Table 1. List of the potential protein targets for the 91 potential miRNAs, grouped by annotated gene family and by biological function.
| Protein annotation | MiRNA | Common function/type |
|---|---|---|
| CCAAT box-binding factor | MIR13, MIR43, MIR47, MIR57, MIR81, MIR87 | |
| CCAAT box-binding factor Hap2a | MIR77 | Core transcription factor |
| CCAAT-binding factor B subunit homolog | MIR13, MIR43, MIR47, MIR57 | |
| CCAAT-binding factor B subunit-related | MIR13, MIR43, MIR57, MIR77, MIR81, MIR87 | |
| Auxin-response transcription factor (ARF) | MIR75 | |
| ARF8 | MIR54 | |
| Transcription factor B3 family similar to ARF10 | MIR40, MIR75 | |
| Transcription factor B3 family | MIR40, MIR47 | |
| NAC1/NAM protein family | MIR29, MIR82 | Auxin signaling |
| NAM-related protein | MIR29, MIR82 | |
| NAM-like protein | MIR29, MIR82 | |
| NAM-related protein | MIR82 | |
| NAM protein CUC2 | MIR82 | |
| Scarecrow transcription factor family | MIR30, MIR46, MIR58 | Asymmetric cell division |
| Scarecrow-like transcription factor 14 (SCL14) | MIR14 | Specify meristem quiescent Center and radial patterning |
| SCL6 | MIR30, MIR46, MIR58 | |
| Squamosa promoter-binding protein-related 2 | MIR17, MIR85, MIR91 | |
| Squamosa promoter-binding protein homologs | MIR17, MIR63, MIR85, MIR91 | |
| Squamosa promoter-binding protein 4 (SPL4) | MIR17, MIR43, MIR63, MIR85, MIR91 | Homeotic MADS box genes controling floral development |
| AP2 domain transcription factor RAP2.7 | MIR21, MIR84 | |
| AP2 domain transcription factor, potential | MIR18, MIR21, MIR84 | |
| Floral homeotic protein APETALA2 | MIR18, MIR21, MIR84 | |
| HD-Zip transcription factor Athb-15 | MIR5, MIR70 | Vascular development and leaf development |
| Phabulosa HD-Zip TF Athb-14 | MIR70 | |
| HD-Zip transcription factor Athb-9 | MIR70 | |
| PIL6 Myc-related bHLH transcription factor | MIR32 | Circadian rhythm control by light |
| Myb family transcription factor MYB33 | MIR89 | |
| Myb family transcription factor MYB30, MYB120, MYB65 | MIR88 | Myb family transcription factor |
| Zinc finger (C3HC4-type RING finger) family | MIR12, MIR44, MIR56, MIR76, MIR80, MIR86 | Zinc finger transcription factor |
| TIR1, E3 ubiquitin ligase SCF complex F-box subunit | MIR10 | |
| TIR1-like genes, E3 ubiquitin ligase F-box subunit | MIR10, MIR20 | Ubiquitination pathway |
| F-box protein GRR1-like protein 1, AtFBL 18 | MIR10 | Controling targeted |
| E2 UBC, ubiquitin-conjugating enzyme family | MIR16, MIR27, MIR67 | Protein degradation (auxin-related for many) |
| CDC48 domain-containing AAA-type ATPase/NSF | MIR2 | |
| TAZ RING BTB/POZ domain protein | MIR47 | |
| F-box protein family | MIR63 | |
| FLU, TPR-containing protein | MIR15 | Chloroplast import of PORA |
| VQ-motif containing protein | MIR60 | Control of plastid genes |
| Thioredoxin-like protein 3 | MIR59 | Redox control in chloroplast |
| ATP sulfurylase | MIR64 | Sulfur metabolism |
| Sulfate transporter | MIR64 | |
| Acyl transferase-containing multifunctional enzyme | MIR64 | |
| Copper/zinc superoxidase dismutase (CSD1) | MIR1 | Cell death |
| Potential cytosine/deoxycytidine deaminase | MIR55 | Purine salvage |
| Amine oxidase-related | MIR83 | Overlaps auxin gene NAC1 |
| Ypt/Rab GTPase-activating protein | MIR4 | Intracellular trafficking |
| WASP domain containing-protein | MIR11 | Signal transduction to actin |
| SAG101, leaf senescence-associated acyl hydrolase | MIR73 | Senescence |
| Target of rapamycin, phosphatidylinositol 3-kinase | MIR34 | Embryo development |
| Potential (glycerol) phosphate acyltransferase | MIR31, MIR72 | Phospholipid synthesis |
| Laccase (diphenol oxidase), potential | MIR9 | |
| Lucine-rich repeat receptor kinase, potential | MIR55 | |
| ABC transporter family protein | MIR51 | Specific function unknown |
| Proline-rich protein family | MIR53 | |
| Expressed protein | MIR21 | |
| Expressed protein | MIR25 | |
| Hypothetical protein | MIR6, MIR15 | |
| Gypsy family retrotransposon gag protein | MIR88 | Retrotransposon |
An extended version of this table, which includes the gene loci (At codes) for each protein, appears as Table 2, which is published as supporting information on the PNAS web site.