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Table 1 List of Drosophila miRNAs and additional unverified candidates supported by third-species conservation

From: Computational identification of DrosophilamicroRNA genes

Reference set miRNAs

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

-

-

 

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

+

+

 

In the intron of spi (sense)

[10]; 3 miR cluster

(8)

24.01*

miR-2b-1

2L:8250840

28B

UAUCACAGCCAGCUUUGAGGAGC

-

-

 

895 upstream of Btk29A

[10]; failed conservation filter

8

23.52

miR-13b-2 (4)

X:8830202

8C

UAUCACAGCCAUUUUGACGAGU

-

-

 

In the intron of CG7033 (sense)

[10]

9

23.45

miR6-3 (5)

2R:14724424

56E

UAUCACAGUGGCUGUUCUUUUU

-

-

 

1732 upstream of CG11018

[10]; 7 miR cluster

12

22.89

miR-12 (6)

X:15240478

13D

UGAGUAUUACAUCAGGUACUGGU

+

+

 

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

+

+

 

5855 upstream of Or45b

[10]

27

20.94

miR-9 (9)

3L:19515075

76C

UCUUUGGUUAUCUAGCUGUAUGA

+

+

 

6462 upstream of Shal

[10]

29

20.77

miR6-2 (10)

2R:14724582

56E

UAUCACAGUGGCUGUUCUUUUU

-

-

 

1574 upstream of CG11018

[10]; 7 miR cluster

31

20.65

miR6-1 (11)

2R:14724711

56E

UAUCACAGUGGCUGUUCUUUUU

-

-

 

1445 upstream of CG11018

[10]; 7 miR cluster

33

20.38

miR-13a (12)

3R:11243269

88F

UAUCACAGCCAUUUUGAUGAGU

+

+

 

4626 upstream of CG6118

[10]; 3 miR cluster

36

20.08

miR-5 (13)

2R:14724858

56E

AAAGGAACGAUCGUUGUGAUAUG

-

-

 

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

-

-

 

843 upstream of CG11018

[10]; 7 miR cluster

114

17.49

miR-11 (17)

3R:17439181

93E

CAUCACAGUCUGAGUUCUUGC

-

-

 

In the intron of E2f (sense)

[10]

124

17.36

miR-4 (18)

2R:14724998

56E

AUAAAGCUAGACAACCAUUGA

-

-

 

1158 upstream of CG11018

[10]; 7 miR cluster

172

16.54

miR-13b-1 (19)

3R:11243135

88F

UAUCACAGCCAUUUUGACGAGU

+

+

 

4760 upstream of CG6118

[10]; 3 miR cluster

192

16.27

miR-8 (20)

2R:11895154

53D

UAAUACUGUCAGGUAAAGAUGUC

+

+

 

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

-

-

 

In the intron of CG32085 (antisense)

Expression verified

10

23.10

miR-275

2L:7418027

27F

cAGUCAGGUACCUGAAGUAGCGCGCG

+

+

 

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

+

+

 

47587 upstream of CG12362

Duplicated, 45 kb apart; expression verified; 1copy in Ano and Apis

28

20.88

miR-277

3R:5925763

85F

UGUAAAUGCACUAUCUGGUACGACAU

+

+

 

1391 upstream of Fmr1

2 miR cluster; expression verified

30

20.73

miR-278

2R:10720792

52B

ggUGGGACUUUCGUCCGUUUGUAA

+

-

 

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

+

+

 

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)

 

39

19.77

miR-280

2R:3358854

44C

UGUAUUUACGUUGCAUAUGAAAUGAUA

-

-

 

21740 upstream of CG30358

Expression verified

41

19.73

miR-281a

2R:7235078

48E

ACUGUCGACGGACAGCUCUCUU

-

-

 

356 downstream of SmD3

Duplicated cluster; expression verified; 1 copy in Ano

43

19.64

miR-282

3L:3231652

63C

aaucUAGCCUCUACUAGGCUUUGUCUGU

+

-

 

7132 upstream of CG14959

Expression verified

44

19.55

miR-283

X:15238971

13D

AAAUAUCAGCUGGUAAUUCUGGG

+

+

 

3493 upstream of Ac13E

2 miR cluster; expression verified

46

19.52

miR-284

3R:8377257

87C

UGAAGUCAGCAACUUGAUUCCAGCAAUUG

-

-

 

1128 upstream of CG6989

Expression verified

47

19.47

miR-281b

2R:7234866

48E

ACUGUCGACGGAUAGCUCUCUU

+

-

 

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

 

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

+

-

 

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

-

-

 

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

 

2R:4681879

46A

CAUCACACCCAGGUUGAGUGAGU

+

+

 

In the intron of Mmp2 (antisense)

NT

5

24.35

 

3R:121090

82A

AAAUUGACUCUAGUAGGGAGUCC

+

+

 

533 downstream of CG9780

NT

14

22.63

 

X:1545630

2B

UGCAGGUUUCGUCGACAACGA

+

-

 

732 upstream of CG32806

NT

19

22.13

 

3L:21585985

79A

CGAUUUGUCUUUUUCCGCUUACUG

+

-

 

1727 downstream of CG7160

NT

20

21.95

 

3L:18809845

75E

UUUUGAUUGUUGCUCAGAAAGCC

+

+

 

3283 upstream of CG6865

No expression seen either strand

23

21.38

 

3L:8530512

66D

GUGAGAUAUGUUUGAUAUUCUUGGUUGUU

+

+

 

2374 upstream of CG6638

NT

40

19.75

 

X:12366993

11B

UAUCAUAAGACACACGCGGCUAU

+

-

 

in the intron of tomosyn (sense)

NT

54

19.06

 

2R:11128979

52E

guUAUUGCUUGAGAAUACACGUAGUU

+

+

 

15915 upstream of Dg

No expression seen either strand

61

18.86

 

2L:859210

21D

AGUUUGUUCGUUUGGCUCGAGUUAU

+

-

 

2208 downstream of CG13949

NT

104

17.64

 

2L:16676008

36A

UCUUUGGUAUUCUAGCUGUAGA

+

-

 

1453 upstream of CG31782

No expression seen; miR-79 cluster

117

17.44

 

3R:21403955

96E

UGAUAUUGUCCUGUCACAGCAGUA

+

-

 

3265 upstream of CG12250

No expression seen

123

17.36

 

2L:7418192

27F

AUUGUACUUCAUCAGGUGCUCUGGUG

+

+

 

905 upstream of CG5261

NT

126

17.31

 

3R:16621175

92F

UUUGUUUUGCAAUUUUCGCUUU

+

-

 

In the intron of CG17838 (sense)

NT

130

17.24

 

2L:16676828

36A

CUUUGGUGAUUUUAGCUGUAUG

+

-

 

633 upstream of CG31782

No expression seen; miR-79 cluster

183

16.39

 

2R:7223583

48E

UCAUCCCCUUGUUGCAAACCUCACGC

+

-

 

In the intron of CG8877 (sense)

NT

190

16.28

 

3R:5916861

85F

UGGGAUACACCCUGUGCUCGCU

+

-

 

17107 upstream of CG5361

NT

195

16.24

 

2L:243049

21B

CAUAAGCGUAUAGCUUUUCCC

+

+

 

In the intron of kis (sense)

NT

  1. These sequences were identified as high-scoring candidates through miRseeker analysis of drosophilid genomes (except as noted) and are ordered by their rank and score. The first part of the table includes members of the reference set, whose rank within the reference set is given in parentheses after the gene name; thus miR-4 ranked 18th among the reference set and 124th overall. The second part of the table includes miRNAs newly identified in this study. In general, we defined a candidate miRNA sequence on the basis of the bounds of conserved sequence; this is often longer than the presumed 21-22 nucleotide mature product. The third part of the table includes unverified gene predictions supported by conservation in Anopheles and/or Apis. Drosophila-specific predictions without confirming expression data may be viewed on the web [43]. References in the comments are to miRNAs that have been independently identified in previous or concurrent studies. n/a, score not available; NT, expression not tested; Hom, miRNA identified solely by homology to other miRNAs. The following miRs were not identifed by miRseeker: miR-10 was not aligned using the first release of the D. pseudoobscura genome while miR-2b-1 and miR-100 failed the conservation filters. These three received very high miRseeker scores, however, and they have been placed into the list for the sake of comparison, although they are not ranked. Six additional miRNAs scored poorly but are genuine. These include two members of the reference set (miR-125 and miR-2c), two that were identified by homology to miRNAs cloned from other species (miR-87 and miR-263b), and two that were identified as Anopheles-conserved stem-loops located in proximity to other Drosophila miRNAs whose expression was verified by northern analysis (miR-287 and miR-288). Most miRNAs are located in intragenic regions, and there is an apparent bias for intronic miRNAs to be located on the transcribed strand.