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. 2012 Jul 17;7(7):e40859. doi: 10.1371/journal.pone.0040859

Table 2. High-confidence predicted miRNA coding sequences on chromosome 1AL.

miRNA from chromosome 1AL Conserved miRNA1 Mature miRNA location Pre-miRNA statistics Matched sequence read2
ID Sequence3 Length(nt) ID Start End Arm Length MFE4 GC% MFEI5 ID
tae-miR156a UGACAGAAGAGAGUGAGCAC 20 aly-miR156a 20 39 5′ 125 −62 53.60 0.93 F2MIQBM02DWQ3H
tae-miR156a UGACAGAAGAGAGUGAGCAC 20 aly-miR156a 20 39 5′ 124 −69 58.87 0.95 F2MIQBM02DWQ3H
tae-miR164a UGGAGAAGCAGGGCACGUGCA 21 aly-miR164a 20 40 5′ 140 −75 55.71 0.96 F0RUNSI02GP0XY
tae-miR164a UGGAGAAGCAGGGCACGUGCA 21 aly-miR164a 20 40 5′ 140 −75 55.71 0.96 F1NBZEY01BCHIA
tae-miR166b* GGAAUGUUGUCUGGUUCAAGG 21 zma-miR166b* 20 40 5′ 136 −55 46.32 0.87 F1ADE5F01D77GU
tae-miR166e CUCGGACCAGGCUUCAUUCCC 21 bdi-miR166e 94 114 3′ As above F1ADE5F01D77GU
tae-miR166a UCGGACCAGGCUUCAUUCCCC 21 aly-miR166a 95 115 3′ 136 −54 47.06 0.84 F1ADE5F01DOFSZ
tae-miR166b* GGAAUGUUGUCUGGUUCAAGG 21 zma-miR166b* 20 40 5′ As above F1ADE5F01DOFSZ
tae-miR166a UCGGACCAGGCUUCAUUCCCC 21 aly-miR166a 96 116 3′ 137 −55 46.72 0.86 F1ADE5F01E2LUR
tae-miR166b* GGAAUGUUGUCUGGUUCAAGG 21 zma-miR166b* 20 40 5′ As above F1ADE5F01E2LUR
tae-miR171a UGAUUGAGCCGCGCCAAUAU 20 zma-miR171a 78 97 3′ 118 −59 48.31 1.04 F003IAL01EKU7V
tae-miR171b UUGAGCCGUGCCAAUAUCAC 20 zma-miR171b 82 101 3′ 122 −59 59.02 0.82 F1ADE5F01DL80Q
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 133 152 3′ 173 −74 45.09 0.94 F2MIQBM01BUBWA
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 133 152 3′ 173 −73 45.66 0.92 F1NBZEY02GWGQ1
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 134 153 3′ 174 −69 45.98 0.86 F1ADE5F01BAC6G
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 136 155 3′ 176 −70 44.32 0.90 F1ADE5F01AFV6T
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 135 154 3′ 175 −73 44.00 0.95 F1ADE5F01DARNZ
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 136 155 3′ 176 −74 44.32 0.95 F1ADE5F01AJ0FQ
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 133 152 3′ 173 −69 45.66 0.87 F1ADE5F01BL63C
tae-miR172a AGAAUCUUGAUGAUGCUGCA 20 csi-miR172a 136 155 3′ 176 −70 43.75 0.91 F1ADE5F01AY2DE
tae-miR399b UGCCAAAGGAGAAUUGCCCUG 21 bdi-miR399b 100 120 3′ 141 −64 59.57 0.76 F1NBZEY01CXBWQ
tae-miR399b UGCCAAAGGAGAAUUGCCCUG 21 bdi-miR399b 139 159 3′ 180 −84 59.44 0.78 F2MIQBM01AUXGN
tae-miR399b UGCCAAAGGAGAAUUGCCCUG 21 bdi-miR399b 138 158 3′ 179 −84 59.22 0.79 F2MIQBM01B24OQ
tae-miR399k UGCCAAAGGAAAUUUGCCCCA 21 osa-miR399k 93 113 3′ 134 −54 58.96 0.68 F1ADE5F01C5M0T
tae-miR1138 GUUUAGAUGUGACAUCCUUAAAA 23 tae-miR1138 20 42 5′ 173 −57 32.37 1.01 F0RUNSI01BXR55
tae-miR2118g UUCCUAAUGCCUCCCAUUCCUA 22 osa-miR2118g 97 118 3′ 139 −71 43.88 1.17 F003IAL01CL16O 6
tae-miR2118b UUCCCGAUGCCUCUCAUUCCUA 22 osa-miR2118b 96 117 3′ 138 −59 46.38 0.92 F003IAL01CL16O 6
tae-miR2118e UUUCUGAUGUCUCCCAUUCCUA 22 zma-miR2118e 98 119 3′ 140 −53 42.14 0.90 F1ADE5F01C34UT 6
tae-miR2118f UUUCUGAUGCCUCCCAUUCCUA 22 osa-miR2118f 96 117 3′ 138 −49 40.58 0.88 F1ADE5F01C68L2
tae-miR2118f UUCCUGAUGCCUCCCAUUCCUA 22 osa-miR2118f 101 122 3′ 143 −49 47.55 0.73 F1ADE5F01D1MVB
tae-miR2905 CACAUGUCAGUGCCAAAGGCA 21 osa-miR2905 61 81 3′ 102 −53 54.90 0.94 F1ADE5F01EPHEM
tae-miR2905 CACAUGUCAGUGACCAAGGCA 21 osa-miR2905 61 81 3′ 102 −57 54.90 1.02 F2MIQBM02EQP10
tae-miR5049 ACCUAAAUACUUGUAGUUGGG 21 hvu-miR5049 20 40 5′ 88 −56 38.64 1.65 F0RUNSI02HO6UW
tae-miR5050 GUGAGGUCGUUCAACCGGCAA 21 hvu-miR5050 94 114 3′ 135 −74 61.48 0.89 F1ADE5F01D1QBQ
1

Where two similar known miRNAs gave equally close matches to a sequence, the evolutionarily closest match is given.

2

Matched sequence reads shown in bold were also predicted to form miRNA hairpins by miRPara.

3

Mismatches to the conserved miRNA sequence are underlined and in bold.

4

MFE  =  Minimum Folding free Energy of predicted hairpin secondary structure.

5

MFEI  =  Minimum Folding Energy Index, calculated as described by Yin et al. [40].

6

miRPara did not predict these hairpins, but predicted a pre-miRNA on the complementary strand. For F003IAL01CL160, which contains two adjacent pre-miRNA hairpins, miRPara predicted the same strand for one but the complementary strand for the other.