From: Computational identification of DrosophilamicroRNA genes
Reference set miRNAs | ||||||||||
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Rank | Score | miR name | miR position | Cytological position | Sequence | Ano | Apis | Other | Nearest gene | Comment |
2 | 26.15 | miR-2a-2 (1) | 2L:19547562 | 37E | UAUCACAGCCAAGCUUUGAUGAGC | - | - | Â | In the intron of spi (sense) | [10]; 3 miR cluster |
3 | 26.00 | miR-2a-1 (2) | 2L:19547974 | 37E | UAUCACAGCCAGCUUUGAUGAGC | + | + | Worm | In the intron of spi (sense) | [10]; 3 miR cluster |
6 | 24.16 | miR-2b-2 (3) | 2L:19548259 | 37E | UAUCACAGCCAGCUUUGAGGAGC | + | + | Â | In the intron of spi (sense) | [10]; 3 miR cluster |
(8) | 24.01* | miR-2b-1 | 2L:8250840 | 28B | UAUCACAGCCAGCUUUGAGGAGC | - | - | Â | 895 upstream of Btk29A | [10]; failed conservation filter |
8 | 23.52 | miR-13b-2 (4) | X:8830202 | 8C | UAUCACAGCCAUUUUGACGAGU | - | - | Â | In the intron of CG7033 (sense) | [10] |
9 | 23.45 | miR6-3 (5) | 2R:14724424 | 56E | UAUCACAGUGGCUGUUCUUUUU | - | - | Â | 1732 upstream of CG11018 | [10]; 7 miR cluster |
12 | 22.89 | miR-12 (6) | X:15240478 | 13D | UGAGUAUUACAUCAGGUACUGGU | + | + | Â | 1986 upstream of Ac13E | [10]; 2 miR cluster |
13 | 22.84 | miR-7 (7) | 2R:15669777 | 57A | UGGAAGACUAGUGAUUUUGUUGU | + | + | Vertebrate | 816 upstream of CG30147 | [10] |
17 | 22.45 | miR-14 (8) | 2R:4614375 | 45E | UCAGUCUUUUUCUCUCUCCUA | + | + | Â | 5855 upstream of Or45b | [10] |
27 | 20.94 | miR-9 (9) | 3L:19515075 | 76C | UCUUUGGUUAUCUAGCUGUAUGA | + | + | Â | 6462 upstream of Shal | [10] |
29 | 20.77 | miR6-2 (10) | 2R:14724582 | 56E | UAUCACAGUGGCUGUUCUUUUU | - | - | Â | 1574 upstream of CG11018 | [10]; 7 miR cluster |
31 | 20.65 | miR6-1 (11) | 2R:14724711 | 56E | UAUCACAGUGGCUGUUCUUUUU | - | - | Â | 1445 upstream of CG11018 | [10]; 7 miR cluster |
33 | 20.38 | miR-13a (12) | 3R:11243269 | 88F | UAUCACAGCCAUUUUGAUGAGU | + | + | Â | 4626 upstream of CG6118 | [10]; 3 miR cluster |
36 | 20.08 | miR-5 (13) | 2R:14724858 | 56E | AAAGGAACGAUCGUUGUGAUAUG | - | - | Â | 1298 upstream of CG11018 | [10]; 7 miR cluster |
62 | 18.86 | let-7 (14) | 2L:18450101 | 36E | UGAGGUAGUAGGUUGUAUAGU | + | + | Vertebrate/ worm | 932 upstream of CG10283 | [9]; 3 miR cluster |
 | 18.45* | miR-10 | 3R:2635277 | 84B | ACCCUGUAGAUCCGAAUUUGU | + | + | Vertebrate | 13566 upstream of Scr | [10]; (not on aligned contig) |
74 | 18.42 | miR-1 (15) | 2L:20457182 | 38D | UGGAAUGUAAAGAAGUAUGGAG | + | - | Vertebrate/ worm | 14444 upstream of CG15476 | [10] |
96 | 17.79 | miR-3 (16) | 2R:14725313 | 56E | UCACUGGGCAAAGUGUGUCUCA | - | - | Â | 843 upstream of CG11018 | [10]; 7 miR cluster |
114 | 17.49 | miR-11 (17) | 3R:17439181 | 93E | CAUCACAGUCUGAGUUCUUGC | - | - | Â | In the intron of E2f (sense) | [10] |
124 | 17.36 | miR-4 (18) | 2R:14724998 | 56E | AUAAAGCUAGACAACCAUUGA | - | - | Â | 1158 upstream of CG11018 | [10]; 7 miR cluster |
172 | 16.54 | miR-13b-1 (19) | 3R:11243135 | 88F | UAUCACAGCCAUUUUGACGAGU | + | + | Â | 4760 upstream of CG6118 | [10]; 3 miR cluster |
192 | 16.27 | miR-8 (20) | 2R:11895154 | 53D | UAAUACUGUCAGGUAAAGAUGUC | + | + | Â | 3783 downstream of CG6301 | [10] |
 | 14.20 | miR-125 | 2L:18450405 | 36E | UCCCUGAGACCCUAACUUGUGA | + | + | Vertebrate/ worm | 628 upstream of CG10283 | [29]: low score; 3 miR cluster |
 |  | miR-2c | 3R:11243493 | 88F | UAUCACAGCCAGCUUUGAUGGGC | - | - |  | 4402 upstream of CG6118 | Hom; score n/a; 3 miR cluster |
Newly verified miRNAs | ||||||||||
Rank | Score | miR name | miR position | Cytological position | Sequence | Anos | Apis | Other | Nearest gene | Comment |
4 | 24.67 | miR-184 | 2R:8394117 | 50A | UGGACGGAGAACUGAUAAGGG | + | + | Vertebrate | 24406 upstream of CG17048 | Expression verified |
7 | 24.15 | miR-274 | 3L:11614451 | 68C | UUUUGUGACCGACACUAACGGGUAAU | - | - | Â | In the intron of CG32085 (antisense) | Expression verified |
10 | 23.10 | miR-275 | 2L:7418027 | 27F | cAGUCAGGUACCUGAAGUAGCGCGCG | + | + | Â | 1070 upstream of CG5261 | 2miR cluster (+Ano and Apis); expression verified |
16 | 22.57 | miR-92a | 3R:21461594 | 96E | CAUUGCACUUGUCCCGGCCUG | + | + | Vertebrate | 6578 upstream of BcDNA:LD22548 | 2miR cluster |
21 | 21.72 | miR-219 | 3L:17263886 | 74A | UGAUUGUCCAAACGCAAUUCUUG | + | + | Vertebrate | 4955 upstream of CG6485 | Expression not seen |
25 | 21.12 | miR-276a | 3L:10322758 | 67E | CAGCGAGGUAUAGAGUUCCUACG | + | + | Â | 47587 upstream of CG12362 | Duplicated, 45 kb apart; expression verified; 1copy in Ano and Apis |
28 | 20.88 | miR-277 | 3R:5925763 | 85F | UGUAAAUGCACUAUCUGGUACGACAU | + | + | Â | 1391 upstream of Fmr1 | 2 miR cluster; expression verified |
30 | 20.73 | miR-278 | 2R:10720792 | 52B | ggUGGGACUUUCGUCCGUUUGUAA | + | - | Â | 386 upstream of fus | Expression verified |
34 | 20.27 | miR-133 | 2L:20586360 | 38D | UUGGUCCCCUUCAACCAGCUGU | + | + | Vertebrate | 1059 downstream of CG15475 | 3 miR cluster; expression verified; [45] |
37 | 20.03 | miR-279 | 3R:25030674 | 99A | UGUGACUAGAUCCACACUCAU | + | + | Â | 1328 upstream of CG31044 | Related to miR-286; expression verified |
38 | 19.90 | miR-33 | 3L:19716503 | 76C | AGGUGCAUUGUAGUCGCAUUG | - | - | Vertebrate | In the intron of HLH106 (sense) | Â |
39 | 19.77 | miR-280 | 2R:3358854 | 44C | UGUAUUUACGUUGCAUAUGAAAUGAUA | - | - | Â | 21740 upstream of CG30358 | Expression verified |
41 | 19.73 | miR-281a | 2R:7235078 | 48E | ACUGUCGACGGACAGCUCUCUU | - | - | Â | 356 downstream of SmD3 | Duplicated cluster; expression verified; 1 copy in Ano |
43 | 19.64 | miR-282 | 3L:3231652 | 63C | aaucUAGCCUCUACUAGGCUUUGUCUGU | + | - | Â | 7132 upstream of CG14959 | Expression verified |
44 | 19.55 | miR-283 | X:15238971 | 13D | AAAUAUCAGCUGGUAAUUCUGGG | + | + | Â | 3493 upstream of Ac13E | 2 miR cluster; expression verified |
46 | 19.52 | miR-284 | 3R:8377257 | 87C | UGAAGUCAGCAACUUGAUUCCAGCAAUUG | - | - | Â | 1128 upstream of CG6989 | Expression verified |
47 | 19.47 | miR-281b | 2R:7234866 | 48E | ACUGUCGACGGAUAGCUCUCUU | + | - | Â | 144 downstream of SmD3 | Duplicated cluster; expression verified |
49 | 19.35 | miR-34 | 3R:5926677 | 85F | UGGCAGUGUGGUUAGCUGGUUG | + | + | Vertebrate/ worm | 477 upstream of Fmr1 | 2 miR cluster; expression verified; [45] |
50 | 19.27 | miR-263a | 2L:11942273 | 33B | aAUGGCACUGGAAGAAUUCACg | + | + | Vertebrate | 4764 downstream of CG16964 | Expression verified; [34] |
59 | 18.89 | miR-124 | 2L:17544454 | 36D | AUAAGGCACGCGGUGAAUGCCA | + | + | Vertebrate/ worm | 10606 downstream of CG7094 | 2 miR cluster; [45] |
66 | 18.58 | miR-79 | 2L:16676639 | 36A | AUAAAGCUAGAUUACCAAAGC | + | + | Worm | 822 upstream of CG31782 | 3 miR cluster; expression verified; [45] |
67 | 18.57 | miR-276b | 3L:10277315 | 67E | CAGCGAGGUAUAGAGUUCCUACG | - | - | Vertebrate | 7073 downstream of CG6559 | Duplicated, 45 kb apart; expression verified; 1copy in Ano and Apis |
77 | 18.36 | miR-210 | X:17859179 | 16F | UUGUGCGUGUGACAGCGGCUA | + | + | Vertebrate | 1193 downstream of CG32553 | Â |
83 | 18.11 | miR-285 | 3L:11903642 | 68E | UAGCACCAUUCGAAAUCAGUGCU | - | - | Vertebrate | 1592 upstream of CG7252 | Similar to miR-29 |
 | 18.08* | miR-100 | 2L:18449518 | 36E | AACCCGUAAAUCCGAACUUGUG | + | - | Vertebrate | 1515 upstream of CG10283 | Failed conservation filter; 3 miR cluster; expression verified; [45] |
91 | 17.93 | miR-92b | 3R:21466486 | 96E | AAUUGCACUAGUCCCGGCCU | + | - | Vertebrate | 1686 upstream of BcDNA:LD22548 | Expression verified; 2 miR cluster; [45] |
145 | 17.12 | miR-286 | 2R:14724858 | 56E | AGUGACUAGACCGAACACUCG | + | - | Â | 1013 upstream of CG11018 | Expression verified; 7 miR cluster; related to miR-279 |
146 | 17.11 | bantam | 3L:622845 | 61C | AGUGAGAUCAUUUUGAAAGCUG | + | - | Worm | 6301 upstream of CG12030 | [44] |
208 | 16.09 | miR-289 | 3L:13578391 | 70C | UAAAUAUUUAAGUGGAGCCUGCGACU | - | - | Â | In the intron of bru-3 (antisense) | Expression verified |
 | 13.73 | miR-287 | 2L:17552694 | 36D | UGUGUUGAAAAUCGUUUGCAC | + | - |  | 14896 upstream of Oli | Very low score;found by proximity to miR-124; expression verified |
 | 13.35 | miR-87 | 2L:9942828 | 30D | UGAGCAAAAUUUCAGGUGUG | - | - | Worm | 2009 upstream of CG13126 | Hom: very low score |
 |  | miR-263b | 3L:15666960 | 72D | cuUGGCACUGGGAGAAUUCACa | + | - | Vertebrate | 4243 upstream of comm | Hom; score n/a |
 |  | miR-288 | 2L:20588106 | 38D | UUUCAUGUCGAUUUCAUUUCAUG | + | - |  | 2805 downstream of CG15475 | Score n/a; found by proximity to miR-133; expression verified |
Unverified Ano-conserved candidates | ||||||||||
Rank | Score | miR name | miR position | Cytological position | Sequence | Ano | Apis | Other | Nearest gene | Comment |
1 | 26.76 | Â | 2R:4681879 | 46A | CAUCACACCCAGGUUGAGUGAGU | + | + | Â | In the intron of Mmp2 (antisense) | NT |
5 | 24.35 | Â | 3R:121090 | 82A | AAAUUGACUCUAGUAGGGAGUCC | + | + | Â | 533 downstream of CG9780 | NT |
14 | 22.63 | Â | X:1545630 | 2B | UGCAGGUUUCGUCGACAACGA | + | - | Â | 732 upstream of CG32806 | NT |
19 | 22.13 | Â | 3L:21585985 | 79A | CGAUUUGUCUUUUUCCGCUUACUG | + | - | Â | 1727 downstream of CG7160 | NT |
20 | 21.95 | Â | 3L:18809845 | 75E | UUUUGAUUGUUGCUCAGAAAGCC | + | + | Â | 3283 upstream of CG6865 | No expression seen either strand |
23 | 21.38 | Â | 3L:8530512 | 66D | GUGAGAUAUGUUUGAUAUUCUUGGUUGUU | + | + | Â | 2374 upstream of CG6638 | NT |
40 | 19.75 | Â | X:12366993 | 11B | UAUCAUAAGACACACGCGGCUAU | + | - | Â | in the intron of tomosyn (sense) | NT |
54 | 19.06 | Â | 2R:11128979 | 52E | guUAUUGCUUGAGAAUACACGUAGUU | + | + | Â | 15915 upstream of Dg | No expression seen either strand |
61 | 18.86 | Â | 2L:859210 | 21D | AGUUUGUUCGUUUGGCUCGAGUUAU | + | - | Â | 2208 downstream of CG13949 | NT |
104 | 17.64 | Â | 2L:16676008 | 36A | UCUUUGGUAUUCUAGCUGUAGA | + | - | Â | 1453 upstream of CG31782 | No expression seen; miR-79 cluster |
117 | 17.44 | Â | 3R:21403955 | 96E | UGAUAUUGUCCUGUCACAGCAGUA | + | - | Â | 3265 upstream of CG12250 | No expression seen |
123 | 17.36 | Â | 2L:7418192 | 27F | AUUGUACUUCAUCAGGUGCUCUGGUG | + | + | Â | 905 upstream of CG5261 | NT |
126 | 17.31 | Â | 3R:16621175 | 92F | UUUGUUUUGCAAUUUUCGCUUU | + | - | Â | In the intron of CG17838 (sense) | NT |
130 | 17.24 | Â | 2L:16676828 | 36A | CUUUGGUGAUUUUAGCUGUAUG | + | - | Â | 633 upstream of CG31782 | No expression seen; miR-79 cluster |
183 | 16.39 | Â | 2R:7223583 | 48E | UCAUCCCCUUGUUGCAAACCUCACGC | + | - | Â | In the intron of CG8877 (sense) | NT |
190 | 16.28 | Â | 3R:5916861 | 85F | UGGGAUACACCCUGUGCUCGCU | + | - | Â | 17107 upstream of CG5361 | NT |
195 | 16.24 | Â | 2L:243049 | 21B | CAUAAGCGUAUAGCUUUUCCC | + | + | Â | In the intron of kis (sense) | NT |