RNA 3D Hub

JAR3D Query RF00210-3.98 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 15 3-way junction loop

Column numbers: 399-410, 461-463, 497-514 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    C--UAAGGAUGC*GGA*UUUAAAAAGCUUCUAU-G   62

    
    C--UAAGGAUGC*GGA*UUUAAAAAGCUUCUAC-G   10

    
    C--UAAGGAUGC*GGA*UUUAAAAAACUUCUAU-G    3

    
    C--UAAGGAUGC*GGG*CUUAAAAAGCUUCUAU-G    3

    
    CACGAAGGAUGC*GGC*GUUAAAAAACGUCUAGUG    1

    
    A--UAAGGAUGC*GGA*UUUAAAAAGCUUCUAU-G    1

    
    C--UAAGGAUGC*GGA*GUUAAAAAGCUUCUAU-G    1

    
    C--UAAGGAUGC*GGA*UUCAAAAAGCUUCUAC-G    1

    
    C--UAAGGAUGC*GGA*UUCAAAAAGCUUCUAU-G    1

    
    C--UAAGGAUGC*GGA*UUUAAAAAACUUCUAC-G    1

    
    C--UAAGGAUGC*GGA*UUUAAAAACCUUCUAU-G    1

    
    C--UAAGGAUGC*GGG*UUUAAAAAGCUUCUAU-G    1

    
    C--UAAGGAUGC*UGA*UUUAAAAAGCUUCUAU-G    1

    
    C--UAAGGAUGU*AGA*UUUAAAAAACGUCUAU-G    1

    
    C--UAAGGAUGU*AGA*UUUAAAAAGCGUCUAU-G    1

    
    C--UAAGGAUGU*GGA*UUUAAAAAGCUUCUAU-G    1

    
    C--UCCGGAUGC*GGA*UUUAAAAAGCUUCUAC-G    1

    
    C--GAAGGAUGC*GGC*GUUAAAAAACGUCUA--G    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 -213.57 21 17

2

Motif group J3_69466.1

Basepair signature:
27

0.00 -221.81 18 15

3

Motif group J3_00458.1

Basepair signature:
20

0.00 -246.42 17 12

4

Motif group J3_93261.1

Basepair signature:
25

0.00 -276.11 16 15

5

Motif group J3_28639.1

Basepair signature:
18

0.00 -311.34 19 16

6

Motif group J3_46173.1

Basepair signature:
16

0.00 -321.35 19 15

7

Motif group J3_68440.1

Basepair signature:
19

0.00 -322.15 18 15

8

Motif group J3_44792.1

Basepair signature:
19

0.00 -331.66 20 16

9

Motif group J3_39320.1

Basepair signature:
21

0.00 -349.56 21 18

10

Motif group J3_28460.1

Basepair signature:
28

0.00 -352.35 24 20

11

Motif group J3_20992.1

Basepair signature:
18

0.00 -359.32 18 17

12

Motif group J3_19664.1

Basepair signature:
22

0.00 -380.36 20 17

13

Motif group J3_21426.1

Basepair signature:
19

0.00 -392.29 17 16

14

Motif group J3_61367.1

Basepair signature:
23

0.00 -395.04 20 18

15

Motif group J3_17791.2

Basepair signature:
19

0.00 -403.42 21 17

16

Motif group J3_58957.1

Basepair signature:
17

0.00 -409.83 19 15

17

Motif group J3_83726.1

Basepair signature:
17

0.00 -413.81 18 15

18

Motif group J3_97280.1

Basepair signature:
19

0.00 -414.80 18 16

19

Motif group J3_63687.1

Basepair signature:
17

0.00 -416.25 20 18

20

Motif group J3_10708.1

Basepair signature:
22

0.00 -418.97 17 16

21

Motif group J3_30040.2

Basepair signature:
24

0.00 -421.40 21 16

22

Motif group J3_47707.1

Basepair signature:
20

0.00 -422.46 22 21

23

Motif group J3_03190.1

Basepair signature:
17

0.00 -427.55 23 20

24

Motif group J3_71753.1

Basepair signature:
17

0.00 -431.43 23 19

25

Motif group J3_53439.1

Basepair signature:
16

0.00 -431.89 17 16

26

Motif group J3_00210.1

Basepair signature:
16

0.00 -436.45 19 15

27

Motif group J3_88257.1

Basepair signature:
14

0.00 -436.92 17 15

28

Motif group J3_58429.1

Basepair signature:
27

0.00 -445.34 24 20

29

Motif group J3_46124.1

Basepair signature:
26

0.00 -446.16 17 16

30

Motif group J3_13378.1

Basepair signature:
38

0.00 -455.49 24 23

31

Motif group J3_75076.1

Basepair signature:
34

0.00 -461.45 26 24

32

Motif group J3_41339.1

Basepair signature:
20

0.00 -464.72 23 20

33

Motif group J3_46317.4

Basepair signature:
19

0.00 -467.14 18 15

34

Motif group J3_98484.1

Basepair signature:
16

0.00 -478.05 23 20

35

Motif group J3_45482.1

Basepair signature:
16

0.00 -482.76 17 15

36

Motif group J3_38098.1

Basepair signature:
25

0.00 -490.17 21 18

37

Motif group J3_76375.1

Basepair signature:
17

0.00 -492.51 19 17

38

Motif group J3_88233.1

Basepair signature:
15

0.00 -493.35 23 18

39

Motif group J3_83516.4

Basepair signature:
22

0.00 -496.06 23 19

40

Motif group J3_46299.2

Basepair signature:
19

0.00 -496.10 20 17

41

Motif group J3_84052.1

Basepair signature:
17

0.00 -498.33 22 18

42

Motif group J3_58525.1

Basepair signature:
20

0.00 -499.87 25 21

43

Motif group J3_38881.1

Basepair signature:
19

0.00 -502.56 20 18

44

Motif group J3_75408.1

Basepair signature:
20

0.00 -503.51 21 19

45

Motif group J3_41596.1

Basepair signature:
17

0.00 -503.53 21 18

46

Motif group J3_25303.4

Basepair signature:
19

0.00 -503.73 21 17

47

Motif group J3_96372.2

Basepair signature:
16

0.00 -513.01 22 17

48

Motif group J3_23373.1

Basepair signature:
17

0.00 -514.92 23 19

49

Motif group J3_32030.1

Basepair signature:
15

0.00 -517.00 21 18

50

Motif group J3_59706.1

Basepair signature:
21

0.00 -518.22 22 19

51

Motif group J3_45099.1

Basepair signature:
19

0.00 -521.84 18 18

52

Motif group J3_22899.1

Basepair signature:
20

0.00 -527.25 21 19

53

Motif group J3_83592.1

Basepair signature:
19

0.00 -529.13 20 17

54

Motif group J3_72012.1

Basepair signature:
16

0.00 -533.45 21 18

55

Motif group J3_04315.1

Basepair signature:
20

0.00 -533.85 23 20

56

Motif group J3_34864.2

Basepair signature:
15

0.00 -534.38 20 16

57

Motif group J3_65214.1

Basepair signature:
28

0.00 -546.69 22 19

58

Motif group J3_65990.1

Basepair signature:
14

0.00 -546.76 19 16

59

Motif group J3_77951.1

Basepair signature:
20

0.00 -550.51 22 18

60

Motif group J3_98379.3

Basepair signature:
16

0.00 -561.20 21 18

61

Motif group J3_65403.1

Basepair signature:
21

0.00 -570.10 20 18

62

Motif group J3_33327.1

Basepair signature:
26

0.00 -572.71 22 18

63

Motif group J3_69441.1

Basepair signature:
14

0.00 -575.17 24 21

64

Motif group J3_19286.1

Basepair signature:
15

0.00 -583.63 23 19

65

Motif group J3_76475.2

Basepair signature:
16

0.00 -585.84 23 21

66

Motif group J3_87797.1

Basepair signature:
15

0.00 -586.54 19 18

67

Motif group J3_99563.1

Basepair signature:
17

0.00 -597.02 23 22

68

Motif group J3_97609.1

Basepair signature:
15

0.00 -599.43 23 20

69

Motif group J3_07703.1

Basepair signature:
16

0.00 -601.07 22 17

70

Motif group J3_44163.2

Basepair signature:
18

0.00 -606.43 21 18

71

Motif group J3_12393.2

Basepair signature:
13

0.00 -612.96 21 18

72

Motif group J3_62630.1

Basepair signature:
12

0.00 -616.84 24 21

73

Motif group J3_35667.2

Basepair signature:
12

0.00 -637.90 20 16

74

Motif group J3_89737.1

Basepair signature:
14

0.00 -663.43 26 22

5S rRNA junction

75

Motif group J3_08394.3

Basepair signature:
20

0.00 -678.23 25 23

76

Motif group J3_32857.1

Basepair signature:
15

0.00 -697.39 21 20

77

Motif group J3_64069.1

Basepair signature:
13

0.00 -699.88 19 18

78

Motif group J3_37047.6

Basepair signature:
15

0.00 -701.31 23 20

79

Motif group J3_04521.1

Basepair signature:
10

0.00 -715.73 19 17

80

Motif group J3_01052.1

Basepair signature:
13

0.00 -722.98 20 18

81

Motif group J3_20574.1

Basepair signature:
14

0.00 -726.25 22 18

82

Motif group J3_44961.1

Basepair signature:
16

0.00 -736.51 21 20

83

Motif group J3_68164.1

Basepair signature:
15

0.00 -742.63 24 21

84

Motif group J3_51249.1

Basepair signature:
13

0.00 -747.52 21 19

85

Motif group J3_36387.1

Basepair signature:
16

0.00 -752.87 24 21

86

Motif group J3_17385.4

Basepair signature:
12

0.00 -759.34 19 17

87

Motif group J3_85054.4

Basepair signature:
14

0.00 -762.16 21 19

88

Motif group J3_21998.1

Basepair signature:
14

0.00 -769.68 22 20

89

Motif group J3_89368.5

Basepair signature:
13

0.00 -770.44 23 19

90

Motif group J3_94999.1

Basepair signature:
12

0.00 -778.63 19 18

91

Motif group J3_31965.2

Basepair signature:
13

0.00 -790.09 22 19

92

Motif group J3_09667.1

Basepair signature:
11

0.00 -792.56 21 18

93

Motif group J3_24127.1

Basepair signature:
13

0.00 -804.35 20 18

94

Motif group J3_97642.1

Basepair signature:
13

0.00 -805.46 22 20

95

Motif group J3_89044.1

Basepair signature:
15

0.00 -807.97 22 18

96

Motif group J3_15893.1

Basepair signature:
14

0.00 -817.02 20 18

C-di-AMP riboswitch

97

Motif group J3_98798.1

Basepair signature:
13

0.00 -837.61 20 18

98

Motif group J3_92705.1

Basepair signature:
12

0.00 -840.02 22 20

99

Motif group J3_28621.5

Basepair signature:
13

0.00 -843.24 17 17

100

Motif group J3_37089.1

Basepair signature:
12

0.00 -847.17 22 19

101

Motif group J3_11934.4

Basepair signature:
13

0.00 -868.05 21 19

102

Motif group J3_06335.1

Basepair signature:
14

0.00 -877.96 22 20

103

Motif group J3_64189.2

Basepair signature:
11

0.00 -879.89 20 19

104

Motif group J3_08040.1

Basepair signature:
29

0.00 -880.31 25 23

105

Motif group J3_76911.2

Basepair signature:
11

0.00 -880.61 21 18

106

Motif group J3_93637.1

Basepair signature:
15

0.00 -891.31 25 20

107

Motif group J3_72575.1

Basepair signature:
13

0.00 -893.04 21 19

108

Motif group J3_33494.1

Basepair signature:
12

0.00 -902.72 21 18

109

Motif group J3_71677.1

Basepair signature:
13

0.00 -914.84 23 21

110

Motif group J3_32601.5

Basepair signature:
12

0.00 -923.15 24 21

111

Motif group J3_76043.3

Basepair signature:
11

0.00 -933.31 21 19

112

Motif group J3_90186.1

Basepair signature:
20

0.00 -953.72 24 20

113

Motif group J3_44724.7

Basepair signature:
12

0.00 -961.47 19 18

114

Motif group J3_19545.2

Basepair signature:
12

0.00 -963.83 21 20

115

Motif group J3_51910.1

Basepair signature:
12

0.00 -969.40 20 18

116

Motif group J3_08158.1

Basepair signature:
36

0.00 -969.97 35 34

117

Motif group J3_47324.1

Basepair signature:
10

0.00 -981.38 24 22

118

Motif group J3_74474.1

Basepair signature:
23

0.00 -989.68 25 22

119

Motif group J3_36821.1

Basepair signature:
11

0.00 -1066.02 20 20

120

Motif group J3_22198.1

Basepair signature:
12

0.00 -1086.65 22 20

121

Motif group J3_67856.4

Basepair signature:
12

0.00 -1108.13 21 19

122

Motif group J3_97971.2

Basepair signature:
14

0.00 -1109.84 24 22

123

Motif group J3_24879.1

Basepair signature:
28

0.00 -1111.86 22 18

124

Motif group J3_81015.1

Basepair signature:
11

0.00 -1113.96 22 20

125

Motif group J3_25217.1

Basepair signature:
9

0.00 -1156.26 21 20

126

Motif group J3_05216.1

Basepair signature:
12

0.00 -1247.34 22 17

127

Motif group J3_70599.1

Basepair signature:
11

0.00 -1309.19 20 19

128

Motif group J3_60031.2

Basepair signature:
12

0.00 -1343.47 21 19

129

Motif group J3_12003.2

Basepair signature:
9

0.00 -1829.08 23 21

130

Motif group J3_99595.1

Basepair signature:
9

0.00 -1883.16 23 21

131

Motif group J3_45941.1

Basepair signature:
13

0.00 -4289.74 25 23

132

Motif group J3_89095.1

Basepair signature:
13

0.00 -4302.00 21 21

133

Motif group J3_83332.1

Basepair signature:
13

0.00 -4534.21 23 21

134

Motif group J3_92134.2

Basepair signature:
26

0.00 -4541.19 20 16

135

Motif group J3_55773.1

Basepair signature:
15

0.00 -4850.12 23 20

136

Motif group J3_79369.1

Basepair signature:
10

0.00 -5262.37 23 21

137

Motif group J3_20650.1

Basepair signature:
13

0.00 -5270.33 26 23

138

Motif group J3_82572.1

Basepair signature:
11

0.00 -5305.72 24 22

139

Motif group J3_36499.1

Basepair signature:
13

0.00 -5830.75 22 20

140

Motif group J3_58090.1

Basepair signature:
13

0.00 -5899.27 20 19

141

Motif group J3_61124.2

Basepair signature:
10

0.00 -5953.60 22 20

142

Motif group J3_31041.1

Basepair signature:
12

0.00 -6163.38 23 20

143

Motif group J3_32852.6

Basepair signature:
12

0.00 -6238.82 21 19

144

Motif group J3_47376.1

Basepair signature:
10

0.00 -6458.40 23 21

145

Motif group J3_41097.1

Basepair signature:
9

0.00 -6462.49 22 21

phi29 pRNA

146

Motif group J3_94652.1

Basepair signature:
10

0.00 -6533.81 22 21

147

Motif group J3_93059.1

Basepair signature:
13

0.00 -6696.00 18 17

148

Motif group J3_52655.4

Basepair signature:
11

0.00 -6712.97 22 22

149

Motif group J3_01425.1

Basepair signature:
9

0.00 -6738.88 22 21

150

Motif group J3_80708.1

Basepair signature:
12

0.00 -6919.33 22 21

151

Motif group J3_80578.1

Basepair signature:
10

0.00 -7121.82 22 21

152

Motif group J3_10118.1

Basepair signature:
7

0.00 -7476.95 21 20

153

Motif group J3_28315.1

Basepair signature:
12

0.00 -7555.15 23 21

154

Motif group J3_41486.2

Basepair signature:
8

0.00 -8068.89 25 24

155

Motif group J3_14360.1

Basepair signature:
10

0.00 -8143.03 24 22

156

Motif group J3_38151.1

Basepair signature:
10

0.00 -8187.96 25 22

157

Motif group J3_82365.4

Basepair signature:
9

0.00 -8277.73 23 19

158

Motif group J3_11375.2

Basepair signature:
10

0.00 -8348.57 22 21

159

Motif group J3_56052.5

Basepair signature:
8

0.00 -8436.83 21 20

160

Motif group J3_59914.1

Basepair signature:
9

0.00 -8573.43 24 22

161

Motif group J3_26675.1

Basepair signature:
9

0.00 -8642.82 23 21

162

Motif group J3_07845.1

Basepair signature:
7

0.00 -9547.84 26 24

163

Motif group J3_30104.1

Basepair signature:
8

0.00 -9999.00 24 23

164

Motif group J3_30478.1

Basepair signature:
8

0.00 -9999.00 26 24

165

Motif group J3_75962.2

Basepair signature:
9

0.00 -9999.00 22 22

Coloring options: