Table 4.
Summary of the bioinformatics prediction against plant transcriptome. For each investigated miRNA (Query), the putative plant target mRNAs showing an expectation (Exp) ≤ 1 (where possible, otherwise the lowest registered values) were listed and described as Unigene-DFCI Gene Index-GORAGI IDs (Accession) and in full (Description). The complete output of this bioinformatics analysis was reported in Supplemental material 1
| Query | Exp | Target | |
|---|---|---|---|
| Accession | Description | ||
| miR156a | 1.0 | CO092899 | Chromosome chr1 scaffold_136 |
| 1.0 | TC6174 | Chromosome chr8 scaffold_34 | |
| 1.0 | TC6994 | Chromosome chr1 scaffold_136 | |
| miR156b | 0.0 | TC5782 | Unknown protein |
| 0.0 | TC7659 | Unknown protein | |
| miR159 | 1.0 | TC9277 | ATP synthase F0 subunit 6 |
| miR159-3p | 2.0 | CO076957 | Amphiregulin long form |
| 2.0 | TC9277 | ATP synthase F0 subunit 6 | |
| miR160a | 1.0 | TC8008 | Chromosome chr6 scaffold_3 |
| 1.0 | TC4570 | Auxin response factor 3 | |
| miR160b-5p | 0.0 | TC8008 | Chromosome chr6 scaffold_3 |
| 0.0 | TC4570 | Auxin response factor 3 | |
| miR164d-5p | 1.5 | CO109521 | NAC domain protein NAC1 |
| miR166f-3p | 1.0 | TC6854 | Class III HD-Zip protein 4 |
| miR166g-3p | 2.5 | CO079323 | Chromosome chr14 scaffold_27 |
| miR167d | 3.0 | TC1436 | Chromosome chr5 scaffold_2 |
| 3.0 | TC3171 | Zinc finger, C3HC4 type family protein | |
| 3.0 | TC484 | Cytochrome P450 | |
| miR167e-5p | 3.0 | TC1436 | Chromosome chr5 scaffold_2 |
| 3.0 | TC3171 | Zinc finger, C3HC4 type family protein | |
| 3.0 | TC484 | Cytochrome P450 | |
| miR168-5p | 2.5 | CO084924 | AGO1-1 |
| miR172b-3p | 0.5 | TC7001 | Chromosome chr6 scaffold_3 |
| 0.5 | TC4318 | Ethylene-responsive transcription factor related to APETALA2 | |
| 0.5 | TC8328 | Chromosome chr6 scaffold_3 | |
| 0.5 | TC8568 | Chromosome chr13 scaffold_17 | |
| miR172c | 2.5 | TC7001 | Chromosome chr6 scaffold_3 |
| 2.5 | TC7575 | Chromosome chr7 scaffold_20 | |
| 2.5 | TC4318 | Ethylene-responsive transcription factor related to APETALA2 | |
| 2.5 | TC8568 | Chromosome chr13 scaffold_17 | |
| miR172c-5p | 3.0 | TC2843 | Plastid division protein |
| 3.0 | CO097477 | NADPH-cytochrome P450 oxydoreductase isoform 3 | |
| 3.0 | TC9053 | Chromosome chr7 scaffold_192 | |
| 3.0 | TC4030 | Chromosome chr12 scaffold_47 | |
| 3.0 | TC8617 | Glycosyl hydrolase | |
| 3.0 | TC7382 | Chromosome chr18 scaffold_1 | |
| 3.0 | TC3352 | Chromosome undetermined scaffold_670 | |
| 3.0 | TC8563 | Chromosome chr4 scaffold_83 | |
| miR393c-5p | 1.0 | TC7732 | Transport inhibitor response 1 |
| miR395c-3p | 2.5 | TC7582 | Pyruvate decarboxylase |
| miR396a | 2.5 | TC9189 | Chromosome chr2 scaffold_132 |
| miR396c-3p | 3.5 | TC4016 | Chromosome chr5 scaffold_64 |
| 3.5 | TC5991 | Calcium binding protein | |
| 3.5 | TC9308 | Chromosome chr19 scaffold_4 | |
| 3.5 | TC21 | Unknown protein | |
| 3.5 | CO099385 | Chromosome chr3 scaffold_8 | |
| 3.5 | CO128430 | Chromosome chr17 scaffold_16 | |
| 3.5 | CO129875 | Chromosome chr17 scaffold_12 | |
| 3.5 | TC1113 | Chromosome undetermined scaffold_254 | |
| miR396f-5p | 2.5 | TC9189 | Chromosome chr2 scaffold_132 |
| miR398b | 3.0 | CO114193 | Chromosome chr1 scaffold_5 |
| miR398b-3p | 2.5 | CO105378 | RING-H2 finger protein ATL3F |
| miR399c | 2.5 | CO072266 | Unknown protein |
| 2.5 | CO092308 | Chromosome chr17 scaffold_12 | |
| 2.5 | CO120548 | Chromosome chr4 scaffold_443 | |
| miR399d | 1.5 | CO072266 | Unknown protein |
| miR399e-3p | 2.0 | TC7413 | Chromosome chr11 scaffold_13 |
| 2.0 | CO124179 | MYB transcription factor | |
| miR399f-3p | 3.0 | CO095104 | ATP-dependent Clp protease proteolytic subunit |
| 3.0 | CO095019 | Os11g0104900 protein | |
| miR403b-3p | 3.0 | TC2550 | Chromosome chr5 scaffold_124 |
| miR482a | 2.5 | CO081126 | ATPase |
| miR530b | 2.0 | TC2909 | Chromosome chr6 scaffold_3 |
| miR2118 | 1.0 | TC5359 | Cytochrome b |
| miR3954b-5p | 3.0 | TC2550 | Chromosome chr5 scaffold_124 |
| miR6300 | 2.0 | TC6704 | Unknown protein |
| miR8051-5p | 2.5 | CO082018 | Chromosome chr4 scaffold_6 |
| 2.5 | CO127801 | Isoform 2 of Q8LPQ8 | |