Table 3.
Potential novel melon specific miRNAs
| Melon sRNA namea | nt | sRNA sequence | Number of sequences | Hits in genome | miRanda scoreb | Potential precursor lenght (nt) | MFEIc |
|---|---|---|---|---|---|---|---|
| a34_130677_ | 21 | AUAGAUAUUGAUAUGCUUUUA | 1 | 4 | 163 | 94 | -1.0573 |
| a24_2602_ | 21 | UGCUACAUGGUUUAUCAGUGA | 2 | 5 | 115 | 72 | -1.2524 |
| a24_177791_ | 21 | UCGCAGAAGAGAUGGCGCCGA | 7 | 1 | 143 | 91 | -0.8587 |
| a23_118111_ | 21 | CAUUGAUAGACACUAAUAGAA | 1 | 5 | 167 | 90 | -1.475 |
| a33_14294_ | 21 | AUAGACUUCUAUUGGUGUCUA | 1 | 1 | 154 | 74 | -1.5105 |
| a32_31625_ | 21 | GUUCCCACGGUAAUGAUAAUA | 2 | 1 | 127 | 72 | -1.1045 |
| a32_1324_ | 21 | AGGUGUCAUCUUGCUGCGAUA | 1 | 1 | 179 | 99 | -1.2 |
| a22_190223_ | 21 | UGUUAUGCAUGGCGUCGGGAG | 1 | 5 | 187 | 157 | -1.2915 |
| a14_98657_ | 21 | AUAGCGAAGUAUAUCAGUGAU | 1 | 1 | 154 | 127 | -1.2423 |
| a14_51701_ | 21 | UGAGCCGUGCCAAUAUCGACG | 1 | 1 | 159 | 97 | -1.1 |
| a14_180374_ | 21 | UAAAUAUUUAGAAAGUCAAUC | 1 | 4 | 159 | 79 | -1.855 |
| a21_80766_f | 21 | UAAUAUUCAUUUUCACUUCUU | 1 | 1 | 116 | 232 | -1.2494 |
| a21_78863_ | 21 | UGCAUCCUGAGGUUUAGGGAG | 3 | 1 | 159 | 194 | -0.9776 |
| a21_244426_ | 21 | AGUAACCACUAAGCUAAUGGC | 1 | 1 | 187 | 597 | -1.0096 |
| a23_1441_f | 21 | UAUAGCAAAGUCUAUCGAUGG | 5d | 1 | 107 | 77 | -1.1435 |
| a13_84447_e | 21 | GGUCAUUCUAGCAGCUUCAAU | 13d | 1 | 139 | 201 | -0.96 |
| a23_370_e | 21 | UGGUGUGCAUGUGAUGGAAUA | 13d | 1 | 163 | 113 | -0.9061 |
| a21_134553_f | 21 | GUUAUACGAGUUGGGUUGGGU | 1 | 1 | 155 | 114 | -0.9571 |
| a11_95657_e | 21 | UUGUGUCAUUGACAUUGUGGU | 1 | 2 | 195 | 191 | -1.1708 |
| a14_9427_ | 21 | UCGUCCUGAGAAUACAUGUCA | 35d | 1 | 159 | 97 | -0.9409 |
| a14_668_ | 21 | UGAGUUAUCGGUGAAUUCAAG | 5d | 3 | 159 | 516 | -0.9675 |
| a13_252112_ | 21 | ACUGCUGCUUGUACUAUUGAA | 1 | 1 | 191 | 255 | -1.9670 |
| a11_33177_ | 21 | UUUAGUUUAGCCUAUUGCUUU | 1 | 3 | 187 | 139 | -1.1035 |
| a11_191362_e | 21 | UUCUAUUGUCUUCAUUUGUGA | 1 | 1 | 191 | 119 | -1.2718 |
| a34_224062_ | 21 | UGAAAUGACUUGUCAAGUGCU | 1 | 1 | 151 | 97 | -0.975 |
| a13_228150_ | 21 | CUUGUACUUGAUUUUGUUGCC | 1 | 1 | 191 | 115 | -1.4469 |
| a12_32299_e | 21 | AAUUUGUUGGUCAAAUGAUUG | 2 | 1 | 195 | 107 | -1.7552 |
| a12_272161_ | 21 | UUGUAUGGUGGAAAGAUGGAA | 1 | 1 | 162 | 96 | -1.4167 |
| a11_33986_ | 21 | GCUGACUUGCUGAUUGAGUUA | 2 | 3 | 179 | 189 | -1.4852 |
| a13_33760_ | 21 | UGAAUUAUCUGCUUAAGUUUU | 1 | 1 | 187 | 95 | -1.2889 |
| a11_389198_ | 21 | ACACGCAGAAGAGACGAUUGA | 1 | 1 | 191 | 120 | -1.5575 |
| a13_357842_ | 21 | UGGAGCAAUAUUGAUGCAUAU | 1 | 1 | 195 | 220 | -0.9548 |
| a11_364692_ | 21 | UUGGGUCUAUUUAAUGGGAGC | 1 | 1 | 155 | 107 | -1.2308 |
| a13_281334_ | 21 | ACUUUCUGUCAAUAUAAUCAG | 1 | 1 | 175 | 115 | -1.3943 |
| a12_71107_ | 21 | UAUCAUAGUUGGUGGUUCAGG | 3 | 1 | 143 | 115 | -1.2167 |
| a13_120551_ | 21 | UCAACGAUAGACAUUGAUAGA | 1 | 1 | 171 | 107 | -1.2875 |
| a12_123886_ | 21 | UUAUCAUUGAUAGACUAGUAU | 1 | 2 | 155 | 174 | -1.0612 |
| a11_227522_ | 21 | CAAGCCCAUGACAAAGCAAGC | 1 | 1 | 187 | 225 | -1.0929 |
| a14_133932_f | 21 | UCAACACGAUCGUCUAGCAUG | 1 | 2 | 173 | 113 | -1.2295 |
| a11_203340_ | 21 | UUUGAGUGUCCUACUCACCUC | 1 | 1 | 191 | 411 | -1.0833 |
| a11_11135_ | 21 | UAGUGCCGCGCUGCGUGCGUC | 85 | 1 | 147 | 102 | -0.98 |
| a11_31022_ | 21 | UUUCGCUUUUCCUCUUUCGUG | 1 | 1 | 191 | 454 | -1.1523 |
| a12_144938_ | 21 | UCGUGGAUAUUGCUCUUUUCU | 2 | 1 | 171 | 504 | -1.3303 |
| a33_181157_ | 22 | GAUAGAUACUAAUAUGCUUCUA | 1 | 2 | 188 | 87 | -1.3227 |
| a33_37151_ | 22 | AGAUUAAUUUAUUGGGCGUUAU | 1 | 2 | 144 | 94 | -1.3313 |
| a12_72169_ | 22 | UUGAGCUAUGCUCAGGUUGACA | 30 | 1 | 176 | 174 | -1.2933 |
| a24_96796_e | 22 | UGAGCUAUGCUCGCUUUGGCAA | 21d | 1 | 175 | 169 | -1.2855 |
| a11_378153_ | 22 | GAGUUCCUAAGUUUUGAUGAAU | 1 | 1 | 144 | 351 | -1.2221 |
| a11_378297_ | 22 | UUUUGGAUUCUAUCGAUGAAAG | 1 | 1 | 155 | 123 | -1.4857 |
| a23_244052_e | 22 | GGGCAGCCCCACGUUGGGCAUG | 5d | 1 | 175 | 353 | -0.9263 |
| a11_85662_ | 22 | AAAUAUAUCGGUGUCUAUCAAU | 1 | 2 | 132 | 85 | -1.2208 |
| a21_388555_ | 22 | GAUAGACGCUGAUAGAUAGACA | 3 | 1 | 124 | 76 | -0.8963 |
| a11_84237_ | 22 | CGGCCAAAAAUGACUUGCCCGG | 2 | 1 | 150 | 105 | -0.8902 |
| a23_124460_ | 22 | AGGUGAGUUCUUUUUAUAGGCU | 1 | 1 | 184 | 179 | -1.6306 |
| a23_163065_ | 22 | AUUUGAUUAGCCAAAUUUAAAC | 2 | 2 | 148 | 130 | -1.0514 |
| a23_71826_ | 22 | CAAUAGUCAGAUGUAAACGAUC | 1 | 1 | 180 | 228 | -1.4282 |
| a22_52587_ | 22 | AAAAUUAUUGGGUGAAUUAGUU | 2 | 1 | 179 | 162 | -0.9013 |
| a13_234225_ | 22 | UGAAUUUUGUUAUGUUUUGUAA | 1 | 2 | 168 | 80 | -2.0417 |
| a13_286453_ | 22 | AGUCUAUCACCGAUAGAAGCCU | 1 | 6 | 182 | 430 | -1.4372 |
| a21_339397_ | 22 | CGCGAGGUUCUUUGUUUGUCUU | 1 | 1 | 192 | 413 | -1.3341 |
| a14_283014_ | 22 | UACCUAGUGAUGCCAUUGUCAA | 1 | 1 | 184 | 533 | -1.2829 |
| a21_170878_ | 22 | CUAAGGUUGCCCAGAGAUGUUC | 1 | 1 | 163 | 271 | -1.2341 |
| a21_63125_f | 22 | GAAUAAUUAUCAAGUGUGUAGC | 1 | 1 | 165 | 210 | -1.7804 |
| a11_146182_ | 24 | UUAAAAUGUUGCUAUAUAAUUAAU | 1 | 6 | 202 | 390 | -1.6207 |
| a21_169735_ | 24 | UAUACGGGCCGUAAAUAGUUUGAU | 2 | 6 | 132 | 369 | -0.8885 |
| a23_3672_ | 24 | UUGCUCAUUGCUAACUGCAAAGAG | 1 | 3 | 198 | 183 | -1.7594 |
| a14_260703_f | 24 | UUAAAAGUAUGAGACGAAAAUGAA | 1 | 1 | 190 | 111 | -1.4204 |
| a14_218837_ | 24 | UUAAAAAGAACUACACGAACGUGC | 1 | 1 | 194 | 342 | -1.1314 |
| a14_148530_f | 24 | AAAUAGCGUCGGGGAAAGGUGUCU | 3 | 1 | 152 | 73 | -1.0167 |
| a21_127379_ | 24 | UGGGACAAAAGAAAACUGUGGGUC | 2 | 1 | 162 | 586 | -1.32 |
| a11_2899_ | 24 | AUGAUGCUUUGGUGCUAAGGAGGU | 1 | 1 | 198 | 470 | -1.6094 |
| a11_248538_ | 24 | AUUUUUGGCAUUUUACACGGUGAG | 2 | 2 | 192 | 218 | -1.5206 |
| a13_59670_ | 24 | AGUGGAGUGGGCUAUUUUAGUCCA | 6 | 1 | 166 | 570 | -1.1249 |
| a32_72333_ | 24 | AACUAUUUUAUUGGAACAUGUUGA | 3 | 1 | 170 | 96 | -1.0391 |
| a33_22103_ | 24 | AGUAUGAUCUCGGGCUAAGGUUGC | 1 | 4 | 202 | 246 | -1.4138 |
| a24_224684_ | 24 | AACAAAACGAAUGAUCAAAAUGGU | 3 | 1 | 134 | 80 | -0.8871 |
| a13_225824_ | 24 | ACCAAAUGGAUCUAUUCUUAUAAU | 1 | 1 | 198 | 311 | -1.3393 |
| a24_82972_ | 24 | AACGAUCGGGUUGACUACGUAAAU | 3 | 1 | 190 | 146 | -0.9354 |
| a21_98074_ | 24 | AAUUUUUAGUGGUCCCGAAAUGCA | 3 | 1 | 166 | 112 | -0.9033 |
| a11_350684_ | 24 | UGAGUGUAUCAUCGAGAUAGUGCG | 1 | 1 | 190 | 307 | -1.1642 |
| a21_216237_ | 24 | AAAUUUCAGGGUCUAAAUUGAUGC | 2 | 1 | 138 | 447 | -1.2096 |
| a33_49599_ | 24 | CAGCGUGAUUGAUGGGGCAUUUUU | 3 | 1 | 118 | 287 | -1.4678 |
| a33_58155_ | 24 | AUGGUCGAUCUCAACCGAGAUUGA | 1 | 1 | 194 | 298 | -1.3188 |
| a23_103110_ | 24 | CGUGAAGAUUGUGGAUAUUGGAGA | 1 | 1 | 190 | 414 | -1.5507 |
a Precursor secondary structures of sRNAs in bold are represented in Figure 4.
b miRanda score calculated for the identification of the complementary region to the putative miRNA.
c MFEI index calculated as described [35].
d Include cases where sequence variants with up to two mismatches were identified and counted
e Indicates miRNAs for which a miRNA* sequence was identified.
f Indicates miRNAs for which an asymmetric bulge of more than 2 bases was identified in the miRNA/miRNA* duplex of the precursor, not meeting exactly the structural criteria previously set forth [36,37].