Table 3.
Predicted Targets of Newly Identified Rice miRNAs
| miRNA | Target Gene | Target Site | Target Protein | Count | Mean | sd |
|---|---|---|---|---|---|---|
| miR390 | 11668.m00935(1); 11674.m03433(3); 11687.m03320(3) | ORF | Leu-rich repeat proteins | 3 | 0.24 | 0.7 |
| miR396d | 11668.m04403(1); 11668.m04580(1); 11669.m04718(1); 11670.m04997(1); 11670.m04998(1); 11680.m00165(1); 11680.m00999(1); 11669.m05248(1); 11670.m02258(1); 11687.m03206(1); 11686.m02909(1); 11687.m03206(2); 11670.m04996(1); 11680.m00166(1); 11670.m04758(1) | ORF | GRL transcription factors | 15 | 0.19 | 0.6 |
| miR435 | 11687.m03448(3) | ORF | F-box protein | 1 | 0.75 | 1.3 |
| miR436 | 11686.m04227(0); 11686.m04226(1) | ORF | Unknown proteins | 2 | 0.07 | 0.3 |
| miR437 | 11680.m04605(1); 11680.m04606(1) | ORF | Glu receptor proteins | 2 | 0.22 | 0.6 |
| miR439 | 11667.m02576 (3 target sites with 0, 2, and 4 mismatches) | ORF | Dirigent-like protein | 4 | 0.15 | 0.5 |
| 11680.m01869(1); 11668.m02918(3) | ORF | Unknown proteins | ||||
| 11673.m02474(3) | ORF | Retrotransposon | ||||
| miR441 | 11669.m05042(3) | ORF | Unknown protein | 10 | 0.00 | 0.0 |
| 11667.m06876(2); 11674.m00346(2); 11674.m00582(2); 11680.m01945(2); | 3′UTR | Unknown proteins | ||||
| 3′UTR | Unknown proteins | |||||
| 11682.m04930(3); 11687.m00089(3) 11682.m03939(3); | 3′UTR | Unknown proteins | ||||
| 11668.m04341(2) | 3′UTR | F-box protein | ||||
| 11686.m03687(3) | 3′UTR | UDP-glucoronosyl and UDP-glucosyltransferase | ||||
| miR443 | 11687.m04039(3) | ORF | Unknown protein | 1 | 0.13 | 0.4 |
| miR444 | 11668.m04852(0) | ORF | MADS box transcription factor | 1 | 0.19 | 0.6 |
| miR445 | 11680.m05074(3) | 5′UTR | RNA binding protein | 1 | 0.00 | 0.0 |
| miR446 | 11668.m04341(2) | 3′UTR | F-box protein | 6 | 0.01 | 0.1 |
| 11674.m00582(2); 11680.m01945(2); 11682.m04930(3); 11682.m03939(3) | 3′UTR | Unknown proteins | ||||
| 3′UTR | Unknown protein | |||||
| 11680.m01730(2) | 3′UTR | Unknown plant | ||||
| Specific protein |
For each potential target gene, the number of mismatches between the miRNA and mRNA is indicated in parentheses. Annotated rice mRNAs were also searched for sites complementary to randomized miRNAs (100 repeats), applying the same criteria that were used for predicting targets. The mean of the hit frequency of the randomized data and their standard deviations are recorded.