Table 1.
Identified potential miRNAs in neem (Azadirachta indica)
| Putative miRNA | miRNA sequence 5′ 3′ | LM (nt) | Position | LP (nt) | G + C content (%) | MFE/ ΔG (kcal/mol) | MFEI |
|---|---|---|---|---|---|---|---|
| ain-miR156a-5p | UGACAGAAGAGAGUGAGCAC | 20 | 5′ | 82 | 48.78 | − 45.40 | 1.14 |
| ain-miR156g | ACAGAAGAUAGAGAGCACAG | 20 | 5′ | 80 | 38.75 | − 40.30 | 1.30 |
| ain-miR156j-3p | AUCCAACGAAGCAGGAGCUGC | 21 | 3′ | 85 | 44.71 | − 35.50 | 0.93 |
| ain-miR156l | UUGACAGAAGAUAGAGAGCAC | 21 | 5′ | 86 | 38.37 | − 45.60 | 1.38 |
| ain-miR157d | UGACAGAAGAUAGAGAGCAC | 20 | 5′ | 84 | 39.29 | − 44.90 | 1.36 |
| ain-miR159c-3p | CUUGGACUGAAGGGAGCUCCC | 21 | 3′ | 168 | 49.70 | − 92.60 | 1.11 |
| ain-miR159e-3p | UUUGGAUUGAAGGGAGCUCUA | 21 | 3′ | 178 | 44.94 | − 81.80 | 1.02 |
| ain-miR159f-3p | AUUGGAGUGAAGGGAGCUCCA | 21 | 3′ | 173 | 50.85 | − 83.70 | 0.95 |
| ain-miR160a-3p | GCGUAUGAGGAGCCAUGCAUA | 21 | 3′ | 83 | 53.01 | − 51.10 | 1.16 |
| ain-miR160a-5p | GCCUGGCUCCCUGUAUGCCAU | 21 | 5′ | 78 | 56.41 | − 40.80 | 0.93 |
| ain-miR160c-3p | GCGUGCGAGGAGCCAUGCAUG | 21 | 3′ | 84 | 53.57 | − 44.50 | 0.99 |
| ain-miR160f | UGCCUGGCUCCCUGUAUGCCA | 21 | 5′ | 80 | 58.75 | − 46.30 | 0.99 |
| ain-miR164i | UGGAGAAGCAGGGCACGUGCA | 21 | 5′ | 73 | 42.47 | − 35.80 | 1.15 |
| ain-miR166a-3p | UCGGACCAGGCUUCAUUCCCCC | 22 | 3′ | 164 | 36.59 | − 52.10 | 0.87 |
| ain-miR166c-5p | GGGAAUGUUGUCUGGUUCGAG | 21 | 5′ | 90 | 45.56 | − 44.80 | 1.09 |
| ain-miR166d | UCGGACCAGGCUUCAUUCCCC | 21 | 3′ | 118 | 40.68 | − 41.70 | 0.87 |
| ain-miR166l | GGAAUGUUGUCUGGCUCGAGG | 21 | 5′ | 158 | 34.81 | − 47.30 | 0.86 |
| ain-miR166m | CGGACCAGGCUUCAUUCCCC | 20 | 3′ | 116 | 41.38 | − 40.70 | 0.85 |
| ain-miR167a | UGAAGCUGCCAGCAUGAUCUA | 21 | 5′ | 78 | 46.15 | − 41.80 | 1.16 |
| ain-miR169a-5p | CAGCCAAGGAUGACUUGCCGA | 21 | 5′ | 74 | 41.89 | − 31.10 | 1.00 |
| ain-miR169c | CAGCCAAGGAUGACUUGCCGG | 21 | 5′ | 152 | 36.18 | − 43.90 | 0.80 |
| ain-miR169h | UAGCCAAGGAUGACUUGCCUG | 21 | 3′ | 192 | 40.10 | − 58.60 | 0.76 |
| ain-miR171b-3p | CGAGCCGAAUCAAUAUCACUC | 21 | 3′ | 76 | 34.21 | − 28.50 | 1.10 |
| ain-miR171c-3p | UUGAGCCGUGCCAAUAUCACG | 21 | 3′ | 83 | 50.60 | − 46.60 | 1.11 |
| ain-miR171j-3p | UGAUUGAGCCGUGCCAAUAUC | 21 | 3′ | 77 | 48.05 | − 44.60 | 1.21 |
| ain-miR171k-3p | UUGAGCCGCGCCAAUAUCACU | 21 | 3′ | 90 | 41.11 | − 38.70 | 1.05 |
| ain-miR172a | AGAAUCUUGAUGAUGCUGCAU | 21 | 3′ | 120 | 38.33 | − 56.10 | 1.22 |
| ain-miR172d-3p | AGAAUCUUGAUGAUGCUGCAG | 21 | 3′ | 124 | 42.74 | − 53.40 | 1.01 |
| ain-miR172d-5p | GCGGCAUCAUCAAGAUUCACA | 21 | 5′ | 115 | 46.09 | − 53.80 | 1.02 |
| ain-miR172i-3p | GGAAUCUUGAUGAUGCUGCAU | 21 | 3′ | 120 | 45.00 | − 56.60 | 1.05 |
| ain-miR319k | UUGGACUGAAGGGAGCUCCCU | 21 | 3′ | 168 | 49.40 | − 89.30 | 1.08 |
| ain-miR390a-3p | CGCUAUCCAUCCUGAGUUUCA | 21 | 3′ | 80 | 47.50 | − 38.50 | 1.01 |
| ain-miR390g | AAGCUCAGGAGGGAUAGCGCC | 21 | 5′ | 75 | 48.00 | − 38.40 | 1.07 |
| ain-miR394b-5p | UUGGCAUUCUGUCCACCUCC | 20 | 5′ | 75 | 44.00 | − 27.60 | 0.84 |
| ain-miR395d | CUGAAGUGUUUGGGGGAACUC | 21 | 3′ | 65 | 52.31 | − 38.70 | 1.14 |
| ain-miR396b-3p | GCUCAAGAAAGCUGUGGGAAA | 21 | 3′ | 86 | 40.70 | − 39.20 | 1.12 |
| ain-miR396k-5p | UUCCACAGCUUUCUUGAACUU | 21 | 5′ | 86 | 40.70 | − 39.20 | 1.12 |
| ain-miR397b-5p | UCAUUGAGUGCAGCGUUGAUG | 21 | 5′ | 72 | 45.83 | − 34.60 | 1.05 |
| ain-miR399f-5p | GGGCAAUUCUCCUUUGGCAGA | 21 | 5′ | 68 | 47.06 | − 42.40 | 1.32 |
| ain-miR403-3p | UUAGAUUCACGCACAAACUCG | 21 | 3′ | 89 | 41.57 | − 35.70 | 0.96 |
| ain-miR408d | UGCACUGCCUCUUCCCUGGC | 20 | 3′ | 82 | 52.43 | − 39.90 | 0.93 |
| ain-miR827 | UUAGAUGACCAUCAACAAACA | 21 | 3′ | 76 | 28.95 | − 29.20 | 1.33 |
| ain-miR2111-5p | UAAUCUGCAUCCUGAGGUUUG | 21 | 5′ | 68 | 39.71 | − 37.70 | 1.40 |
| ain-miR2275a-3p | UUUAGUUUCCUCCAAUAUCUUA | 22 | 3′ | 72 | 31.94 | − 32.20 | 1.40 |
LM Length of mature miRNAs, LP length of precursor