RNA 3D Hub

JAR3D Query RF00210-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF00210 maps to these 3 chains: 2NBX|1|A, 8HUJ|1|C, 8J7R|1|C See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 25 3-way junction loop

Column numbers: 410-411, 460-461, 499-505 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CC*GG*UAAAAAG   79

    
    CC*GG*UAAAAAA    6

    
    CC*GG*CAAAAAG    2

    
    CC*GG*UAAAAAC    1

    
    CC*GU*UAAAAAG    1

    
    UC*GA*UAAAAAA    1

    
    UC*GA*UAAAAAG    1

    
    UC*GG*UAAAAAG    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_10118.1

Basepair signature:
7

90.22 5.34 7 3

2

Motif group J3_70599.1

Basepair signature:
11

3.26 -11.70 5 2

3

Motif group J3_31041.1

Basepair signature:
12

0.00 -14.18 7 3

4

Motif group J3_36821.1

Basepair signature:
11

0.00 -27.86 4 3

5

Motif group J3_01052.1

Basepair signature:
13

0.00 -38.29 4 2

6

Motif group J3_26675.1

Basepair signature:
9

0.00 -39.33 9 4

7

Motif group J3_47324.1

Basepair signature:
10

0.00 -45.48 8 5

8

Motif group J3_33494.1

Basepair signature:
12

0.00 -52.94 7 3

9

Motif group J3_61124.2

Basepair signature:
10

0.00 -68.14 4 3

10

Motif group J3_11375.2

Basepair signature:
10

0.00 -70.72 7 3

11

Motif group J3_28621.5

Basepair signature:
13

0.00 -80.08 4 4

12

Motif group J3_62630.1

Basepair signature:
12

0.00 -82.49 10 6

13

Motif group J3_47376.1

Basepair signature:
10

0.00 -93.53 11 5

14

Motif group J3_35667.2

Basepair signature:
12

0.00 -96.16 10 4

15

Motif group J3_69441.1

Basepair signature:
14

0.00 -96.54 6 6

16

Motif group J3_67856.4

Basepair signature:
12

0.00 -96.54 7 3

17

Motif group J3_93059.1

Basepair signature:
13

0.00 -100.10 4 4

18

Motif group J3_83332.1

Basepair signature:
13

0.00 -103.05 10 7

19

Motif group J3_88257.1

Basepair signature:
14

0.00 -105.63 11 7

20

Motif group J3_45941.1

Basepair signature:
13

0.00 -108.18 13 10

21

Motif group J3_19545.2

Basepair signature:
12

0.00 -110.38 8 5

22

Motif group J3_60031.2

Basepair signature:
12

0.00 -111.38 3 2

23

Motif group J3_51910.1

Basepair signature:
12

0.00 -118.72 7 4

24

Motif group J3_58090.1

Basepair signature:
13

0.00 -119.65 9 6

25

Motif group J3_00210.1

Basepair signature:
16

0.00 -121.29 11 5

26

Motif group J3_98484.1

Basepair signature:
16

0.00 -122.84 9 9

27

Motif group J3_45482.1

Basepair signature:
16

0.00 -123.85 11 7

28

Motif group J3_92705.1

Basepair signature:
12

0.00 -123.88 11 6

29

Motif group J3_37089.1

Basepair signature:
12

0.00 -125.64 11 6

30

Motif group J3_41486.2

Basepair signature:
8

0.00 -133.10 6 4

31

Motif group J3_19286.1

Basepair signature:
15

0.00 -134.74 12 8

32

Motif group J3_58957.1

Basepair signature:
17

0.00 -138.69 11 6

33

Motif group J3_89095.1

Basepair signature:
13

0.00 -139.14 9 8

34

Motif group J3_97642.1

Basepair signature:
13

0.00 -141.84 10 6

35

Motif group J3_75962.2

Basepair signature:
9

0.00 -143.05 8 3

36

Motif group J3_55773.1

Basepair signature:
15

0.00 -144.62 10 7

37

Motif group J3_32601.5

Basepair signature:
12

0.00 -146.29 6 5

38

Motif group J3_71677.1

Basepair signature:
13

0.00 -147.42 10 5

39

Motif group J3_31965.2

Basepair signature:
13

0.00 -150.17 11 7

40

Motif group J3_65990.1

Basepair signature:
14

0.00 -152.37 10 7

41

Motif group J3_56052.5

Basepair signature:
8

0.00 -152.78 7 4

42

Motif group J3_72012.1

Basepair signature:
16

0.00 -154.22 13 9

43

Motif group J3_11934.4

Basepair signature:
13

0.00 -157.09 10 7

44

Motif group J3_04521.1

Basepair signature:
10

0.00 -157.50 10 5

45

Motif group J3_96372.2

Basepair signature:
16

0.00 -158.64 13 8

46

Motif group J3_12003.2

Basepair signature:
9

0.00 -161.10 7 3

47

Motif group J3_72575.1

Basepair signature:
13

0.00 -162.16 10 7

48

Motif group J3_71753.1

Basepair signature:
17

0.00 -164.79 13 9

49

Motif group J3_68164.1

Basepair signature:
15

0.00 -165.00 12 7

50

Motif group J3_76043.3

Basepair signature:
11

0.00 -165.75 9 5

51

Motif group J3_82572.1

Basepair signature:
11

0.00 -166.73 10 7

52

Motif group J3_32030.1

Basepair signature:
15

0.00 -171.67 8 7

53

Motif group J3_76375.1

Basepair signature:
17

0.00 -173.46 12 9

54

Motif group J3_28315.1

Basepair signature:
12

0.00 -175.99 8 5

55

Motif group J3_81015.1

Basepair signature:
11

0.00 -179.10 9 6

56

Motif group J3_51249.1

Basepair signature:
13

0.00 -179.11 10 5

57

Motif group J3_89737.1

Basepair signature:
14

0.00 -179.28 10 9

5S rRNA junction

58

Motif group J3_98798.1

Basepair signature:
13

0.00 -180.26 10 8

59

Motif group J3_87797.1

Basepair signature:
15

0.00 -180.47 10 10

60

Motif group J3_80708.1

Basepair signature:
12

0.00 -181.18 9 5

61

Motif group J3_12393.2

Basepair signature:
13

0.00 -182.88 8 4

62

Motif group J3_22198.1

Basepair signature:
12

0.00 -183.15 8 6

63

Motif group J3_98379.3

Basepair signature:
16

0.00 -184.99 12 7

64

Motif group J3_20574.1

Basepair signature:
14

0.00 -187.28 11 7

65

Motif group J3_41596.1

Basepair signature:
17

0.00 -190.20 16 11

66

Motif group J3_83726.1

Basepair signature:
17

0.00 -192.60 14 10

67

Motif group J3_53439.1

Basepair signature:
16

0.00 -194.02 8 8

68

Motif group J3_80578.1

Basepair signature:
10

0.00 -194.67 9 4

69

Motif group J3_23373.1

Basepair signature:
17

0.00 -197.10 14 10

70

Motif group J3_21426.1

Basepair signature:
19

0.00 -198.91 14 11

71

Motif group J3_44724.7

Basepair signature:
12

0.00 -202.80 10 6

72

Motif group J3_41097.1

Basepair signature:
9

0.00 -203.17 8 6

phi29 pRNA

73

Motif group J3_94652.1

Basepair signature:
10

0.00 -203.34 8 6

74

Motif group J3_76475.2

Basepair signature:
16

0.00 -204.59 13 10

75

Motif group J3_64189.2

Basepair signature:
11

0.00 -206.49 10 6

76

Motif group J3_46299.2

Basepair signature:
19

0.00 -207.31 12 9

77

Motif group J3_44961.1

Basepair signature:
16

0.00 -209.18 12 10

78

Motif group J3_20650.1

Basepair signature:
13

0.00 -209.46 11 8

79

Motif group J3_32852.6

Basepair signature:
12

0.00 -210.59 9 6

80

Motif group J3_94999.1

Basepair signature:
12

0.00 -211.05 9 6

81

Motif group J3_21998.1

Basepair signature:
14

0.00 -211.18 11 8

82

Motif group J3_79369.1

Basepair signature:
10

0.00 -213.18 10 7

83

Motif group J3_47707.1

Basepair signature:
20

0.00 -216.63 13 11

84

Motif group J3_97609.1

Basepair signature:
15

0.00 -217.00 13 8

85

Motif group J3_46173.1

Basepair signature:
16

0.00 -218.73 16 11

86

Motif group J3_36387.1

Basepair signature:
16

0.00 -218.91 13 8

87

Motif group J3_14360.1

Basepair signature:
10

0.00 -220.84 7 4

88

Motif group J3_07703.1

Basepair signature:
16

0.00 -221.36 11 7

89

Motif group J3_06335.1

Basepair signature:
14

0.00 -221.46 12 8

90

Motif group J3_76911.2

Basepair signature:
11

0.00 -224.61 9 6

91

Motif group J3_25217.1

Basepair signature:
9

0.00 -224.85 9 7

92

Motif group J3_07845.1

Basepair signature:
7

0.00 -225.41 6 4

93

Motif group J3_64069.1

Basepair signature:
13

0.00 -226.99 11 8

94

Motif group J3_99563.1

Basepair signature:
17

0.00 -227.03 13 11

95

Motif group J3_83592.1

Basepair signature:
19

0.00 -229.04 13 11

96

Motif group J3_84052.1

Basepair signature:
17

0.00 -230.22 15 9

97

Motif group J3_04315.1

Basepair signature:
20

0.00 -230.83 14 11

98

Motif group J3_85054.4

Basepair signature:
14

0.00 -235.39 10 8

99

Motif group J3_34864.2

Basepair signature:
15

0.00 -237.12 10 5

100

Motif group J3_32857.1

Basepair signature:
15

0.00 -237.62 13 10

101

Motif group J3_93637.1

Basepair signature:
15

0.00 -242.66 13 9

102

Motif group J3_45099.1

Basepair signature:
19

0.00 -244.20 11 11

103

Motif group J3_00458.1

Basepair signature:
20

0.00 -245.25 14 13

104

Motif group J3_89044.1

Basepair signature:
15

0.00 -246.93 11 7

105

Motif group J3_38881.1

Basepair signature:
19

0.00 -247.31 11 11

106

Motif group J3_24127.1

Basepair signature:
13

0.00 -248.07 8 5

107

Motif group J3_30478.1

Basepair signature:
8

0.00 -250.97 7 4

108

Motif group J3_89368.5

Basepair signature:
13

0.00 -255.11 11 7

109

Motif group J3_15893.1

Basepair signature:
14

0.00 -258.18 10 7

C-di-AMP riboswitch

110

Motif group J3_08394.3

Basepair signature:
20

0.00 -258.98 14 12

111

Motif group J3_01425.1

Basepair signature:
9

0.00 -259.75 12 7

112

Motif group J3_44792.1

Basepair signature:
19

0.00 -260.61 15 12

113

Motif group J3_44163.2

Basepair signature:
18

0.00 -263.24 13 12

114

Motif group J3_75408.1

Basepair signature:
20

0.00 -264.02 13 12

115

Motif group J3_41339.1

Basepair signature:
20

0.00 -264.02 15 12

116

Motif group J3_63687.1

Basepair signature:
17

0.00 -267.27 15 14

117

Motif group J3_20992.1

Basepair signature:
18

0.00 -274.12 15 13

118

Motif group J3_58525.1

Basepair signature:
20

0.00 -277.71 18 13

119

Motif group J3_22899.1

Basepair signature:
20

0.00 -294.63 17 14

120

Motif group J3_99595.1

Basepair signature:
9

0.00 -296.76 9 5

121

Motif group J3_97971.2

Basepair signature:
14

0.00 -298.20 13 9

122

Motif group J3_38151.1

Basepair signature:
10

0.00 -305.98 12 7

123

Motif group J3_59706.1

Basepair signature:
21

0.00 -306.06 13 13

124

Motif group J3_88233.1

Basepair signature:
15

0.00 -306.85 12 10

125

Motif group J3_65403.1

Basepair signature:
21

0.00 -307.44 18 14

126

Motif group J3_28639.1

Basepair signature:
18

0.00 -310.75 16 14

127

Motif group J3_59914.1

Basepair signature:
9

0.00 -315.71 8 6

128

Motif group J3_25303.4

Basepair signature:
19

0.00 -316.60 12 10

129

Motif group J3_37047.6

Basepair signature:
15

0.00 -317.58 14 13

130

Motif group J3_01596.1

Basepair signature:
23

0.00 -322.01 18 14

131

Motif group J3_83516.4

Basepair signature:
22

0.00 -324.04 19 14

132

Motif group J3_36499.1

Basepair signature:
13

0.00 -324.09 12 10

133

Motif group J3_39320.1

Basepair signature:
21

0.00 -326.31 18 15

134

Motif group J3_46317.4

Basepair signature:
19

0.00 -334.64 13 11

135

Motif group J3_17385.4

Basepair signature:
12

0.00 -338.80 10 8

136

Motif group J3_52655.4

Basepair signature:
11

0.00 -345.51 9 8

137

Motif group J3_82365.4

Basepair signature:
9

0.00 -363.01 8 7

138

Motif group J3_30104.1

Basepair signature:
8

0.00 -364.89 9 5

139

Motif group J3_97280.1

Basepair signature:
19

0.00 -367.83 14 13

140

Motif group J3_19664.1

Basepair signature:
22

0.00 -367.84 19 15

141

Motif group J3_05216.1

Basepair signature:
12

0.00 -387.55 12 6

142

Motif group J3_61367.1

Basepair signature:
23

0.00 -388.64 18 17

143

Motif group J3_68440.1

Basepair signature:
19

0.00 -407.34 17 15

144

Motif group J3_93261.1

Basepair signature:
25

0.00 -412.10 19 17

145

Motif group J3_77951.1

Basepair signature:
20

0.00 -418.56 18 16

146

Motif group J3_38098.1

Basepair signature:
25

0.00 -422.48 18 18

147

Motif group J3_69466.1

Basepair signature:
27

0.00 -427.71 19 17

148

Motif group J3_03190.1

Basepair signature:
17

0.00 -443.83 23 20

149

Motif group J3_17791.2

Basepair signature:
19

0.00 -455.28 18 17

150

Motif group J3_90186.1

Basepair signature:
20

0.00 -456.07 20 18

151

Motif group J3_30040.2

Basepair signature:
24

0.00 -460.09 17 15

152

Motif group J3_10708.1

Basepair signature:
22

0.00 -465.94 15 13

153

Motif group J3_46124.1

Basepair signature:
26

0.00 -469.28 20 19

154

Motif group J3_09667.1

Basepair signature:
11

0.00 -525.97 11 8

155

Motif group J3_74474.1

Basepair signature:
23

0.00 -527.36 21 20

156

Motif group J3_08040.1

Basepair signature:
29

0.00 -553.45 23 22

157

Motif group J3_58429.1

Basepair signature:
27

0.00 -568.05 23 22

158

Motif group J3_65214.1

Basepair signature:
28

0.00 -617.44 22 21

159

Motif group J3_28460.1

Basepair signature:
28

0.00 -630.57 28 25

160

Motif group J3_75076.1

Basepair signature:
34

0.00 -685.19 27 26

161

Motif group J3_33327.1

Basepair signature:
26

0.00 -751.84 28 27

162

Motif group J3_24879.1

Basepair signature:
28

0.00 -752.79 22 20

163

Motif group J3_92134.2

Basepair signature:
26

0.00 -824.09 29 27

164

Motif group J3_08158.1

Basepair signature:
36

0.00 -840.79 33 33

165

Motif group J3_13378.1

Basepair signature:
38

0.00 -849.79 32 32

Coloring options: