Table 3.
Predicted target genes of two novel miRNAs from meiocytes.
| Gene expression (RPM) | ||||||||
|---|---|---|---|---|---|---|---|---|
| Target accession | InterPro description | Note | Meiocytes | Anthers | Seedlings | Inhibition | UPE | MFE |
| For zma-MIR11969 (UUAUACCCAUCUCUCACCUUGCAA) | ||||||||
| GRMZM5G868767 | HCNGP-like | Putative transcription factor | 62.06 | 42.60 | 21.89 | Translation | 19.804 | -32.8 |
| GRMZM2G060061 | Glycosyl transferase, family 14 | 22.82 | 36.57 | 16.65 | Cleavage | 18.606 | -37.8 | |
| GRMZM2G030139 | ATPase-like, ATP-binding domain | Putative pyruvate Dehydrogenase kinase | 38.05 | 19.56 | 39.68 | Cleavage | 20.325 | -35.6 |
| GRMZM2G041247 | 0 | Ribonuclease H-like | 0.01 | 0.00 | 0.04 | Cleavage | 16.515 | -34.2 |
| GRMZM2G087406 | 0 | Ribonuclease H-like | #N/A | #N/A | #N/A | Cleavage | 16.515 | -34.2 |
| GRMZM2G119261 | Zinc finger, ZZ-type | Homeodomain-like | 20.27 | 12.85 | 7.62 | Cleavage | 22.181 | -33.1 |
| GRMZM2G336583 | RNA recognition motif, RNP-1 | Zinc finger like | 19.79 | 26.35 | 13.29 | Translation | 12.477 | -25.4 |
| GRMZM5G821637 | Ankyrin repeat | 3.22 | 6.05 | 363.23 | Translation | 18.004 | -27.0 | |
| For zma-MIR11970 (UGGUUUGGUUGCACGUUUGCA) | ||||||||
| GRMZM2G048366 | 0 | 50.06 | 76.63 | 26.79 | Cleavage | 17.496 | -35.3 | |
| GRMZM2G078924 | Membrane-anchored ubiquitin-fold protein, HCG-1 | Ubiquitin fusion protein | 10.05 | 3.52 | 5.76 | Cleavage | 13.847 | -35.3 |
| GRMZM2G134430 | Uncharacterized protein family UPF0220 | Transmembrane protein | 114.60 | 93.53 | 34.97 | Cleavage | 15.45 | -32.9 |
| GRMZM2G097106 | GTPase EngC | 165.27 | 119.39 | 52.91 | Cleavage | 20.168 | -29.2 | |
| GRMZM2G123089 | DNA recombination and repair protein Rad51, C-terminal | Rad51C | 19.12 | 14.47 | 8.97 | Cleavage | 17.826 | -33.4 |
| GRMZM5G889052 | Protein of unknown function DUF946 | 1.71 | 0.70 | 1.96 | Cleavage | 18.226 | -33.1 | |
| GRMZM2G126197 | Zinc finger, CCCH-type | Zinc finger | 1.13 | 2.15 | 2.55 | Cleavage | 12.39 | -28.7 |
| GRMZM2G022787 | Zinc finger, CCHC-type | Zinc finger | 17.99 | 10.52 | 11.06 | Cleavage | 16.134 | -31.6 |
| GRMZM2G124143 | Ribosomal protein S28e | Ribosomal protein | 94.23 | 66.37 | 87.60 | Cleavage | 15.076 | -31.4 |
| GRMZM2G177052 | Protein of unknown function DUF966 | 4.62 | 3.82 | 10.24 | Translation | 21.539 | -31.2 | |
| GRMZM2G447785 | Proteinase inhibitor I12, Bowman-Birk | 286.86 | 244.96 | 47.03 | Cleavage | 15.814 | -28.2 | |
| GRMZM2G304274 | Glycosyl transferase, family 20 | 27.88 | 20.07 | 7.95 | Translation | 16.26 | -29.9 | |
Target genes predicted with psRNATarget. Gene expression values from our B73 RNA-seq data. UPE, unpair energy (required minimum energy to open secondary structure around target site, values 0–100, the smaller the better). MFE, Minimum free energy (in kcal/mol, the lower the better).