Table 1.
High-probability rice miRNA targets proposed for experimental work
| No. | miRNA family | No. of target transcripts | Predicted function (Known) | Predicted function (Novel) | Mark* |
|---|---|---|---|---|---|
| 1 | miR156 | 13 | Squamosa promoter-binding protein SPL2, SPL9, SPL10 | Jakalin homolog of barley | C, K |
| 2 | miR159 | 10 | MYB family transcription factor MYB33, MYB65 | Inositol 1,3,4-trisphosphate 5/6-kinase family protein; calcium-binding protein | C |
| 3 | miR160 | 4 | Transcriptional factor B3 family protein | Far-red impaired responsive protein | C |
| 4 | miR164 | 10 | Transcription activator NAC1-No apical meristem (NAM) | Dihydrolipoamide S-acetyltransferase | C |
| 5 | miR166 | 8 | Homeobox-leucine zipper transcription factor (HB-14); homeodomain-leucine zipper protein Revoluta (REV) | Stress-inducible protein | C |
| 6 | miR167 | 3 | Probable leucine zipper; isoleucyl-tRNA synthetase | – | |
| 7 | miR168 | 8 | Argonaute protein (AGO1) | Quinone reductase family protein DNAJ heat shock N-terminal domain; flavin-containing monooxygenase family protein | K |
| 8 | miR169 | 12 | CCAAT-binding transcription factor | Glycine-rich RNA-binding protein (GRP7); leucine-rich repeat transmembrane protein kinase; multi-zipper protein | C |
| 9 | miR171 | 5 | Scarecrow-like transcription factor 6 (SCL6) | – | C |
| 10 | miR172 | 4 | Floral homeotic protein APETALA2 (AP2) | Starch synthase-related protein | C, K |
| 11 | miR319 | 4 | MYB family transcription factor MYB33, MYB65 | – | C |
| 12 | miR390 | 3 | Leucine-rich repeat family protein | – | |
| 13 | miR395 | 7 | Sulfate transporter, sulfate adenylyl-transferase 1/ATP-sulfurylase 1 (APS1) | – | C |
| 14 | miR396 | 10 | Transcription activator GRL1, GRL2, GRL3, GRL5 | Phytochrome A-related containing 7 WD-40 repeats; ATP-binding region containing non-consensus splice site | K |
| 15 | miR397 | 4 | Laccase | Pyruvate dehydrogenase E1 beta subunit, mitochondrial; diphenol oxidase | C |
| 16 | miR398 | 2 | Copper/zinc superoxide dismutase (CSD1) | – | |
| 17 | miR399 | 9 | Phosphate transporter (PT2) | Disease resistance protein (NBS-LRR class); pentatricopeptide (PPR) repeat-containing protein; DNAJ heat shock N-terminal domain | K |
| 18 | miR408 | 6 | – | Auxin-responsive AUX/IAA7 family protein; E2F transcription factor-3; multi-copper oxidase type I family protein; plastocyanin-like domain-containing protein/plantacyanin; helicase domain-containing protein; laccase | C, K |
| 19 | miR415 | 5 | – | Auxin-responsive AUX/IAA7 family protein; leucine-rich repeat family protein; AP2 domain-containing transcription factor; viviparous-14 protein (maize) | C, K |
| 20 | miR443 | 2 | – | Beta-expansin (EXBP2) | K |
| 21 | miR444 | 1 | Expressed protein supported by MPSS (similar to AT1G54385) | – | |
| 22 | miR445 | 2 | – | Transformer serine/arginine-rich ribonucleoprotein | K |
| 23 | miR446 | 20 | – | CAAX protease (STE24); DNA repair and recombination protein PIF1, mitochondrial pre-cursor; fucosyltransferase-like protein FucT2; glutaredoxin family protein; metallo-beta-lactamase family protein; PPR repeat-containing protein; C3HC4-type zinc finger family protein | K |
| 24 | miR528 | 7 | – | F-box family protein (ORE9) E3 ubiquitin ligase SCF; L-ascorbate oxidase; uclacyanin I | K |
| 25 | miR531 | 5 | – | Nodulin family protein; cell division cycle protein 48 (CDC48) | K |
| 26 | miR806 | 2 | L1P family of ribosomal protein | ATP-dependent protease domain-containing protein; epoxidehydrolase (ATsEH) | C |
| 27 | miR808 | 4 | Helicase associated domain; cytochrome P-450; cysteine protease; plant protein family | – | C |
| 28 | miR809 | 8 | Mlo (pathogen resistance) protein; helicase associated domain; new cDNA-based gene; zinc finger protein; F-box domain protein; isoflavone reductase; cytochrome P-450; plant protein family | GTP-binding regulatory protein beta chain; exportin-related protein; glutaredoxin family protein | C |
| 29 | miR812 | 3 | Protein kinase; glycosyl hydrolases; chloroplast import receptor | – | C |
| 30 | miR814 | 1 | Peroxidase | Nucleolar protein similar to proliferating-cell nucleolar antigen p120 | |
| 31 | miR815 | 5 | – | Zinc finger (C2H2-type) family protein; dentin sialophosphoprotein-type protein; exocyst complex subunit Sec15-like family protein; disease resistance protein (CC-NBS-LRR class); protein phosphatase 2C-like protein; 5′–3′ exoribonuclease XRN4 | C |
| 32 | miR818 | 25 | Serine threonine kinase; hydrolase; ENT domain; isoflavone reductase; leucine-rich repeat; new cDNA-basegene; pyruvate kinase | UDP-glucose:indole-3-acetate beta-D-glucosyl-transferase; suppressor of lin-12-like protein; MYB family transcription factor (MYB20); 3-hydroxy isobutyryl-coenzyme A hydrolase; 2′-hydroxy isoflavone reductase; beta-glucosidase; WRKY family transcription factor; probable DNA replication licensing factor; PPR repeat-containing protein; expressed protein similar to At1g70550; phospho inositide-specific phospholipase C | C |
| 33 | miR819 | 7 | Elongation factor; diacylglycerol kinase; strubble Ig receptor family; ABC transporter | Leucine-rich repeat family protein; probable LRR receptor-like protein kinase | |
| 34 | miR820 | 3 | DNA cytosine methyltransferase | WWE domain-containing protein |
*
The multiple hits conserved between indica and japonica rice subspecies are marked as “C”. Those targets that are predicted both by miRanda and miRU algorithms (consensus targets) are marked as “K”.