RNA 3D Hub

JAR3D Query RF00011-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF00011 maps to these 104 chains: 1NBS|1|A, 1NBS|1|B, 2A64|1|A, 3DHS|1|A, 9OV3|1|A, 9OV6|1|A, 9OV7|1|A, 9OV8|1|A, 9OVB|1|A, 9OVC|1|A, 9OWJ|1|A, 9OWK|1|A, 9OWL|1|A, 9OWM|1|A, 9OWN|1|A, 9OWO|1|A, 9OWP|1|A, 9OWQ|1|A, 9OWS|1|A, 9OWT|1|A, 9OWU|1|A, 9OWV|1|A, 9OWW|1|A, 9OWX|1|A, 9OWY|1|A, 9OY2|1|A, 9OY3|1|A, 9OY4|1|A, 9ZDV|1|A, 9ZF2|1|A, 9ZF3|1|A, 9ZF5|1|A, 9ZF9|1|A, 9ZFC|1|A, 9ZFD|1|A, 9ZGM|1|A, 9ZGN|1|A, 9ZGO|1|A, 9ZGP|1|A, 9ZGQ|1|A, 9ZGR|1|A, 9ZGS|1|A, 9ZGT|1|A, 9ZGU|1|A, 9ZGV|1|A, 9ZGW|1|A, 9ZGX|1|A, 9ZGY|1|A, 9ZGZ|1|A, 9ZH0|1|A, 9ZH1|1|A, 9ZH2|1|A, 9ZH5|1|A, 9ZH7|1|A, 9ZH9|1|A, 9ZHA|1|A, 9ZHB|1|A, 9ZHC|1|A, 9ZHD|1|A, 9ZHE|1|A, 9ZHF|1|A, 9ZHG|1|A, 9ZHI|1|A, 9ZHJ|1|A, 9ZHK|1|A, 9ZHL|1|A, 9ZHO|1|A, 9ZHP|1|A, 9ZHR|1|A, 9ZHS|1|A, 9ZHT|1|A, 9ZHU|1|A, 9ZHV|1|A, 9ZHW|1|A, 9ZHX|1|A, 9ZHZ|1|A, 9ZI0|1|A, 9ZI2|1|A, 9ZI3|1|A, 9ZI4|1|A, 9ZI5|1|A, 9ZI6|1|A, 9ZI7|1|A, 9ZI8|1|A, 9ZI9|1|A, 9ZIB|1|A, 9ZIC|1|A, 9ZID|1|A, 9ZIE|1|A, 9ZIF|1|A, 9ZIG|1|A, 9ZIH|1|A, 9ZII|1|A, 9ZIJ|1|A, 9ZIK|1|A, 9ZIL|1|A, 9ZIM|1|A, 9ZIN|1|A, 9ZIU|1|A, 9ZIV|1|A, 9ZIW|1|A, 9ZIX|1|A, 9ZIY|1|A, 9ZIZ|1|A See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Rfam family RF00011 is part of clan CL00002, which includes Rfam families RF00009, RF00373, RF02357, RF01577, RF00011, RF00010, RF00030 .
There are 130 chains in PDB that we map to these Rfam families: 1NBS|1|A, 1NBS|1|B, 1U9S|1|A, 2A2E|1|A, 2A64|1|A, 3DHS|1|A, 3OK7|1|B, 3OKB|1|B, 3Q1Q|1|B, 3Q1R|1|B, 6AGB|1|A, 6AH3|1|A, 6AHR|1|A, 6AHU|1|A, 6K0A|1|X, 6K0A|1|Y, 6K0B|1|X, 6K0B|1|Y, 6W6V|1|A, 7C79|1|A, 7C7A|1|A, 7DA7|1|C, 7DAS|1|C, 7UO0|1|B, 7UO1|1|B, 7UO2|1|B, 7UO5|1|B, 9OV3|1|A, 9OV6|1|A, 9OV7|1|A, 9OV8|1|A, 9OVB|1|A, 9OVC|1|A, 9OWJ|1|A, 9OWK|1|A, 9OWL|1|A, 9OWM|1|A, 9OWN|1|A, 9OWO|1|A, 9OWP|1|A, 9OWQ|1|A, 9OWS|1|A, 9OWT|1|A, 9OWU|1|A, 9OWV|1|A, 9OWW|1|A, 9OWX|1|A, 9OWY|1|A, 9OY2|1|A, 9OY3|1|A, 9OY4|1|A, 9UH7|1|A, 9UH9|1|A, 9UHA|1|A, 9ZDV|1|A, 9ZF2|1|A, 9ZF3|1|A, 9ZF5|1|A, 9ZF9|1|A, 9ZFC|1|A, 9ZFD|1|A, 9ZGM|1|A, 9ZGN|1|A, 9ZGO|1|A, 9ZGP|1|A, 9ZGQ|1|A, 9ZGR|1|A, 9ZGS|1|A, 9ZGT|1|A, 9ZGU|1|A, 9ZGV|1|A, 9ZGW|1|A, 9ZGX|1|A, 9ZGY|1|A, 9ZGZ|1|A, 9ZH0|1|A, 9ZH1|1|A, 9ZH2|1|A, 9ZH5|1|A, 9ZH7|1|A, 9ZH9|1|A, 9ZHA|1|A, 9ZHB|1|A, 9ZHC|1|A, 9ZHD|1|A, 9ZHE|1|A, 9ZHF|1|A, 9ZHG|1|A, 9ZHI|1|A, 9ZHJ|1|A, 9ZHK|1|A, 9ZHL|1|A, 9ZHO|1|A, 9ZHP|1|A, 9ZHR|1|A, 9ZHS|1|A, 9ZHT|1|A, 9ZHU|1|A, 9ZHV|1|A, 9ZHW|1|A, 9ZHX|1|A, 9ZHZ|1|A, 9ZI0|1|A, 9ZI2|1|A, 9ZI3|1|A, 9ZI4|1|A, 9ZI5|1|A, 9ZI6|1|A, 9ZI7|1|A, 9ZI8|1|A, 9ZI9|1|A, 9ZIB|1|A, 9ZIC|1|A, 9ZID|1|A, 9ZIE|1|A, 9ZIF|1|A, 9ZIG|1|A, 9ZIH|1|A, 9ZII|1|A, 9ZIJ|1|A, 9ZIK|1|A, 9ZIL|1|A, 9ZIM|1|A, 9ZIN|1|A, 9ZIU|1|A, 9ZIV|1|A, 9ZIW|1|A, 9ZIX|1|A, 9ZIY|1|A, 9ZIZ|1|A . See them at RNA 3D Hub by filtering on Rfam family, clan, or chain.

Loop 8 3-way junction loop

Column numbers: 198-199, 261-273, 354-364 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GC*GUGCCACAGUGAC*G-CGGUAAACC   67

    
    GC*GUGCCACAGUGAC*G-AGGUAAACC   17

    
    GC*GUGCCACAGAGAC*G-CGGUAAACC    6

    
    AC*GUGCCACAGAGAC*G-CGGUAAACU    5

    
    GC*GUGCCACAGAAAC*G--GGUAAACC    3

    
    GC*GUGCCACAGAGAC*GUUGGUAAACC    2

    
    GC*GUGCCAUAGAGAC*G-UGGUAAACC    2

    
    GC*GUGCCACAGAGAC*G--GGUAAACC    2

    
    GC*GUGCCACAGUGAC*G--GGUAAACC    2

    
    GC*GUGG-AUAGAGAC*G-A-CUAAACC    2

    
    AC*GUACCACAGAGAC*G-CGGUAAACU    1

    
    AC*GUGCAACAGAGAC*G-AUGUAAACU    1

    
    GC*GUGCCACAGAAAC*G-CGGUAAACC    1

    
    GC*GUGCCACAGUAAC*G-CGGUAAACC    1

    
    GC*GUGCCAUAGAAAC*G-AGGUAAACC    1

    
    GC*GUGCUAUAGCGAC*G-ACGUAAACC    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_01596.1

Basepair signature:
23

0.00 -168.49 16 12

2

Motif group J3_00458.1

Basepair signature:
20

0.00 -205.08 16 12

3

Motif group J3_20992.1

Basepair signature:
18

0.00 -208.61 11 11

4

Motif group J3_39320.1

Basepair signature:
21

0.00 -219.25 13 13

5

Motif group J3_46173.1

Basepair signature:
16

0.00 -222.13 15 13

6

Motif group J3_53439.1

Basepair signature:
16

0.00 -234.28 12 10

7

Motif group J3_58957.1

Basepair signature:
17

0.00 -234.65 14 11

8

Motif group J3_17791.2

Basepair signature:
19

0.00 -248.21 13 12

9

Motif group J3_44792.1

Basepair signature:
19

0.00 -254.00 14 14

10

Motif group J3_83726.1

Basepair signature:
17

0.00 -260.26 15 12

11

Motif group J3_72012.1

Basepair signature:
16

0.00 -275.62 15 12

12

Motif group J3_97280.1

Basepair signature:
19

0.00 -287.35 17 14

13

Motif group J3_00210.1

Basepair signature:
16

0.00 -289.48 16 12

14

Motif group J3_21426.1

Basepair signature:
19

0.00 -290.07 15 14

15

Motif group J3_46317.4

Basepair signature:
19

0.00 -294.78 13 11

16

Motif group J3_69466.1

Basepair signature:
27

0.00 -302.90 22 17

17

Motif group J3_71753.1

Basepair signature:
17

0.00 -316.87 16 15

18

Motif group J3_58525.1

Basepair signature:
20

0.00 -320.81 15 14

19

Motif group J3_34864.2

Basepair signature:
15

0.00 -323.17 14 12

20

Motif group J3_61367.1

Basepair signature:
23

0.00 -325.14 21 16

21

Motif group J3_41339.1

Basepair signature:
20

0.00 -325.92 15 14

22

Motif group J3_37047.6

Basepair signature:
15

0.00 -326.54 14 14

23

Motif group J3_88233.1

Basepair signature:
15

0.00 -331.92 16 13

24

Motif group J3_41596.1

Basepair signature:
17

0.00 -334.67 19 15

25

Motif group J3_68440.1

Basepair signature:
19

0.00 -338.39 21 17

26

Motif group J3_83332.1

Basepair signature:
13

0.00 -338.86 15 12

27

Motif group J3_28639.1

Basepair signature:
18

0.00 -339.91 17 15

28

Motif group J3_65214.1

Basepair signature:
28

0.00 -343.72 17 15

29

Motif group J3_19664.1

Basepair signature:
22

0.00 -350.36 20 17

30

Motif group J3_93261.1

Basepair signature:
25

0.00 -354.13 24 19

31

Motif group J3_36387.1

Basepair signature:
16

0.00 -355.05 15 12

32

Motif group J3_32030.1

Basepair signature:
15

0.00 -357.43 17 13

33

Motif group J3_47707.1

Basepair signature:
20

0.00 -358.62 20 17

34

Motif group J3_83516.4

Basepair signature:
22

0.00 -366.71 17 15

35

Motif group J3_98484.1

Basepair signature:
16

0.00 -368.17 19 16

36

Motif group J3_75408.1

Basepair signature:
20

0.00 -369.11 17 12

37

Motif group J3_38881.1

Basepair signature:
19

0.00 -371.20 13 12

38

Motif group J3_25303.4

Basepair signature:
19

0.00 -379.83 17 12

39

Motif group J3_30040.2

Basepair signature:
24

0.00 -381.32 14 12

40

Motif group J3_55773.1

Basepair signature:
15

0.00 -383.93 15 12

41

Motif group J3_98379.3

Basepair signature:
16

0.00 -387.64 16 14

42

Motif group J3_45099.1

Basepair signature:
19

0.00 -388.02 13 12

43

Motif group J3_12393.2

Basepair signature:
13

0.00 -389.90 17 13

44

Motif group J3_46299.2

Basepair signature:
19

0.00 -392.11 16 12

45

Motif group J3_63687.1

Basepair signature:
17

0.00 -397.11 18 17

46

Motif group J3_44163.2

Basepair signature:
18

0.00 -398.17 15 14

47

Motif group J3_04315.1

Basepair signature:
20

0.00 -399.70 19 16

48

Motif group J3_28460.1

Basepair signature:
28

0.00 -407.39 24 21

49

Motif group J3_84052.1

Basepair signature:
17

0.00 -408.81 21 15

50

Motif group J3_22899.1

Basepair signature:
20

0.00 -410.27 17 17

51

Motif group J3_38098.1

Basepair signature:
25

0.00 -414.47 18 16

52

Motif group J3_96372.2

Basepair signature:
16

0.00 -414.93 15 13

53

Motif group J3_89095.1

Basepair signature:
13

0.00 -415.72 14 13

54

Motif group J3_45482.1

Basepair signature:
16

0.00 -416.80 19 16

55

Motif group J3_58429.1

Basepair signature:
27

0.00 -417.13 22 20

56

Motif group J3_88257.1

Basepair signature:
14

0.00 -417.44 19 16

57

Motif group J3_59706.1

Basepair signature:
21

0.00 -417.86 17 15

58

Motif group J3_03190.1

Basepair signature:
17

0.00 -426.70 24 21

59

Motif group J3_65990.1

Basepair signature:
14

0.00 -429.27 17 13

60

Motif group J3_99563.1

Basepair signature:
17

0.00 -430.35 18 16

61

Motif group J3_19286.1

Basepair signature:
15

0.00 -435.19 20 16

62

Motif group J3_69441.1

Basepair signature:
14

0.00 -439.72 18 15

63

Motif group J3_76375.1

Basepair signature:
17

0.00 -444.14 19 16

64

Motif group J3_65403.1

Basepair signature:
21

0.00 -445.78 20 16

65

Motif group J3_07703.1

Basepair signature:
16

0.00 -450.01 16 12

66

Motif group J3_51249.1

Basepair signature:
13

0.00 -457.21 15 14

67

Motif group J3_35667.2

Basepair signature:
12

0.00 -459.28 16 14

68

Motif group J3_97609.1

Basepair signature:
15

0.00 -462.19 15 14

69

Motif group J3_23373.1

Basepair signature:
17

0.00 -463.92 17 17

70

Motif group J3_46124.1

Basepair signature:
26

0.00 -466.99 24 19

71

Motif group J3_06335.1

Basepair signature:
14

0.00 -474.78 17 14

72

Motif group J3_76475.2

Basepair signature:
16

0.00 -475.56 21 17

73

Motif group J3_31965.2

Basepair signature:
13

0.00 -480.06 15 13

74

Motif group J3_44961.1

Basepair signature:
16

0.00 -483.55 21 16

75

Motif group J3_08394.3

Basepair signature:
20

0.00 -483.94 19 18

76

Motif group J3_01052.1

Basepair signature:
13

0.00 -490.16 15 14

77

Motif group J3_83592.1

Basepair signature:
19

0.00 -491.49 20 17

78

Motif group J3_04521.1

Basepair signature:
10

0.00 -492.51 14 13

79

Motif group J3_62630.1

Basepair signature:
12

0.00 -495.15 19 16

80

Motif group J3_87797.1

Basepair signature:
15

0.00 -510.42 19 16

81

Motif group J3_32857.1

Basepair signature:
15

0.00 -511.79 15 15

82

Motif group J3_58090.1

Basepair signature:
13

0.00 -511.97 14 13

83

Motif group J3_89737.1

Basepair signature:
14

0.00 -513.01 16 16

5S rRNA junction

84

Motif group J3_09667.1

Basepair signature:
11

0.00 -525.78 18 15

85

Motif group J3_75076.1

Basepair signature:
34

0.00 -536.95 25 25

86

Motif group J3_13378.1

Basepair signature:
38

0.00 -552.36 29 25

87

Motif group J3_92705.1

Basepair signature:
12

0.00 -552.67 16 14

88

Motif group J3_20650.1

Basepair signature:
13

0.00 -559.73 18 15

89

Motif group J3_24127.1

Basepair signature:
13

0.00 -560.02 17 13

90

Motif group J3_76911.2

Basepair signature:
11

0.00 -564.59 16 13

91

Motif group J3_71677.1

Basepair signature:
13

0.00 -569.50 15 14

92

Motif group J3_20574.1

Basepair signature:
14

0.00 -572.87 17 15

93

Motif group J3_64069.1

Basepair signature:
13

0.00 -572.96 16 14

94

Motif group J3_68164.1

Basepair signature:
15

0.00 -577.79 19 15

95

Motif group J3_11934.4

Basepair signature:
13

0.00 -587.00 16 12

96

Motif group J3_45941.1

Basepair signature:
13

0.00 -588.00 21 19

97

Motif group J3_94999.1

Basepair signature:
12

0.00 -590.85 18 14

98

Motif group J3_89368.5

Basepair signature:
13

0.00 -591.84 18 14

99

Motif group J3_17385.4

Basepair signature:
12

0.00 -594.60 17 14

100

Motif group J3_51910.1

Basepair signature:
12

0.00 -595.13 14 13

101

Motif group J3_85054.4

Basepair signature:
14

0.00 -599.49 17 14

102

Motif group J3_37089.1

Basepair signature:
12

0.00 -601.77 17 15

103

Motif group J3_21998.1

Basepair signature:
14

0.00 -614.51 19 14

104

Motif group J3_97971.2

Basepair signature:
14

0.00 -622.86 16 13

105

Motif group J3_90186.1

Basepair signature:
20

0.00 -638.60 16 13

106

Motif group J3_77951.1

Basepair signature:
20

0.00 -645.56 18 15

107

Motif group J3_31041.1

Basepair signature:
12

0.00 -652.91 15 15

108

Motif group J3_89044.1

Basepair signature:
15

0.00 -655.87 17 14

109

Motif group J3_97642.1

Basepair signature:
13

0.00 -657.84 19 15

110

Motif group J3_93059.1

Basepair signature:
13

0.00 -674.12 16 14

111

Motif group J3_19545.2

Basepair signature:
12

0.00 -678.16 15 14

112

Motif group J3_15893.1

Basepair signature:
14

0.00 -680.89 17 15

C-di-AMP riboswitch

113

Motif group J3_76043.3

Basepair signature:
11

0.00 -686.68 17 15

114

Motif group J3_93637.1

Basepair signature:
15

0.00 -688.68 16 16

115

Motif group J3_80708.1

Basepair signature:
12

0.00 -692.75 16 13

116

Motif group J3_47376.1

Basepair signature:
10

0.00 -695.85 16 15

117

Motif group J3_94652.1

Basepair signature:
10

0.00 -699.26 17 14

118

Motif group J3_28621.5

Basepair signature:
13

0.00 -724.99 15 15

119

Motif group J3_98798.1

Basepair signature:
13

0.00 -726.22 21 19

120

Motif group J3_32852.6

Basepair signature:
12

0.00 -729.63 16 14

121

Motif group J3_08040.1

Basepair signature:
29

0.00 -747.14 27 22

122

Motif group J3_33494.1

Basepair signature:
12

0.00 -761.88 18 16

123

Motif group J3_47324.1

Basepair signature:
10

0.00 -765.56 18 16

124

Motif group J3_82572.1

Basepair signature:
11

0.00 -768.68 20 17

125

Motif group J3_32601.5

Basepair signature:
12

0.00 -777.96 19 16

126

Motif group J3_64189.2

Basepair signature:
11

0.00 -799.20 18 16

127

Motif group J3_28315.1

Basepair signature:
12

0.00 -800.10 18 17

128

Motif group J3_72575.1

Basepair signature:
13

0.00 -801.30 19 17

129

Motif group J3_67856.4

Basepair signature:
12

0.00 -803.30 15 13

130

Motif group J3_44724.7

Basepair signature:
12

0.00 -817.36 19 15

131

Motif group J3_25217.1

Basepair signature:
9

0.00 -822.67 19 15

132

Motif group J3_36821.1

Basepair signature:
11

0.00 -839.71 17 15

133

Motif group J3_74474.1

Basepair signature:
23

0.00 -856.91 18 18

134

Motif group J3_10118.1

Basepair signature:
7

0.00 -857.00 18 15

135

Motif group J3_61124.2

Basepair signature:
10

0.00 -860.90 18 16

136

Motif group J3_08158.1

Basepair signature:
36

0.00 -863.17 33 32

137

Motif group J3_05216.1

Basepair signature:
12

0.00 -897.72 15 14

138

Motif group J3_24879.1

Basepair signature:
28

0.00 -899.04 16 12

139

Motif group J3_36499.1

Basepair signature:
13

0.00 -899.74 20 16

140

Motif group J3_22198.1

Basepair signature:
12

0.00 -919.17 18 17

141

Motif group J3_70599.1

Basepair signature:
11

0.00 -954.83 16 15

142

Motif group J3_60031.2

Basepair signature:
12

0.00 -1007.85 15 13

143

Motif group J3_81015.1

Basepair signature:
11

0.00 -1012.50 20 16

144

Motif group J3_33327.1

Basepair signature:
26

0.00 -1019.44 28 27

145

Motif group J3_38151.1

Basepair signature:
10

0.00 -1089.96 21 17

146

Motif group J3_80578.1

Basepair signature:
10

0.00 -1097.53 19 17

147

Motif group J3_41486.2

Basepair signature:
8

0.00 -1119.20 18 16

148

Motif group J3_52655.4

Basepair signature:
11

0.00 -1144.28 19 18

149

Motif group J3_12003.2

Basepair signature:
9

0.00 -1191.58 17 15

150

Motif group J3_59914.1

Basepair signature:
9

0.00 -1398.57 22 18

151

Motif group J3_79369.1

Basepair signature:
10

0.00 -1427.26 18 15

152

Motif group J3_99595.1

Basepair signature:
9

0.00 -1490.19 18 16

153

Motif group J3_92134.2

Basepair signature:
26

0.00 -4143.58 11 11

154

Motif group J3_10708.1

Basepair signature:
22

0.00 -4451.24 26 24

155

Motif group J3_41097.1

Basepair signature:
9

0.00 -6412.88 19 17

phi29 pRNA

156

Motif group J3_01425.1

Basepair signature:
9

0.00 -6650.36 18 18

157

Motif group J3_82365.4

Basepair signature:
9

0.00 -7692.79 17 16

158

Motif group J3_14360.1

Basepair signature:
10

0.00 -7967.12 15 15

159

Motif group J3_11375.2

Basepair signature:
10

0.00 -8191.12 17 15

160

Motif group J3_56052.5

Basepair signature:
8

0.00 -8405.40 18 17

161

Motif group J3_26675.1

Basepair signature:
9

0.00 -8466.62 19 15

162

Motif group J3_07845.1

Basepair signature:
7

0.00 -9370.93 20 18

163

Motif group J3_30104.1

Basepair signature:
8

0.00 -9999.00 22 19

164

Motif group J3_30478.1

Basepair signature:
8

0.00 -9999.00 21 18

165

Motif group J3_75962.2

Basepair signature:
9

0.00 -9999.00 18 16

Coloring options: