RNA 3D Hub

JAR3D Query RF03087-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03087 maps to these 30 chains: 9ISV|1|A, 9J3R|1|A, 9J3R|1|B, 9J3R|1|C, 9J3R|1|D, 9J3T|1|A, 9J3T|1|B, 9J3T|1|C, 9J3T|1|D, 9J3T|1|E, 9J3T|1|F, 9J3T|1|G, 9J3T|1|H, 9MM6|1|A, 9MM6|1|E, 9MM6|1|I, 9MM6|1|M, 9MM6|1|Q, 9MM6|1|U, 9MM6|1|Y, 9MM6|1|c, 9MME|1|U, 9MME|1|Y, 9MME|1|c, 9MME|1|g, 9MME|1|k, 9MME|1|o, 9MME|1|s, 9MME|1|w, 9MMG|1|c See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 33 3-way junction loop

Column numbers: 1026-1027, 1134-1139, 1250-1251 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AG*CU--AG*CU   22

    
    GU*----UC*GC   21

    
    GG*C---UG*CC   19

    
    UC*G----A*GA   11

    
    AG*C----G*CU   10

    
    GG*C----A*CC    9

    
    UG*GG--UU*CA    6

    
    AG*C---UG*CU    6

    
    AG*U---UG*CU    6

    
    AG*----AG*CU    6

    
    GG*U----G*CC    5

    
    AG*U---GG*CU    4

    
    CU*U---CG*GG    4

    
    GG*U---GG*CC    4

    
    GC*----CC*GC    4

    
    GC*----UC*GC    4

    
    AG*G---UG*CU    3

    
    GA*C---CA*UC    3

    
    UU*C---CC*AA    3

    
    AA*----GC*UU    3

    
    GG*C----G*CC    3

    
    AC*G---AU*GU    2

    
    AG*C---UA*CU    2

    
    GG*C---AG*CC    2

    
    GG*C---GG*CC    2

    
    UA*A---UU*UA    2

    
    AG*----UU*CU    2

    
    AG*U----A*CU    2

    
    CA*U----A*UG    2

    
    CG*U----U*CG    2

    
    GG*----AC*CC    2

    
    UG*----AG*CA    2

    
    UG*----CG*CA    2

    
    UU*C----C*AA    2

    
    AG*UGUCUA*CU    1

    
    UU*CCUUCA*AA    1

    
    AG*CC--AG*CU    1

    
    GU*CU--AG*GC    1

    
    UG*UC--UU*CU    1

    
    AA*C---UA*UU    1

    
    AC*A---AC*GU    1

    
    AC*A---UA*GU    1

    
    AG*A---UA*CU    1

    
    AG*A---UG*CU    1

    
    AG*C---AA*CU    1

    
    AG*C---AG*CU    1

    
    AG*C---CC*CU    1

    
    AG*C---GG*CU    1

    
    AG*C---UC*CU    1

    
    AG*C---UU*CU    1

    
    AG*U---AG*CU    1

    
    AG*U---CU*CU    1

    
    AG*U---UA*CU    1

    
    CA*A---UA*UG    1

    
    CA*U---GG*UG    1

    
    GA*C---GG*UC    1

    
    GC*U---GA*GC    1

    
    GG*A---UA*CC    1

    
    GG*A---UG*CC    1

    
    GG*A---UG*CU    1

    
    GG*C---GG*CU    1

    
    GG*C---UG*CU    1

    
    GG*C---UU*CC    1

    
    GG*U---UA*CC    1

    
    GG*UU---A*CC    1

    
    GU*U---UG*GC    1

    
    UA*G---UU*UA    1

    
    UC*A---GA*GA    1

    
    UC*A---UU*GA    1

    
    UG*A---CU*CA    1

    
    UG*C---AG*CA    1

    
    UG*C---UU*CA    1

    
    UU*A---UU*AA    1

    
    UU*A---UU*GA    1

    
    UU*C---GG*AA    1

    
    AA*----AC*UU    1

    
    AA*C----G*CU    1

    
    AG*A----A*CU    1

    
    AG*C----C*CU    1

    
    AG*U----G*CU    1

    
    AG*U----U*CU    1

    
    AU*C----A*AU    1

    
    CA*G----A*UG    1

    
    CC*C----C*AG    1

    
    CU*----UU*AG    1

    
    GA*U----G*UC    1

    
    GC*----AC*GC    1

    
    GC*----UU*GC    1

    
    GU*----CC*AC    1

    
    GU*----UA*GC    1

    
    GU*A----U*AC    1

    
    GU*C----G*AC    1

    
    UA*C----G*UA    1

    
    UA*U----U*UA    1

    
    UG*----AA*CA    1

    
    UG*----UA*CA    1

    
    UG*U----U*CA    1

    
    UG*U----U*UA    1

    
    Omitted sequenced and counts

    
    UG*-----G*CA   18

    
    AU*-----U*AU    7

    
    UG*-----A*CA    5

    
    GG*-----G*CC    3

    
    AC*-----G*GU    2

    
    AU*-----U*GU    1

    
    GC*-----A*GC    1

    
    UA*-----G*UA    1

    
    UC*-----G*GA    1

    
    UG*-----G*CG    1

    
    AA*------*UU    1

    
    AC*------*GU    1

    
    CG*------*CG    1

    
    GC*------*GC    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_07845.1

Basepair signature:
7

80.08 13.01 4 1

2

Motif group J3_41486.2

Basepair signature:
8

18.29 -22.83 4 2

3

Motif group J3_30478.1

Basepair signature:
8

12.20 -59.52 5 2

4

Motif group J3_30104.1

Basepair signature:
8

10.16 -65.22 4 2

5

Motif group J3_56052.5

Basepair signature:
8

8.94 -72.21 5 2

6

Motif group J3_75962.2

Basepair signature:
9

8.94 -110.39 6 2

7

Motif group J3_11375.2

Basepair signature:
10

0.41 -131.71 7 3

8

Motif group J3_79369.1

Basepair signature:
10

0.00 -61.87 7 4

9

Motif group J3_41097.1

Basepair signature:
9

0.00 -78.90 6 4

phi29 pRNA

10

Motif group J3_25217.1

Basepair signature:
9

0.00 -78.92 6 3

11

Motif group J3_59914.1

Basepair signature:
9

0.00 -100.78 6 3

12

Motif group J3_47376.1

Basepair signature:
10

0.00 -101.07 8 4

13

Motif group J3_99595.1

Basepair signature:
9

0.00 -111.00 6 3

14

Motif group J3_94652.1

Basepair signature:
10

0.00 -113.61 7 4

15

Motif group J3_80578.1

Basepair signature:
10

0.00 -114.75 8 3

16

Motif group J3_76043.3

Basepair signature:
11

0.00 -126.17 8 5

17

Motif group J3_01425.1

Basepair signature:
9

0.00 -128.15 7 3

18

Motif group J3_14360.1

Basepair signature:
10

0.00 -130.75 6 4

19

Motif group J3_81015.1

Basepair signature:
11

0.00 -131.42 8 4

20

Motif group J3_38151.1

Basepair signature:
10

0.00 -132.72 8 4

21

Motif group J3_12393.2

Basepair signature:
13

0.00 -132.84 10 7

22

Motif group J3_45941.1

Basepair signature:
13

0.00 -136.66 10 7

23

Motif group J3_92705.1

Basepair signature:
12

0.00 -145.11 10 6

24

Motif group J3_37089.1

Basepair signature:
12

0.00 -146.23 9 6

25

Motif group J3_01052.1

Basepair signature:
13

0.00 -150.86 10 6

26

Motif group J3_82572.1

Basepair signature:
11

0.00 -152.01 8 6

27

Motif group J3_52655.4

Basepair signature:
11

0.00 -155.56 8 5

28

Motif group J3_61124.2

Basepair signature:
10

0.00 -157.69 6 5

29

Motif group J3_12003.2

Basepair signature:
9

0.00 -158.82 7 3

30

Motif group J3_20650.1

Basepair signature:
13

0.00 -161.05 9 6

31

Motif group J3_62630.1

Basepair signature:
12

0.00 -162.67 11 8

32

Motif group J3_44724.7

Basepair signature:
12

0.00 -162.79 7 5

33

Motif group J3_31965.2

Basepair signature:
13

0.00 -166.53 9 6

34

Motif group J3_47324.1

Basepair signature:
10

0.00 -167.43 9 6

35

Motif group J3_31041.1

Basepair signature:
12

0.00 -167.82 10 6

36

Motif group J3_67856.4

Basepair signature:
12

0.00 -169.07 8 5

37

Motif group J3_83332.1

Basepair signature:
13

0.00 -169.35 11 8

38

Motif group J3_80708.1

Basepair signature:
12

0.00 -171.83 9 5

39

Motif group J3_97642.1

Basepair signature:
13

0.00 -174.59 10 7

40

Motif group J3_35667.2

Basepair signature:
12

0.00 -175.37 10 7

41

Motif group J3_32030.1

Basepair signature:
15

0.00 -177.05 11 8

42

Motif group J3_04521.1

Basepair signature:
10

0.00 -178.53 11 6

43

Motif group J3_82365.4

Basepair signature:
9

0.00 -183.91 7 4

44

Motif group J3_89095.1

Basepair signature:
13

0.00 -184.91 11 9

45

Motif group J3_76911.2

Basepair signature:
11

0.00 -187.02 9 6

46

Motif group J3_19286.1

Basepair signature:
15

0.00 -190.64 11 10

47

Motif group J3_98798.1

Basepair signature:
13

0.00 -192.22 10 7

48

Motif group J3_34864.2

Basepair signature:
15

0.00 -194.04 13 9

49

Motif group J3_69441.1

Basepair signature:
14

0.00 -195.69 12 10

50

Motif group J3_36499.1

Basepair signature:
13

0.00 -197.20 8 7

51

Motif group J3_98484.1

Basepair signature:
16

0.00 -199.79 11 9

52

Motif group J3_89737.1

Basepair signature:
14

0.00 -201.50 11 10

5S rRNA junction

53

Motif group J3_33494.1

Basepair signature:
12

0.00 -204.33 9 6

54

Motif group J3_24127.1

Basepair signature:
13

0.00 -204.70 10 6

55

Motif group J3_17385.4

Basepair signature:
12

0.00 -207.06 8 7

56

Motif group J3_00210.1

Basepair signature:
16

0.00 -207.35 14 9

57

Motif group J3_55773.1

Basepair signature:
15

0.00 -207.46 11 8

58

Motif group J3_97609.1

Basepair signature:
15

0.00 -210.11 12 10

59

Motif group J3_32852.6

Basepair signature:
12

0.00 -210.47 8 6

60

Motif group J3_19545.2

Basepair signature:
12

0.00 -212.20 9 7

61

Motif group J3_36387.1

Basepair signature:
16

0.00 -212.23 12 9

62

Motif group J3_88257.1

Basepair signature:
14

0.00 -212.96 13 10

63

Motif group J3_94999.1

Basepair signature:
12

0.00 -213.20 9 7

64

Motif group J3_71677.1

Basepair signature:
13

0.00 -213.90 11 8

65

Motif group J3_15893.1

Basepair signature:
14

0.00 -214.81 9 7

C-di-AMP riboswitch

66

Motif group J3_22198.1

Basepair signature:
12

0.00 -215.66 10 6

67

Motif group J3_21998.1

Basepair signature:
14

0.00 -219.17 11 9

68

Motif group J3_89368.5

Basepair signature:
13

0.00 -219.99 10 8

69

Motif group J3_51910.1

Basepair signature:
12

0.00 -220.83 9 7

70

Motif group J3_06335.1

Basepair signature:
14

0.00 -221.51 11 8

71

Motif group J3_11934.4

Basepair signature:
13

0.00 -224.71 10 7

72

Motif group J3_37047.6

Basepair signature:
15

0.00 -225.84 12 10

73

Motif group J3_53439.1

Basepair signature:
16

0.00 -226.28 12 10

74

Motif group J3_36821.1

Basepair signature:
11

0.00 -228.02 10 6

75

Motif group J3_72012.1

Basepair signature:
16

0.00 -228.53 13 10

76

Motif group J3_93637.1

Basepair signature:
15

0.00 -229.00 10 8

77

Motif group J3_45482.1

Basepair signature:
16

0.00 -229.92 13 10

78

Motif group J3_58957.1

Basepair signature:
17

0.00 -233.73 14 11

79

Motif group J3_23373.1

Basepair signature:
17

0.00 -234.54 11 10

80

Motif group J3_70599.1

Basepair signature:
11

0.00 -237.08 8 4

81

Motif group J3_68164.1

Basepair signature:
15

0.00 -237.76 12 10

82

Motif group J3_72575.1

Basepair signature:
13

0.00 -237.90 9 7

83

Motif group J3_85054.4

Basepair signature:
14

0.00 -243.62 10 9

84

Motif group J3_58090.1

Basepair signature:
13

0.00 -245.36 11 8

85

Motif group J3_20574.1

Basepair signature:
14

0.00 -248.50 9 8

86

Motif group J3_44961.1

Basepair signature:
16

0.00 -251.68 13 11

87

Motif group J3_32857.1

Basepair signature:
15

0.00 -252.15 12 9

88

Motif group J3_99563.1

Basepair signature:
17

0.00 -254.82 13 12

89

Motif group J3_76375.1

Basepair signature:
17

0.00 -258.41 13 11

90

Motif group J3_65990.1

Basepair signature:
14

0.00 -261.41 12 10

91

Motif group J3_87797.1

Basepair signature:
15

0.00 -261.86 13 11

92

Motif group J3_76475.2

Basepair signature:
16

0.00 -264.26 13 11

93

Motif group J3_88233.1

Basepair signature:
15

0.00 -265.02 14 11

94

Motif group J3_41596.1

Basepair signature:
17

0.00 -265.34 16 12

95

Motif group J3_84052.1

Basepair signature:
17

0.00 -266.67 15 11

96

Motif group J3_89044.1

Basepair signature:
15

0.00 -266.92 11 8

97

Motif group J3_83726.1

Basepair signature:
17

0.00 -269.17 14 11

98

Motif group J3_96372.2

Basepair signature:
16

0.00 -269.95 14 11

99

Motif group J3_07703.1

Basepair signature:
16

0.00 -271.43 12 10

100

Motif group J3_32601.5

Basepair signature:
12

0.00 -275.28 10 8

101

Motif group J3_51249.1

Basepair signature:
13

0.00 -276.68 10 8

102

Motif group J3_93059.1

Basepair signature:
13

0.00 -278.94 8 6

103

Motif group J3_98379.3

Basepair signature:
16

0.00 -279.79 10 9

104

Motif group J3_21426.1

Basepair signature:
19

0.00 -279.82 15 12

105

Motif group J3_28315.1

Basepair signature:
12

0.00 -281.33 11 7

106

Motif group J3_71753.1

Basepair signature:
17

0.00 -286.52 15 13

107

Motif group J3_28621.5

Basepair signature:
13

0.00 -290.19 9 7

108

Motif group J3_26675.1

Basepair signature:
9

0.00 -298.09 9 4

109

Motif group J3_46317.4

Basepair signature:
19

0.00 -298.79 15 12

110

Motif group J3_68440.1

Basepair signature:
19

0.00 -299.06 15 13

111

Motif group J3_44163.2

Basepair signature:
18

0.00 -299.06 13 12

112

Motif group J3_38881.1

Basepair signature:
19

0.00 -300.74 14 12

113

Motif group J3_64069.1

Basepair signature:
13

0.00 -301.10 13 10

114

Motif group J3_25303.4

Basepair signature:
19

0.00 -302.73 14 12

115

Motif group J3_47707.1

Basepair signature:
20

0.00 -311.87 16 13

116

Motif group J3_04315.1

Basepair signature:
20

0.00 -313.26 15 13

117

Motif group J3_46299.2

Basepair signature:
19

0.00 -313.44 14 13

118

Motif group J3_83592.1

Basepair signature:
19

0.00 -318.42 15 13

119

Motif group J3_97280.1

Basepair signature:
19

0.00 -318.99 14 13

120

Motif group J3_45099.1

Basepair signature:
19

0.00 -319.38 14 13

121

Motif group J3_64189.2

Basepair signature:
11

0.00 -331.47 9 8

122

Motif group J3_08394.3

Basepair signature:
20

0.00 -331.75 15 13

123

Motif group J3_60031.2

Basepair signature:
12

0.00 -334.61 8 5

124

Motif group J3_44792.1

Basepair signature:
19

0.00 -335.90 16 14

125

Motif group J3_58525.1

Basepair signature:
20

0.00 -337.12 16 14

126

Motif group J3_97971.2

Basepair signature:
14

0.00 -338.57 11 8

127

Motif group J3_75408.1

Basepair signature:
20

0.00 -339.02 15 14

128

Motif group J3_17791.2

Basepair signature:
19

0.00 -340.00 15 14

129

Motif group J3_20992.1

Basepair signature:
18

0.00 -343.84 16 14

130

Motif group J3_09667.1

Basepair signature:
11

0.00 -344.82 11 8

131

Motif group J3_22899.1

Basepair signature:
20

0.00 -348.04 17 14

132

Motif group J3_77951.1

Basepair signature:
20

0.00 -353.21 17 14

133

Motif group J3_00458.1

Basepair signature:
20

0.00 -355.81 18 15

134

Motif group J3_05216.1

Basepair signature:
12

0.00 -376.92 11 7

135

Motif group J3_41339.1

Basepair signature:
20

0.00 -379.08 17 16

136

Motif group J3_90186.1

Basepair signature:
20

0.00 -379.30 18 16

137

Motif group J3_59706.1

Basepair signature:
21

0.00 -383.42 16 15

138

Motif group J3_65403.1

Basepair signature:
21

0.00 -396.84 19 17

139

Motif group J3_39320.1

Basepair signature:
21

0.00 -410.92 18 17

140

Motif group J3_01596.1

Basepair signature:
23

0.00 -424.88 19 17

141

Motif group J3_10708.1

Basepair signature:
22

0.00 -444.01 20 17

142

Motif group J3_83516.4

Basepair signature:
22

0.00 -445.78 20 18

143

Motif group J3_74474.1

Basepair signature:
23

0.00 -449.10 19 18

144

Motif group J3_61367.1

Basepair signature:
23

0.00 -449.91 19 18

145

Motif group J3_19664.1

Basepair signature:
22

0.00 -489.01 21 19

146

Motif group J3_38098.1

Basepair signature:
25

0.00 -517.57 23 21

147

Motif group J3_93261.1

Basepair signature:
25

0.00 -547.00 23 21

148

Motif group J3_46124.1

Basepair signature:
26

0.00 -547.17 22 21

149

Motif group J3_69466.1

Basepair signature:
27

0.00 -553.84 23 21

150

Motif group J3_30040.2

Basepair signature:
24

0.00 -554.41 22 19

151

Motif group J3_65214.1

Basepair signature:
28

0.00 -604.00 23 22

152

Motif group J3_08040.1

Basepair signature:
29

0.00 -635.96 24 23

153

Motif group J3_92134.2

Basepair signature:
26

0.00 -654.57 24 23

154

Motif group J3_58429.1

Basepair signature:
27

0.00 -673.89 27 25

155

Motif group J3_24879.1

Basepair signature:
28

0.00 -686.33 25 23

156

Motif group J3_33327.1

Basepair signature:
26

0.00 -692.84 27 25

157

Motif group J3_28460.1

Basepair signature:
28

0.00 -752.04 30 29

158

Motif group J3_75076.1

Basepair signature:
34

0.00 -800.69 30 29

159

Motif group J3_08158.1

Basepair signature:
36

0.00 -890.11 33 32

160

Motif group J3_13378.1

Basepair signature:
38

0.00 -964.70 36 35

161

Motif group J3_03190.1

Basepair signature:
17

0.00 -9999.00 24 23

162

Motif group J3_10118.1

Basepair signature:
7

0.00 -9999.00 9 7

163

Motif group J3_28639.1

Basepair signature:
18

0.00 -9999.00 19 17

164

Motif group J3_46173.1

Basepair signature:
16

0.00 -9999.00 17 15

165

Motif group J3_63687.1

Basepair signature:
17

0.00 -9999.00 19 17

Coloring options: