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. 2014 Oct 8;9(10):e108851. doi: 10.1371/journal.pone.0108851

Table 2. Conserved miRNAs in chickpea.

miR_ID miR Family Sequence L Conserved in miRNA* Start End PL MFE Adjusted Hairpin
gma mtr vun ath os Y/N MFE G/C%
miR156_1 mir156 UUGACAGAAGAGAGAGAGCAC 21 + - - - - N 52925 52945 85 -41.8 -49.176468 44.705883
miR156_2 UUGACAGAAGAUAGAGGGCAC 21 + - - - - N 17629788 17629808 109 −42.6 −39.08257 38.532112
miR156_3 UGACAGAAGAGAGUGAGCAC 20 + + + + + Y 44874629 44874648 92 −53.1 −57.71739 44.56522
miR156_4 UGACAGAAGAGAGUGAGCAC 20 Y 35818615 35818634 91 −52.8 −58.021973 43.956043
miR156_5 UGACAGAAGAGAGUGAGCAC 20 N 35226603 35226622 85 −39.6 −46.588234 42.352943
miR156_6 UGACAGAAGAGAGUGAGCAC 20 N 1284221 1284240 145 −65.1 −44.896553 37.931034
miR156_7 UGACAGAAGAGGGUGAGCAC 20 + + + - - N 3228450 3228469 77 −30.7 −39.870132 32.467533
miR156_8 UGACAGACGAGAGUGAGCAC 20 + - + - - N 7424 7443 91 −52.7 −57.912086 42.857143
miR156_9 UUGACAGAAGAUAGAAAGCAC 21 + + + + - N 2202 2222 94 −42.7 −45.42553 39.361702
miR156_10 UUGACAGAAGAUAGAGAGCAC 21 + + + - - Y 134 154 155 −60.3 −38.903225 32.258064
miR156_11 UUGACAGAAGAUAGAGAGCAC 21 Y 2528278 2528298 81 −47.1 −58.148148 39.506172
miR156_12 UUGACAGAAGAUAGAGAGCAC 21 N 25200808 25200828 82 −45.9 −55.97561 32.92683
miR156_13 UUGACAGAAGAUAGAGAGCAC 21 N 14260671 14260691 100 −46.4 −46.4 34
miR156_14 UUGACAGAAGAUAGAGAGCAC 21 N 14160024 14160044 119 −51.1 −42.941174 35.294117
miR159_1 mir159 UUUGGAUUGAAGGGAGCUCUA 21 + + - + - Y 14884652 14884672 195 −97.2 −49.846153 38.46154
miR159_2 UUUGGAUUGAAGGGAGCUCUA 21 Y 11393460 11393480 195 −94.2 −48.30769 38.97436
miR159_3 AUUGGAGUGAAGGGAGCUCCA 21 + + - - - N 13935752 13935772 188 −83.4 −44.361702 41.489365
miR160_1 mir160 UGCCUGGCUCCCUGAAUGCCA 21 - + - - + N 6658138 6658158 85 −42.8 −50.352943 40
miR160_2 UGCCUGGCUCCCUGUAUGCCA 21 + + + + + Y 32984804 32984824 86 −45.6 −53.023254 48.837208
miR160_3 UGCCUGGCUCCCUGUAUGCCA 21 + + + + + Y 10315830 10315850 86 −47.1 −54.76744 47.674416
miR160_4 UGCCUGGCUCCCUGUAUGCCA 21 + + + + + N 19971530 19971550 86 −48.8 −56.744186 48.837208
miR162_1 mir162 UCGAUAAACCUCUGCAUCCAG 21 + + + + + N 7679640 7679660 124 −47.5 −38.30645 42.741936
miR164_1 mir164 UGGAGAAGCAGGGCACAUGCU 21 - + - - - N 33442678 33442698 75 −34.34 −45.786667 45.333336
miR164_2 UGGAGAAGCAGGGCACGUGCA 21 + + + + + N 20759462 20759482 175 −68.1 −38.914284 39.42857
miR164_3 UGGAGAAGCAGGGCACGUGCA 21 N 38007519 38007539 86 −37.3 −43.372093 41.860466
miR164_4 UGGAGAAGCAGGGCACGUGCA 21 N 7727761 7727781 118 −45.93 −38.92373 47.457626
miR166_1 mir166 UCGGACCAGGCUUCAUUCCCC 21 + + - + + Y 47802209 47802229 101 −42.15 −41.732674 47.524754
miR166_2 UCGGACCAGGCUUCAUUCCCC 21 Y 34613199 34613219 80 −41.9 −52.375 47.5
miR166_3 UCGGACCAGGCUUCAUUCCCC 21 N 2982935 2982955 98 −46.2 −47.142857 41.836735
miR166_4 UCGGACCAGGCUUCAUUCCCG 21 + - - - - Y 609780 609800 163 −59.7 −36.625767 34.969322
miR166_5 UCGGACCAGGCUUCAUUCCCU 21 - - - - + N 10985854 10985874 168 −60.8 −36.190475 39.88095
miR166_6 UCGGACCAGGCUUCAUUCCUC 21 - + - - + N 45773545 45773565 94 −39.78 −42.31915 46.80851
miR166_7 UCGGACCAGGCUUCAUUCCUC 21 N 788963 788983 99 −48.07 −48.555557 40.40404
miR166_8 UCUCGGACCAGGCUUCAUUCC 21 + - - - - Y 609782 609802 163 −59.7 −36.625767 34.969322
miR167_1 mir167 UGAAGCUGCCAGCAUGAUCU 20 + + - - - N 32102772 32102791 71 −37.4 −52.676056 39.43662
miR167_2 UGAAGCUGCCAGCAUGAUCUA 21 + + - + + N 30873622 30873642 161 −67.2 −41.73913 37.8882
miR167_3 UGAAGCUGCCAGCAUGAUCUA 21 N 1691349 1691369 101 −48.9 −48.415844 39.603962
miR167_4 UGAAGCUGCCAGCAUGAUCUG 21 + + - - + N 34009600 34009620 210 −79.6 −37.90476 32.380955
miR167_5 UGAAGCUGCCAGCAUGAUCUGA 22 + - - - - Y 5038949 5038970 102 −49.1 −48.137253 39.215687
miR167_6 UGAAGCUGCCAGCAUGAUCUGA 22 Y 38728619 38728640 108 −44.93 −41.601852 48.148148
miR167_7 UGAAGCUGCCAGCAUGAUCUGG 22 - - - + - Y 2509 2530 158 −57.8 −36.58228 42.405064
miR167_8 UGAAGCUGCCAGCAUGAUCUUA 22 N 57870929 57870950 75 −36.3 −48.4 45.333336
miR168_1 mir168 UCGCUUGGUGCAGGUCGGGAA 21 + + + + - Y 7328597 7328617 136 −65.9 −48.455883 55.88235
miR169_1 mir169 AGCCAAGGAUGACUUGCCGG 20 + + + + + N 19659099 19659118 86 −38.3 −44.53488 46.51163
miR169_2 CAGCCAAGGAUGACUUGCCGA 21 + + - + + N 10422873 10422893 200 −83.7 −41.85 34
miR169_3 CAGCCAAGGAUGACUUGCCGG 21 + + + + + N 2353405 2353425 95 −40.7 −42.842106 46.31579
miR169_4 CAGCCAAGGAUGACUUGCCGG 21 N 3920369 3920389 135 −63.5 −47.037037 44.444447
miR169_5 CAGCCAAGGAUGACUUGCCGG 21 Y 2526196 2526216 119 −50.17 −42.15966 30.252102
miR169_6 CAGCCAAGGGUGAUUUGCCGG 21 + + - - - N 19606166 19606186 134 −57.6 −42.985073 40.298508
miR169_9 GAGCCAAGGAUGACUUGCCGG 21 - + - - - N 19659098 19659118 86 −38.3 −44.53488 46.51163
miR169_10 UGAGCCAGGAUGACUUGCCGG 21 - + - - - Y 19609060 19609080 76 −37.4 −49.21053 42.105263
miR169_11 CAGCCAAGGAUAACUUGCCGG 21 + + + + + N 4770 4790 94 −38.5 −40.957447 43.617023
miR171_1 mir171 UGAUUGAGCCGCGUCAAUAUC 21 - + - - - N 14153792 14153812 102 −47.7 −46.76471 40.19608
miR171_3 UGAUUGAGCCGUGCCAAUAUC 21 + + - + + Y 1004434 1004454 97 −49.6 −51.13402 36.082474
miR171_4 UGAUUGAGCCGUGCCAAUAUC 21 N 5540425 5540445 78 −34.4 −44.102566 34.615387
miR171_5 UGAUUGAGCCGUGCCAAUAUC 21 N 15207158 15207178 94 −40.2 −42.765957 39.361702
miR171_6 UGAUUGAGCCGUGCCAAUAUC 21 N 6250414 6250434 117 −45.7 −39.05983 30.769232
miR171_7 UGAUUGAGUCGUGCCAAUAUC 21 - + - - - N 73 93 77 −32.6 −42.337658 35.064934
miR171_8 AGAUAUUGGUGCGGUUCAAUC 21 + - - - - Y 36014922 36014942 102 −52.4 −51.37255 38.235294
miR171_9 CGAUGUUGGUGAGGUUCAAUC 21 + - - - - Y 27995981 27996001 95 −39.8 −41.894737 40
miR171_10 UUGAGCCGCGCCAAUAUCAC 20 - - - - - N 1567139 1567158 92 −41.5 −45.108696 47.826088
miR171_11 UUGAGCCGCGCCAAUAUCACU 21 + - - - - Y 6636919 6636939 94 −42.6 −45.319145 39.361702
miR171_12 UUGAGCCGUGCCAAUAUCAC 20 - - - - - N 14104770 14104789 85 −35.7 −42 36.47059
miR171_13 UUGAGCCGUGCCAAUAUCACA 21 + - - - - N 5540422 5540442 78 −34.4 −44.102566 34.615387
miR172_1 mir172 AGAAUCCUGAUGAUGCUGCAG 21 - + - - - N 33800439 33800459 134 −69.8 −52.089554 38.059704
miR172_2 AGAAUCUUGAUGAUGCUGCA 20 - - - + - N 1018482 1018501 106 −48.7 −45.943398 40.56604
miR172_3 AGAAUCUUGAUGAUGCUGCAG 21 - - - + - Y 1018481 1018501 106 −48.7 −45.943398 40.56604
miR172_4 AGAAUCUUGAUGAUGCUGCAU 21 + + + + + Y 11960794 11960814 108 −47.4 −43.88889 29.62963
miR172_5 AGAAUCUUGAUGAUGCUGCAU 21 Y 28871865 28871885 112 −47.51 −42.419643 39.285713
miR172_6 AGAAUCUUGAUGAUGCUGCAU 21 N 11265321 11265341 82 −39.1 −47.682926 34.146343
miR172_8 GCAGCAGCAUCAAGAUUCACA 21 + - - - - Y 2893096 2893116 184 −71.7 −38.96739 39.673912
miR172_9 GGAGCAUCAUCAAGAUUCACA 21 - - - - - Y 2969008 2969028 126 −58 −46.031746 43.650795
miR172_10 GAAUCUUGAUGAUGCUGCAG 20 + + + + - Y 2969100 2969119 124 −57.1 −46.048386 44.35484
miR319_1 mir319 UUGGACUGAAGGGAGCUCCCU 21 + + + + + Y 4935256 4935276 216 −74.03 −34.273148 39.814816
miR319_2 UUGGACUGAAGGGAGCUCCCU 21 N 27801302 27801322 216 −93.6 −43.333332 35.185184
miR319_4 UUGGACUGAAGGGGCCUCUU 20 + - - - - N 15212722 15212741 207 −90.71 −43.821255 44.927536
miR319_5 UGGACUGAAGGGGAGCUCCUUC 22 + - - - - N 46353126 46353147 213 −90.2 −42.347416 35.21127
miR319_6 GAGCUUCCUUCAGUCCACUC 20 + + + + - Y 31787184 31787203 199 −86.6 −43.517586 38.693466
miR319_7 UGGACUGAAGGGAGCUCCUUC 21 + + + + + N 9436191 9436211 93 −49.3 −53.01075 47.31183
miR390_1 mir390 AAGCUCAGGAGGGAUAGCGCC 21 + + - + - N 26531589 26531609 82 −47 −57.317074 43.90244
miR390_2 AAGCUCAGGAGGGAUAGCGCC 21 N 26325697 26325717 71 −39.4 −55.49296 40.84507
miR393_1 mir393 UCCAAAGGGAUCGCAUUGAUCC 22 + - - + - N 30299002 30299023 121 −53.2 −43.96694 34.710743
miR393_2 UCCAAAGGGAUCGCAUUGAUCC 22 N 1754148 1754169 77 −32.4 −42.077923 28.57143
miR393_3 AUCAUGCUAUCCCUUUGGAUU 21 + + - + + Y 34480633 34480653 141 −57.7 −40.921986 39.00709
miR394_1 mir394 UUGGCAUUCUGUCCACCUCC 20 + - - + + N 49015076 49015095 129 −62.3 −48.294575 41.08527
miR394_2 UUGGCAUUCUGUCCACCUCC 20 N 31533893 31533912 67 −26.03 −38.85075 47.761192
miR394_3 UUGGCAUUCUGUCCACCUCC 20 N 8950170 8950189 125 −36.35 −29.079998 40.8
miR396_1 mir396 UUCCACAGCUUUCUUGAACUG 21 + + - + + N 35366632 35366652 114 −45.6 v39.999996 39.473686
miR396_2 UUCCACAGCUUUCUUGAACUU 21 + + - + + N 556766 556786 85 -35.9 -42.2353 35.294117
miR396_3 CUCAAGAAAGCUGUGGGAGA 20 + + - - - Y 6590654 6590673 108 -47.9 -44.351852 37.962963
miR396_4 GCUCAAGAAAGCUGUGGGAGA 21 + + - - - Y 6590654 6590674 108 -47.9 -44.351852 37.962963
miR396_5 UUCCACAGUUUUCUUGAACUG 21 + + - + + N 31162290 31162310 121 -47.8 -39.50413 41.322315
miR397_1 mir397 UCAUUGAGUGCAGCGUUGAUG 21 + - - + + N 1821127 1821147 153 -60.1 -39.281044 30.065361
miR398_1 mir398 UGUGUUCUCAGGUCGCCCCUG 21 + + - - + N 33289822 33289842 80 −29.04 −36.3 50
miR398_2 UGUGUUCUCAGGUCGCCCCUG 21 N 33373257 33373277 108 −47.8 −44.25926 50
miR399_1 mir399 UGCCAAAGAAGAUUUGCCCCG 21 - + - - - N 103 123 79 −33.4 −42.278484 41.772152
miR399_2 UGCCAAAGGAGAGCUGCCCUA 21 - + - - - N 254628 254648 124 −48.8 −39.354836 35.48387
miR399_3 UGCCAAAGGAGAGCUGCCCUG 21 - + - - + N 216204 216224 110 −47.8 −43.454544 36.363636
miR399_4 UGCCAAAGGAGAGCUGCUCUU 21 + + + + + N 29007702 29007722 172 −60.23 −35.01744 29.651161
miR399_5 UGCCAAAGGAGAGUUGCCCUG 21 + + + + + Y 441789 441809 103 −44.9 −43.592236 43.68932
miR399_6 UGCCAAAGGAGAGUUGCCCUG 21 N 12886367 12886387 89 −43.3 −48.651684 41.573032
miR408_1 mir408 AUGCACUGCCUCUUCCCUGGC 21 + + + + + N 21952158 21952178 82 −36.6 −44.634144 51.219513
miR530_1 mir530 UGCAUUUGCACCUGCACUUUA 21 + + - - + N 40319328 40319348 181 −79.3 −43.812157 38.674034
miR2111_1 mir2111 UAAUCUGCAUCCUGAGGUUUA 21 + + - + - N 37594 37614 81 −30.5 −37.654324 33.333336
miR2111_2 UAAUCUGCAUCCUGAGGUUUA 21 N 93808 93828 66 −27.5 −41.666664 36.363636
miR2111_3 UAAUCUGCAUCCUGAGGUUUA 21 N 19125 19145 67 −33.1 −49.40298 31.343285
miR2111_4 UAAUCUGCAUCCUGAGGUUUA 21 N 37881 37901 81 −35.7 −44.074078 33.333336
miR2118_1 mir2118 UUACCGAUUCCACCCAUUCCUA 22 - + - - - N 112 133 155 −41.2 −26.580647 40
miR2118_2 GGAUAUGGGAGGGUCGGUAAAG 22 + - - - - Y 15537249 15537270 150 −60.54 −40.36 38
miR5213_1 mir5213 UACGUGUGUCUUCACCUCUGAA 22 + - - - - N 16737686 16737707 119 −42.1 −35.37815 36.974792
miR5213_2 UACGUGUGUCUUCACCUCUGA 21 - + - - - N 16737686 16737706 119 −42.1 −35.37815 36.974792
miR5213_3 UACGGGUGUCUUCACCUCUGA 21 - + - - - Y 31172531 31172551 114 −47.7 −41.842106 38.59649
miR5232_1 mir5232 UACAUGUCGCUCUCACCUGGA 21 - + - - - Y 29987519 29987539 167 −69.8 −41.79641 44.31138

gma- Glycin max; mtr- Medicago tranculata; vun- Vigna unguiculata; ath- Arabidopsis thaliana; os- Oryza sativa.

MFE- Minimum Folding Energy; L: Length; PL: Precursor Length.