List of the potential protein targets for the 91 potential miRNAs, grouped by annotation family, and by biological function. This table is an extended version of table 1 in the manuscript.
| Protein annotation | miRNA | Target gene locus | Common function / type |
|---|---|---|---|
| Transcription factor proteins | |||
| CCAAT box binding factor | MIR13 MIR43 MIR47 MIR57 MIR81 MIR87 | At1g17590.1 | Core transcription factor |
| CCAAT box binding factor Hap2a | MIR77 | At5g12840.1 | |
| At5g12840.2 | |||
| CCAAT-binding factor B subunit homolog | MIR13 MIR43 MIR47 MIR57 | At1g72830.1 | |
| CCAAT-binding factor B subunit -related | MIR13 MIR43 MIR57 MIR77 MIR81 MIR87 | At1g54160.1 | |
| Auxin response transcription factor | MIR75 | At2g28350.1 | Auxin signaling |
| Auxin response transcription factor (ARF8) | MIR54 | At5g37020.1 | |
| Transcription Factor B3 family similar to ARF10 | MIR40 MIR75 | At1g77850.1 | |
| Transcription Factor B3 family | MIR40 MIR47 | At5g06510.1 | |
| At4g30080.1 | |||
| NAC1 / No apical meristem (NAM) protein family | MIR29 MIR82 | At1g56010.1 | |
| At1g56010.2 | |||
| NAM (no apical meristem)-related protein | MIR29 MIR82 | At5g07680.1 | |
| At5g07680.2 | |||
| NAM, no apical meristem, - like protein | MIR29 MIR82 | At5g61430.1 | |
| NAM-related protein | MIR82 | At3g15170.1 | |
| No apical meristem (NAM) protein CUC2 | MIR82 | At5g53950.1 | |
| Scarecrow transcription factor family | MIR30 MIR46 MIR58 | At2g45160.1 | Asymmetric cell division specify meristem quiescent center and radial patterning |
| At3g60630.1 | |||
| Scarecrow-like transcription factor 14 (SCL14) | MIR14 | At1g07530.1 | |
| Scarecrow-like transcription factor 6 (SCL6) | MIR30 MIR46 MIR58 | At4g00150.1 | |
| Squamosa promoter binding protein-related 2 | MIR17 MIR85 MIR91 | At5g43270.1 | Homeotic MADS box genes controlling floral development |
| At5g43270.2 | |||
| Squamosa-promoter binding protein homologs | MIR17 MIR63 MIR85 MIR91 | At2g42200.1 | |
| At2g33810.1 | |||
| At2g42200.2 | |||
| At1g69170.1 | |||
| At5g50570.1 | |||
| At5g50570.2 | |||
| At5g50670.1 | |||
| At3g57920.1 | |||
| SPL4, Squamosa Promoter-Binding Protein 4 | MIR17 MIR43 MIR63 MIR85 MIR91 | At1g53160.1 | |
| AP2 domain transcription factor RAP2.7 | MIR21 MIR84 | At2g28550.1 | |
| AP2 domain transcription factor, potential | MIR18 MIR21 MIR84 | At5g60120.1 | |
| Floral homeotic protein APETALA2 | MIR18 MIR21 MIR84 | At4g36920.1 | |
| HD-Zip transcription factor Athb-15 | MIR5 MIR70 | At1g52150.1 | Vascular development and leaf development |
| At1g52150.2 | |||
| Phabulosa HD-Zip TF Athb-14 | MIR70 | At2g34710.1 | |
| HD-Zip transcription factor Athb-9 | MIR70 | At1g30490.1 | |
| PIL6 Myc-related bHLH transcription factor | MIR32 | At3g59060.1 | Circadian rhymth control by light |
| At3g59060.2 | |||
| Myb family transcription factor MYB33 | MIR89 | At3g28910.1 | Myb family transcription factor |
| Myb family transcription factor MYB30, MYB120, MYB65 | MIR88 | At5g06100.1 | |
| At5g06100.2 | |||
| At3g11440.1 | |||
| At5g55020.1 | |||
| At2g26950.1 | |||
| Zinc finger (C3HC4-type RING finger) family | MIR12 MIR44 MIR56 MIR76 MIR80 MIR86 | At1g54150.1 | Zinc finger transcription factor |
| Non-transcription factor proteins | |||
| TIR1, E3 Ubiquitin ligase SCF complex F-box subunit | MIR10 | At3g62980.1 | Ubiquitination pathway controlling targeted protein degradation (auxin-related for many) |
| TIR1-like genes, E3 Ubiquitin ligase F-box subunit | MIR10 MIR20 | At1g12820.1 | |
| At3g26810.1 | |||
| F-box protein GRR1-like protein 1, AtFBL18 | MIR10 | At4g03190.1 | |
| E2 UBC, ubiquitin-conjugating enzyme family | MIR16 MIR27 MIR67 | At2g33770.1 | |
| CDC48 domain-containing AAA-type ATPase/NSF | MIR2 | At4g04910.1 | |
| TAZ RING BTB/POZ domain protein | MIR47 | At3g05690.1 | |
| F-box protein family | MIR63 | At3g17480.1 | |
| FLU, TPR-containing protein | MIR15 | At3g14110.1 | Chloroplast import of PORA |
| VQ-motif containing protein | MIR60 | At1g68450.1 | Control of plastid genes |
| Thioredoxin-like protein 3 | MIR59 | At5g61440.1 | Redox control in chloroplast |
| ATP sulfurylase | MIR64 | At5g43780.1 | Sulfur metabolism |
| At3g22890.1 | |||
| At4g14680.1 | |||
| Sulfate transporter | MIR64 | At5g10180.1 | |
| Acyl transferase-containing multifunctional enzyme | MIR64 | At2g28780.1 | |
| Copper/zinc superoxidase dismutase (CSD1) | MIR1 | At1g08830.1 | Cell death |
| Potential cytosine/deoxycytidine deaminase | MIR55 | At1g68720.1 | Purine salvage |
| Amine oxidase-related | MIR83 | At1g56000.1 | Overlaps auxin gene NAC1 |
| Ypt/Rab GTPase-activating protein | MIR4 | At3g55020.1 | Intracellular trafficking |
| WASP domain containing- protein | MIR11 | At4g18600.1 | Signal transduction to actin |
| SAG101, leaf senescence-associated acyl hydrolase | MIR73 | At5g14930.2 | Senescence |
| TOR, phosphatidylinositol 3-kinase | MIR34 | At1g50030.1 | Embryo development |
| Potential (glycerol)phosphate acyltransferase | MIR31 MIR72 | At2g45670.1 | Phospholipid synthesis |
| At2g45670.2 | |||
| Laccase (diphenol oxidase), potential | MIR9 | At2g29130.1 | Specific function unknown |
| LRR receptor kinase, potential | MIR55 | At1g14390.1 | |
| ABC transporter family protein | MIR51 | At3g53510.1 | |
| Proline-rich protein family | MIR53 | At3g06870.1 | |
| Expressed protein | MIR21 | At5g12900.1 | Unknown |
| Expressed protein | MIR25 | At5g52870.1 | |
| Hypothetical protein | MIR6 MIR15 | At2g34530.1 | |
| At1g37050.1 | |||
| Gypsy family retrotransposon gag protein | MIR88 | At3g33076.1 | Retrotransposon |