RNA 3D Hub

JAR3D Query RF02032-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF02032 maps to these 73 chains: 9L0R|1|A, 9L0R|1|B, 9L0R|1|C, 9L0R|1|D, 9L0R|1|E, 9L0R|1|F, 9L0R|1|G, 9L0R|1|H, 9L0R|1|I, 9L0R|1|J, 9L0R|1|K, 9L0R|1|L, 9LEC|1|J, 9LEE|1|A, 9LEE|1|B, 9LEE|1|C, 9LEE|1|D, 9LEE|1|E, 9LEE|1|F, 9LEE|1|G, 9LEE|1|H, 9LEE|1|I, 9LEE|1|J, 9LEL|1|J, 9LEM|1|A, 9LEM|1|B, 9LEM|1|C, 9LEM|1|D, 9LEM|1|E, 9LEM|1|F, 9LEM|1|G, 9LEM|1|H, 9LEM|1|I, 9LEM|1|J, 9LHK|1|G, 9LHL|1|A, 9LHL|1|B, 9LHL|1|C, 9LHL|1|D, 9LHL|1|E, 9LHL|1|F, 9LHL|1|G, 9LHL|1|H, 9LHL|1|I, 9LHL|1|J, 9LHL|1|K, 9LHL|1|L, 9LHL|1|M, 9LHL|1|N, 9LMF|1|A, 9LMF|1|B, 9LMF|1|C, 9LMF|1|D, 9LMF|1|E, 9LMF|1|F, 9LMF|1|G, 9LMF|1|H, 9LMF|1|I, 9LMF|1|J, 9MEE|1|A, 9MEE|1|B, 9MEE|1|C, 9MEE|1|D, 9MEE|1|E, 9MEE|1|F, 9MEE|1|G, 9MEE|1|H, 9MEE|1|I, 9MEE|1|J, 9MEE|1|K, 9MEE|1|L, 9MEE|1|M, 9MEE|1|N See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 11 3-way junction loop

Column numbers: 319-352, 366-371, 405-406 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UA-------------------------------A*UGAG-U*AA    3

    
    GU-------------------------------A*UUUAGG*CA    2

    
    GU-------------------------------G*CUUAGA*UA    2

    
    UA-------------------------------G*CGAA-U*AA    2

    
    GGCCGCCUCAACAGAGGACGUCUAUGAAUGGUGA*U--U-G*CA    1

    
    CAC-GUUU-------------------------G*UUAA-C*GG    1

    
    GU-------------------------------A*UUUAGA*UA    1

    
    GU-------------------------------G*CUUAGU*GA    1

    
    GU-------------------------------G*CUUUGU*AA    1

    
    GU-------------------------------U*UUAG-A*UA    1

    
    UA-------------------------------A*CGAG-C*GA    1

    
    UA-------------------------------A*CUAG-U*AA    1

    
    UA-------------------------------A*UAAA-U*AA    1

    
    UA-------------------------------A*UGAA-U*AA    1

    
    UA-------------------------------A*UUCA-C*GA    1

    
    UA-------------------------------A*UUCA-U*AA    1

    
    UA-------------------------------G*CGAA-C*GA    1

    
    UA-------------------------------U*AGAG-U*AA    1

    
    Omitted sequenced and counts

    
    -AGCUUAGACUUUUAGC-GGAGUCU-------U-*--C---*--    3

    
    UA----AGGUGAGGAGGCAUCCUCUU------UA*ACU---*-U    1

    
    UA-----AGUGGUUAGC-ACCACCGA-----AUA*UA----*-A    1

    
    ------GGUGGGUUCGCAGCCCUUUA------CU*AG----*-A    1

    
    -AGCUUAGACCUUUAGC-GGGGUUU-------U-*------*-C    1

    
    ------GAGACGUUAGC-GCGUCUCG------CU*AGA---*--    1

    
    AAC--CGAGUGGGUAGCUCCCAUUU---------*------*-A    1

    
    G-----AGGGCGUAAGC--UGCCCUA------GC*G-----*-A    1

    
    UA------GCGACGGCC-AUCGUU----------*------*-G    1

    
    U--------------------------------A*UUAA-U*A-    1
Click on headings to reorder table
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group J3_80578.1

Basepair signature:
10

56.52 -330.46 4 1

2

Motif group J3_14360.1

Basepair signature:
10

56.52 -387.19 7 2

3

Motif group J3_81015.1

Basepair signature:
11

34.78 -365.23 9 4

4

Motif group J3_47376.1

Basepair signature:
10

8.70 -312.99 9 4

5

Motif group J3_41097.1

Basepair signature:
9

4.35 -322.15 8 4

phi29 pRNA

6

Motif group J3_31041.1

Basepair signature:
12

4.35 -344.92 10 4

7

Motif group J3_83726.1

Basepair signature:
17

0.00 -224.31 14 9

8

Motif group J3_45941.1

Basepair signature:
13

0.00 -243.67 11 8

9

Motif group J3_72012.1

Basepair signature:
16

0.00 -254.06 13 10

10

Motif group J3_83332.1

Basepair signature:
13

0.00 -291.71 10 6

11

Motif group J3_19286.1

Basepair signature:
15

0.00 -298.51 10 7

12

Motif group J3_89095.1

Basepair signature:
13

0.00 -304.48 11 7

13

Motif group J3_75408.1

Basepair signature:
20

0.00 -308.27 14 13

14

Motif group J3_20650.1

Basepair signature:
13

0.00 -313.90 9 5

15

Motif group J3_20992.1

Basepair signature:
18

0.00 -318.52 15 13

16

Motif group J3_97609.1

Basepair signature:
15

0.00 -325.28 12 7

17

Motif group J3_44792.1

Basepair signature:
19

0.00 -328.59 16 13

18

Motif group J3_12393.2

Basepair signature:
13

0.00 -328.73 9 6

19

Motif group J3_31965.2

Basepair signature:
13

0.00 -330.29 8 5

20

Motif group J3_98484.1

Basepair signature:
16

0.00 -330.58 11 8

21

Motif group J3_88257.1

Basepair signature:
14

0.00 -330.92 12 9

22

Motif group J3_83592.1

Basepair signature:
19

0.00 -331.62 14 13

23

Motif group J3_36387.1

Basepair signature:
16

0.00 -331.75 10 8

24

Motif group J3_35667.2

Basepair signature:
12

0.00 -334.75 9 6

25

Motif group J3_21426.1

Basepair signature:
19

0.00 -335.94 16 13

26

Motif group J3_76043.3

Basepair signature:
11

0.00 -336.39 8 4

27

Motif group J3_55773.1

Basepair signature:
15

0.00 -336.76 10 6

28

Motif group J3_53439.1

Basepair signature:
16

0.00 -337.11 12 8

29

Motif group J3_23373.1

Basepair signature:
17

0.00 -340.46 11 8

30

Motif group J3_79369.1

Basepair signature:
10

0.00 -343.60 8 4

31

Motif group J3_45482.1

Basepair signature:
16

0.00 -345.53 12 9

32

Motif group J3_89737.1

Basepair signature:
14

0.00 -347.65 12 9

5S rRNA junction

33

Motif group J3_32030.1

Basepair signature:
15

0.00 -350.22 11 8

34

Motif group J3_39320.1

Basepair signature:
21

0.00 -355.85 18 15

35

Motif group J3_96372.2

Basepair signature:
16

0.00 -357.03 12 9

36

Motif group J3_97642.1

Basepair signature:
13

0.00 -359.56 7 5

37

Motif group J3_94652.1

Basepair signature:
10

0.00 -360.75 9 4

38

Motif group J3_80708.1

Basepair signature:
12

0.00 -360.78 7 3

39

Motif group J3_01596.1

Basepair signature:
23

0.00 -361.19 18 15

40

Motif group J3_99563.1

Basepair signature:
17

0.00 -365.71 13 10

41

Motif group J3_46173.1

Basepair signature:
16

0.00 -366.40 17 13

42

Motif group J3_19545.2

Basepair signature:
12

0.00 -366.66 7 5

43

Motif group J3_20574.1

Basepair signature:
14

0.00 -366.74 8 6

44

Motif group J3_01052.1

Basepair signature:
13

0.00 -369.92 12 6

45

Motif group J3_84052.1

Basepair signature:
17

0.00 -370.22 13 9

46

Motif group J3_68164.1

Basepair signature:
15

0.00 -371.19 10 7

47

Motif group J3_06335.1

Basepair signature:
14

0.00 -371.49 10 7

48

Motif group J3_71677.1

Basepair signature:
13

0.00 -371.51 10 5

49

Motif group J3_44961.1

Basepair signature:
16

0.00 -372.62 12 9

50

Motif group J3_58957.1

Basepair signature:
17

0.00 -373.05 13 8

51

Motif group J3_41596.1

Basepair signature:
17

0.00 -373.52 13 10

52

Motif group J3_89368.5

Basepair signature:
13

0.00 -373.75 10 5

53

Motif group J3_17385.4

Basepair signature:
12

0.00 -373.99 8 5

54

Motif group J3_21998.1

Basepair signature:
14

0.00 -374.47 8 7

55

Motif group J3_47324.1

Basepair signature:
10

0.00 -375.63 9 5

56

Motif group J3_82572.1

Basepair signature:
11

0.00 -377.18 9 7

57

Motif group J3_87797.1

Basepair signature:
15

0.00 -377.53 12 10

58

Motif group J3_36499.1

Basepair signature:
13

0.00 -380.18 9 5

59

Motif group J3_85054.4

Basepair signature:
14

0.00 -381.42 9 7

60

Motif group J3_92705.1

Basepair signature:
12

0.00 -382.32 9 5

61

Motif group J3_32852.6

Basepair signature:
12

0.00 -382.69 6 4

62

Motif group J3_98798.1

Basepair signature:
13

0.00 -383.79 9 6

63

Motif group J3_34864.2

Basepair signature:
15

0.00 -383.93 12 7

64

Motif group J3_62630.1

Basepair signature:
12

0.00 -385.78 10 7

65

Motif group J3_00210.1

Basepair signature:
16

0.00 -388.22 13 10

66

Motif group J3_61124.2

Basepair signature:
10

0.00 -389.06 7 3

67

Motif group J3_15893.1

Basepair signature:
14

0.00 -391.43 8 6

C-di-AMP riboswitch

68

Motif group J3_32857.1

Basepair signature:
15

0.00 -392.83 11 8

69

Motif group J3_58090.1

Basepair signature:
13

0.00 -393.06 10 6

70

Motif group J3_93637.1

Basepair signature:
15

0.00 -393.16 10 7

71

Motif group J3_69441.1

Basepair signature:
14

0.00 -394.70 12 9

72

Motif group J3_76375.1

Basepair signature:
17

0.00 -396.34 13 10

73

Motif group J3_44163.2

Basepair signature:
18

0.00 -396.83 12 9

74

Motif group J3_61367.1

Basepair signature:
23

0.00 -396.93 17 16

75

Motif group J3_76911.2

Basepair signature:
11

0.00 -397.60 9 6

76

Motif group J3_37089.1

Basepair signature:
12

0.00 -398.63 10 6

77

Motif group J3_24127.1

Basepair signature:
13

0.00 -399.38 7 5

78

Motif group J3_71753.1

Basepair signature:
17

0.00 -399.40 14 10

79

Motif group J3_25217.1

Basepair signature:
9

0.00 -401.92 8 4

80

Motif group J3_47707.1

Basepair signature:
20

0.00 -407.12 14 10

81

Motif group J3_65990.1

Basepair signature:
14

0.00 -407.43 10 8

82

Motif group J3_44724.7

Basepair signature:
12

0.00 -411.78 7 4

83

Motif group J3_07703.1

Basepair signature:
16

0.00 -412.50 11 7

84

Motif group J3_37047.6

Basepair signature:
15

0.00 -416.44 12 10

85

Motif group J3_88233.1

Basepair signature:
15

0.00 -417.40 11 9

86

Motif group J3_46299.2

Basepair signature:
19

0.00 -417.41 13 10

87

Motif group J3_04315.1

Basepair signature:
20

0.00 -418.51 13 12

88

Motif group J3_83516.4

Basepair signature:
22

0.00 -419.79 20 17

89

Motif group J3_25303.4

Basepair signature:
19

0.00 -420.35 11 10

90

Motif group J3_45099.1

Basepair signature:
19

0.00 -420.77 13 11

91

Motif group J3_38881.1

Basepair signature:
19

0.00 -422.50 12 10

92

Motif group J3_72575.1

Basepair signature:
13

0.00 -426.37 9 6

93

Motif group J3_41486.2

Basepair signature:
8

0.00 -428.07 7 3

94

Motif group J3_98379.3

Basepair signature:
16

0.00 -428.47 11 8

95

Motif group J3_89044.1

Basepair signature:
15

0.00 -429.71 10 6

96

Motif group J3_10118.1

Basepair signature:
7

0.00 -430.33 9 4

97

Motif group J3_58525.1

Basepair signature:
20

0.00 -431.03 14 12

98

Motif group J3_76475.2

Basepair signature:
16

0.00 -431.88 12 10

99

Motif group J3_22198.1

Basepair signature:
12

0.00 -437.33 8 4

100

Motif group J3_08394.3

Basepair signature:
20

0.00 -445.87 14 11

101

Motif group J3_64069.1

Basepair signature:
13

0.00 -446.20 10 8

102

Motif group J3_94999.1

Basepair signature:
12

0.00 -446.85 8 5

103

Motif group J3_52655.4

Basepair signature:
11

0.00 -448.30 7 5

104

Motif group J3_00458.1

Basepair signature:
20

0.00 -449.23 16 12

105

Motif group J3_22899.1

Basepair signature:
20

0.00 -453.47 14 12

106

Motif group J3_01425.1

Basepair signature:
9

0.00 -459.37 8 4

107

Motif group J3_38098.1

Basepair signature:
25

0.00 -465.05 20 19

108

Motif group J3_56052.5

Basepair signature:
8

0.00 -467.28 6 3

109

Motif group J3_04521.1

Basepair signature:
10

0.00 -468.93 9 6

110

Motif group J3_68440.1

Basepair signature:
19

0.00 -472.75 11 9

111

Motif group J3_77951.1

Basepair signature:
20

0.00 -474.59 15 13

112

Motif group J3_51910.1

Basepair signature:
12

0.00 -477.79 11 6

113

Motif group J3_28315.1

Basepair signature:
12

0.00 -479.99 8 5

114

Motif group J3_93261.1

Basepair signature:
25

0.00 -480.88 21 20

115

Motif group J3_46317.4

Basepair signature:
19

0.00 -483.64 12 11

116

Motif group J3_41339.1

Basepair signature:
20

0.00 -484.63 15 13

117

Motif group J3_59706.1

Basepair signature:
21

0.00 -485.75 15 13

118

Motif group J3_69466.1

Basepair signature:
27

0.00 -486.06 22 20

119

Motif group J3_97280.1

Basepair signature:
19

0.00 -489.40 14 11

120

Motif group J3_65403.1

Basepair signature:
21

0.00 -489.58 16 13

121

Motif group J3_11934.4

Basepair signature:
13

0.00 -505.27 11 8

122

Motif group J3_38151.1

Basepair signature:
10

0.00 -505.90 7 4

123

Motif group J3_33494.1

Basepair signature:
12

0.00 -506.39 9 4

124

Motif group J3_97971.2

Basepair signature:
14

0.00 -512.20 10 7

125

Motif group J3_64189.2

Basepair signature:
11

0.00 -519.73 7 5

126

Motif group J3_67856.4

Basepair signature:
12

0.00 -528.63 10 7

127

Motif group J3_82365.4

Basepair signature:
9

0.00 -535.15 8 4

128

Motif group J3_63687.1

Basepair signature:
17

0.00 -545.13 22 18

129

Motif group J3_30040.2

Basepair signature:
24

0.00 -547.91 21 18

130

Motif group J3_90186.1

Basepair signature:
20

0.00 -557.74 18 15

131

Motif group J3_17791.2

Basepair signature:
19

0.00 -559.20 16 14

132

Motif group J3_19664.1

Basepair signature:
22

0.00 -569.53 18 16

133

Motif group J3_51249.1

Basepair signature:
13

0.00 -573.70 9 5

134

Motif group J3_36821.1

Basepair signature:
11

0.00 -574.02 7 4

135

Motif group J3_59914.1

Basepair signature:
9

0.00 -579.41 8 4

136

Motif group J3_32601.5

Basepair signature:
12

0.00 -588.55 10 7

137

Motif group J3_74474.1

Basepair signature:
23

0.00 -629.18 18 15

138

Motif group J3_58429.1

Basepair signature:
27

0.00 -634.34 25 24

139

Motif group J3_07845.1

Basepair signature:
7

0.00 -636.29 7 3

140

Motif group J3_28621.5

Basepair signature:
13

0.00 -638.43 10 7

141

Motif group J3_46124.1

Basepair signature:
26

0.00 -638.78 20 19

142

Motif group J3_09667.1

Basepair signature:
11

0.00 -649.00 9 5

143

Motif group J3_12003.2

Basepair signature:
9

0.00 -652.22 7 4

144

Motif group J3_28460.1

Basepair signature:
28

0.00 -660.58 27 27

145

Motif group J3_30478.1

Basepair signature:
8

0.00 -666.08 8 3

146

Motif group J3_30104.1

Basepair signature:
8

0.00 -670.09 7 3

147

Motif group J3_99595.1

Basepair signature:
9

0.00 -676.77 8 4

148

Motif group J3_33327.1

Basepair signature:
26

0.00 -684.61 26 24

149

Motif group J3_10708.1

Basepair signature:
22

0.00 -688.80 21 18

150

Motif group J3_65214.1

Basepair signature:
28

0.00 -701.27 21 19

151

Motif group J3_93059.1

Basepair signature:
13

0.00 -712.86 12 8

152

Motif group J3_11375.2

Basepair signature:
10

0.00 -721.74 9 6

153

Motif group J3_75076.1

Basepair signature:
34

0.00 -727.54 28 26

154

Motif group J3_08040.1

Basepair signature:
29

0.00 -757.62 22 21

155

Motif group J3_28639.1

Basepair signature:
18

0.00 -772.21 17 15

156

Motif group J3_05216.1

Basepair signature:
12

0.00 -806.35 8 5

157

Motif group J3_70599.1

Basepair signature:
11

0.00 -834.52 9 7

158

Motif group J3_24879.1

Basepair signature:
28

0.00 -842.02 23 20

159

Motif group J3_08158.1

Basepair signature:
36

0.00 -843.33 32 31

160

Motif group J3_26675.1

Basepair signature:
9

0.00 -854.64 9 7

161

Motif group J3_13378.1

Basepair signature:
38

0.00 -869.82 33 32

162

Motif group J3_92134.2

Basepair signature:
26

0.00 -871.40 20 18

163

Motif group J3_75962.2

Basepair signature:
9

0.00 -910.10 7 5

164

Motif group J3_60031.2

Basepair signature:
12

0.00 -963.19 11 8

165

Motif group J3_03190.1

Basepair signature:
17

0.00 -9999.00 22 20

Coloring options: