
0 |
1 |
1 |
3 |
16.578 |
Cleavage |
Pectinacetylesterase family protein [Arabidopsis thaliana] |
3e-108 |
| Stv_8 |
BG525715 |
psRNA/TAPIR |
2 |
0.89 |
303 |
0 |
1 |
0 |
0 |
0 |
0 |
1.5 |
16.677 |
Cleavage |
Predicted protein [Populus trichocarpa] |
2e-06 |
| Stv_10 | BG521995 | TAPIR | 3.5 | 0.82 | 594 | 0 | 1 | 1 | 0 | 0 | 1 | - | --- | ------- | Ribulose-1,5-biphosphate carboxylase activase [Oryza sativa] | 1e-63 |
mfe: free energy ratio; start: start position of the duplex on the mRNA; seed gap: no.of gaps in seed region; seed mismatch: no.of mismatches in seed region; seed gu: number of G–U pairs in seed region; mismatches: number of mismatches, gu: number of G–U pairs; gap: number of gaps introduced by bulges and loop structures; Score: score calculated for each miRNA–mRNA duplex taking into account all the above described parameters. E (Expectation): scores < 3.0 considered as a potential target of miRNA; UPE :Target accessibility - allowed maximum energy to unpair the target site.