Table 3.
Predicted targets of conserved and novel mcr-miRNA.
| miRNA | Predicted function | Expectation | Location | Inhibition | Target gene |
|---|---|---|---|---|---|
| mcr-miR156 | Squamosa promoter-binding protein-like (SPL) | 0 | ORF | Cleavage | tr_25478; 92930; 247074; 130241; 134702; 242974 |
| Glutaredoxin family protein | 2.5 | ORF | Cleavage | tr_222987 | |
| NAD(P)-binding Rossmann-fold superfamily protein | 3 | ORF | Cleavage | tr_112639; 112626 | |
| Oxophytodienoate-reductase 3 | 3 | ORF | Cleavage | tr_8553 | |
| Tetratricopeptide repeat-like superfamily protein | 3 | ORF | Cleavage | tr_211611 | |
| NAD(P)-dehydrogenase | 3 | ORF | Cleavage | tr_20823 | |
| F-box family protein | 3 | ORF | Translation | tr_250578 | |
| Gibberellin receptor GID1B | 3 | 5′ UTR | Translation | tr_131891 | |
| mcr-miR159 | MYB domain protein 33 | 2.5 | ORF | Cleavage | tr_247776 |
| Cytidinediphosphate diacylglycerol synthase 2 | 2.5 | 5′ UTR | Cleavage | tr_24710 | |
| Polyketide cyclase/dehydrase lipid transport protein | 3 | ORF | Cleavage | tr_247457 | |
| Histone H2A protein 9 | 3 | ORF | Cleavage | tr_31155 | |
| ATP binding cassette subfamily B1 | 3 | ORF | Cleavage | tr_75146 | |
| RNA ligase | 3 | ORF | Cleavage | tr_251381 | |
| Glycosylhydrolase superfamily protein | 3 | ORF | Cleavage | tr_63329 | |
| mcr-miR160 | Auxin response factor (ARF) 16 | 0.5 | ORF | Cleavage | tr_131045 |
| Glutathione-regulated potassium-efflux protein | 2.5 | ORF | Cleavage | tr_29190 | |
| mcr-miR162 | Dicer like-1 | 2 | ORF | Cleavage | tr_87681 |
| Pyridoxamine 5′-phosphate oxidase family protein | 3 | ORF | Translation | tr_128506 | |
| mcr-miR164 | NAC domain containing protein | 1 | ORF | Cleavage | tr_20281 |
| mcr-miR166 | Homeobox-leucine zipper family protein (HD-ZIP) | 1.5 | ORF | Cleavage | tr_23906; 16028 |
| NB-ARC domain-containing disease resistance protein | 3 | ORF | Translation | tr_6344 | |
| mcr-miR168 | Argonuate 1 | 3.5 | ORF | Cleavage | tr_23616 |
| Cytochrome P450, family 76 | 3 | ORF | Translation | tr_34562; 106564 | |
| mcr-miR169 | Nuclear factor Y subunit A (NF-YA) | 2 | 3′ UTR | Cleavage | tr_241835 |
| Haloacid dehydrogenase | 3 | ORF | Cleavage | tr_78265 | |
| mcr-miR171 | Scarecrow-like protein (SCL) 6 | 0.5 | ORF | Cleavage | tr_129576 |
| Early-responsive to dehydration stress protein (ERD4) | 3 | ORF | Cleavage | tr_88429 | |
| Cysteine-rich RLK (Receptor-like protein kinase) 25 | 3 | ORF | Cleavage | tr_72609 | |
| Subtilisin-like serine protease 3 | 3 | ORF | Cleavage | tr_23970 | |
| ARM repeat superfamily protein | 3 | ORF | Cleavage | tr_25709 | |
| mcr-miR319 | MYB domain protein 33 | 2.5 | ORF | Cleavage | tr_247776 |
| TCP-4 transcription factor* | 4 | ORF | Cleavage | tr_248183 | |
| mcr-miR396 | Growth-regulating factor (GRF) 2 | 2 | ORF | Cleavage | tr_20229 |
| Alfin-like 3 | 2.5 | ORF | Cleavage | tr_86713 | |
| Heat shock protein 81.4 | 3 | ORF | Translation | tr_24595 | |
| Ribosomal protein L1p/L10e family | 3 | ORF | Cleavage | tr_27243 | |
| Zinc finger protein-related | 3 | ORF | Cleavage | tr_8491 | |
| F-box protein | 3 | 3′ UTR | Cleavage | tr_24495 | |
| Proteasome family protein | 3 | 3′ UTR | Translation | tr_25619 | |
| mcr-miR403 | Argonaute 2 | 1 | 3′ UTR | Cleavage | tr_81134 |
| Ubiquitin-specific protease | 3 | 3′ UTR | Translation | tr_23630 | |
| ADP-ribosylation factor GTPase-activating protein | 3 | ORF | Translation | tr_25728 | |
| mcr-miR1 | Mitochondrial transcription termination factor protein | 1.5 | ORF | Cleavage | tr_26362; 27606 |
| Germin-like protein | 3 | ORF | Cleavage | tr_140178 | |
| Thioredoxin superfamily protein | 3 | ORF | Cleavage | tr_126594 | |
| Ubiquitin-specific protease | 3 | ORF | Cleavage | tr_90873 | |
| BED zinc finger; hAT family dimerisation domain | 3 | ORF | Translation | tr_16919 | |
| mcr-miR3 | Sodium/myo-inositol symporter (ITR) 3 | 3 | ORF | Cleavage | tr_16378 |
| Cytochrome P450, family 81 | 3 | ORF | Translation | tr_127844 | |
| mcr-miR4 | Leucine-rich repeat transmembrane protein kinase | 0.5 | 3′ UTR | Cleavage | tr_124137 |
| Multi-antimicrobial extrusion (MATE) efflux protein | 0.5 | 3′ UTR | Cleavage | tr_15134 | |
| Protein translocase subunit SecA, chloroplastic | 1.5 | 3′ UTR | Cleavage | tr_77781 | |
| Protein kinase superfamily protein | 1.5 | 3′ UTR | Cleavage | tr_91240; 91241; 91239 | |
| NAD(P)-binding Rossmann-fold superfamily protein | 3 | ORF | Cleavage | tr_28492 | |
| mcr-miR5 | Phosphofructokinase 3 (PFK) | 2 | ORF | Cleavage | tr_24929 |
| Tetratricopeptide repeat-like superfamily protein | 2 | ORF | Cleavage | tr_251318 | |
| mcr-miR10 | Germin 3 | 3 | 3′ UTR | Cleavage | tr_32811 |
| mcr-miR11 | Ribosomal protein L34 | 2.5 | ORF | Cleavage | tr_32249 |
| mcr-miR12 | Arginyl-tRNA synthetase | 3 | ORF | Translation | tr_249031 |
| Translin family protein | 3 | ORF | Cleavage | tr_131509 |
*
miR319/TCP-4 pair was aligned manually.