RNA 3D Hub

JAR3D Query RF03072-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03072 maps to these 6 chains: 9CXF|1|A, 9E73|1|A, 9E74|1|A, 9E75|1|A, 9ELY|1|A, 9G7C|1|A See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 8 3-way junction loop

Column numbers: 358-360, 499-503, 610-615 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    C-C*GAGAG*CCA--G  305

    
    C-C*GAGAG*CCG--G   35

    
    C-C*GAGCG*CCG--G   27

    
    C-C*GAGAA*UCA--G   22

    
    C-C*GAGAG*CCU--G   19

    
    C-C*GAGAG*CCC--G    4

    
    C-C*GAGAC*GCA--G    3

    
    U-C*GAGAG*CCA--A    3

    
    U-C*GAGAG*CCG--A    3

    
    C-U*AAGAG*CCG--G    2

    
    C-C*GAGAA*UCC--G    1

    
    C-C*GAGAA*UCG--G    1

    
    C-C*GAGAA*UCU--G    1

    
    C-C*GAGAU*ACC--G    1

    
    C-C*GAGCG*CCA--G    1

    
    C-C*GAGCG*CCC--G    1

    
    C-C*GAGAA*UC---G    1

    
    C-C*GAGAG*CC---G    1

    
    C-C*GAGU-*UCG--G    1

    
    Omitted sequenced and counts

    
    --C*G----*-GUCA-   15

    
    -CC*G----*------    7

    
    --C*G----*------    5

    
    --C*G----*-GCAA-    4

    
    --C*G----*-GUUA-    3

    
    C-G*C----*-----G    3

    
    --C*G----*-AUAA-    2

    
    --C*G----*-AUUA-    2

    
    --U*A----*------    2

    
    C--*-----*-----G    2

    
    C-C*GAGAG*CCM--G    1

    
    ACU*A----*-AC--U    1

    
    --C*G----*-AUCA-    1

    
    --C*G----*-GGAA-    1

    
    --C*G----*-GUAA-    1

    
    --C*G----*-GUAC-    1

    
    -CU*A----*---AU-    1

    
    U-G*C----*--A--A    1

    
    C-C*G----*-----G    1

    
    C-G*C----*------    1

    
    --C*-----*------    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_37089.1

Basepair signature:
12

11.34 -10.75 10 4

2

Motif group J3_92705.1

Basepair signature:
12

0.69 -10.24 9 3

3

Motif group J3_12003.2

Basepair signature:
9

0.46 -65.89 7 4

4

Motif group J3_12393.2

Basepair signature:
13

0.00 -16.39 5 4

5

Motif group J3_04521.1

Basepair signature:
10

0.00 -25.53 8 4

6

Motif group J3_94652.1

Basepair signature:
10

0.00 -32.40 7 3

7

Motif group J3_01052.1

Basepair signature:
13

0.00 -40.79 7 5

8

Motif group J3_76911.2

Basepair signature:
11

0.00 -42.47 5 3

9

Motif group J3_20650.1

Basepair signature:
13

0.00 -49.13 7 5

10

Motif group J3_31965.2

Basepair signature:
13

0.00 -52.79 6 4

11

Motif group J3_24127.1

Basepair signature:
13

0.00 -53.78 6 4

12

Motif group J3_32030.1

Basepair signature:
15

0.00 -54.20 7 5

13

Motif group J3_97642.1

Basepair signature:
13

0.00 -57.82 8 4

14

Motif group J3_76043.3

Basepair signature:
11

0.00 -64.54 8 4

15

Motif group J3_47324.1

Basepair signature:
10

0.00 -67.75 7 5

16

Motif group J3_51910.1

Basepair signature:
12

0.00 -69.48 9 4

17

Motif group J3_22198.1

Basepair signature:
12

0.00 -81.04 11 5

18

Motif group J3_19286.1

Basepair signature:
15

0.00 -81.91 9 7

19

Motif group J3_34864.2

Basepair signature:
15

0.00 -82.53 7 6

20

Motif group J3_41486.2

Basepair signature:
8

0.00 -85.40 3 3

21

Motif group J3_80708.1

Basepair signature:
12

0.00 -86.81 10 4

22

Motif group J3_82572.1

Basepair signature:
11

0.00 -88.13 8 6

23

Motif group J3_35667.2

Basepair signature:
12

0.00 -88.57 8 6

24

Motif group J3_25217.1

Basepair signature:
9

0.00 -92.01 7 5

25

Motif group J3_61124.2

Basepair signature:
10

0.00 -93.50 8 4

26

Motif group J3_44724.7

Basepair signature:
12

0.00 -93.95 7 4

27

Motif group J3_79369.1

Basepair signature:
10

0.00 -94.52 8 2

28

Motif group J3_05216.1

Basepair signature:
12

0.00 -95.00 8 4

29

Motif group J3_00210.1

Basepair signature:
16

0.00 -98.60 11 7

30

Motif group J3_20574.1

Basepair signature:
14

0.00 -98.92 6 6

31

Motif group J3_83332.1

Basepair signature:
13

0.00 -99.07 11 6

32

Motif group J3_82365.4

Basepair signature:
9

0.00 -100.28 5 3

33

Motif group J3_15893.1

Basepair signature:
14

0.00 -101.23 9 6

C-di-AMP riboswitch

34

Motif group J3_45941.1

Basepair signature:
13

0.00 -103.30 13 7

35

Motif group J3_89368.5

Basepair signature:
13

0.00 -105.66 9 5

36

Motif group J3_58957.1

Basepair signature:
17

0.00 -106.93 11 7

37

Motif group J3_94999.1

Basepair signature:
12

0.00 -106.96 8 6

38

Motif group J3_53439.1

Basepair signature:
16

0.00 -109.61 10 7

39

Motif group J3_97609.1

Basepair signature:
15

0.00 -112.63 9 7

40

Motif group J3_55773.1

Basepair signature:
15

0.00 -114.56 11 6

41

Motif group J3_89095.1

Basepair signature:
13

0.00 -115.04 7 6

42

Motif group J3_67856.4

Basepair signature:
12

0.00 -117.31 8 5

43

Motif group J3_89737.1

Basepair signature:
14

0.00 -118.68 11 8

5S rRNA junction

44

Motif group J3_56052.5

Basepair signature:
8

0.00 -120.30 5 3

45

Motif group J3_17385.4

Basepair signature:
12

0.00 -120.49 8 5

46

Motif group J3_06335.1

Basepair signature:
14

0.00 -121.70 9 5

47

Motif group J3_88257.1

Basepair signature:
14

0.00 -125.48 13 9

48

Motif group J3_32857.1

Basepair signature:
15

0.00 -126.24 10 7

49

Motif group J3_47376.1

Basepair signature:
10

0.00 -127.37 10 5

50

Motif group J3_72575.1

Basepair signature:
13

0.00 -128.01 12 6

51

Motif group J3_41097.1

Basepair signature:
9

0.00 -131.89 7 6

phi29 pRNA

52

Motif group J3_80578.1

Basepair signature:
10

0.00 -132.05 9 4

53

Motif group J3_52655.4

Basepair signature:
11

0.00 -136.61 8 4

54

Motif group J3_87797.1

Basepair signature:
15

0.00 -136.78 10 7

55

Motif group J3_21998.1

Basepair signature:
14

0.00 -137.81 11 6

56

Motif group J3_38151.1

Basepair signature:
10

0.00 -138.98 8 4

57

Motif group J3_68164.1

Basepair signature:
15

0.00 -140.46 11 7

58

Motif group J3_83726.1

Basepair signature:
17

0.00 -141.56 9 8

59

Motif group J3_32852.6

Basepair signature:
12

0.00 -141.70 7 5

60

Motif group J3_14360.1

Basepair signature:
10

0.00 -142.91 6 4

61

Motif group J3_19545.2

Basepair signature:
12

0.00 -143.18 8 6

62

Motif group J3_11934.4

Basepair signature:
13

0.00 -143.25 8 6

63

Motif group J3_98379.3

Basepair signature:
16

0.00 -144.17 12 6

64

Motif group J3_98798.1

Basepair signature:
13

0.00 -145.78 12 7

65

Motif group J3_23373.1

Basepair signature:
17

0.00 -146.07 12 8

66

Motif group J3_81015.1

Basepair signature:
11

0.00 -148.23 6 5

67

Motif group J3_72012.1

Basepair signature:
16

0.00 -148.29 13 9

68

Motif group J3_65990.1

Basepair signature:
14

0.00 -148.71 10 7

69

Motif group J3_85054.4

Basepair signature:
14

0.00 -150.51 8 7

70

Motif group J3_99595.1

Basepair signature:
9

0.00 -150.79 4 4

71

Motif group J3_07703.1

Basepair signature:
16

0.00 -152.87 12 7

72

Motif group J3_45482.1

Basepair signature:
16

0.00 -155.46 13 9

73

Motif group J3_99563.1

Basepair signature:
17

0.00 -156.42 12 10

74

Motif group J3_36499.1

Basepair signature:
13

0.00 -159.37 8 6

75

Motif group J3_89044.1

Basepair signature:
15

0.00 -160.25 10 7

76

Motif group J3_71677.1

Basepair signature:
13

0.00 -160.26 9 5

77

Motif group J3_41596.1

Basepair signature:
17

0.00 -163.48 10 9

78

Motif group J3_96372.2

Basepair signature:
16

0.00 -166.51 13 9

79

Motif group J3_36387.1

Basepair signature:
16

0.00 -168.66 11 7

80

Motif group J3_31041.1

Basepair signature:
12

0.00 -171.93 10 6

81

Motif group J3_93637.1

Basepair signature:
15

0.00 -173.91 12 10

82

Motif group J3_76375.1

Basepair signature:
17

0.00 -175.61 13 10

83

Motif group J3_01425.1

Basepair signature:
9

0.00 -176.29 7 4

84

Motif group J3_64069.1

Basepair signature:
13

0.00 -179.50 13 7

85

Motif group J3_84052.1

Basepair signature:
17

0.00 -179.78 15 9

86

Motif group J3_44961.1

Basepair signature:
16

0.00 -180.07 11 9

87

Motif group J3_75962.2

Basepair signature:
9

0.00 -181.83 7 4

88

Motif group J3_30478.1

Basepair signature:
8

0.00 -184.08 5 3

89

Motif group J3_62630.1

Basepair signature:
12

0.00 -186.67 14 9

90

Motif group J3_04315.1

Basepair signature:
20

0.00 -187.55 13 9

91

Motif group J3_10118.1

Basepair signature:
7

0.00 -190.69 8 6

92

Motif group J3_38881.1

Basepair signature:
19

0.00 -190.96 11 9

93

Motif group J3_58090.1

Basepair signature:
13

0.00 -195.12 11 8

94

Motif group J3_37047.6

Basepair signature:
15

0.00 -199.42 9 8

95

Motif group J3_69441.1

Basepair signature:
14

0.00 -201.93 16 10

96

Motif group J3_26675.1

Basepair signature:
9

0.00 -205.84 7 5

97

Motif group J3_11375.2

Basepair signature:
10

0.00 -207.60 7 5

98

Motif group J3_30104.1

Basepair signature:
8

0.00 -211.96 4 4

99

Motif group J3_97971.2

Basepair signature:
14

0.00 -214.55 10 6

100

Motif group J3_98484.1

Basepair signature:
16

0.00 -215.74 11 10

101

Motif group J3_20992.1

Basepair signature:
18

0.00 -218.61 14 11

102

Motif group J3_45099.1

Basepair signature:
19

0.00 -219.35 11 9

103

Motif group J3_25303.4

Basepair signature:
19

0.00 -222.10 12 9

104

Motif group J3_47707.1

Basepair signature:
20

0.00 -222.86 13 11

105

Motif group J3_46173.1

Basepair signature:
16

0.00 -223.03 13 11

106

Motif group J3_76475.2

Basepair signature:
16

0.00 -223.07 12 9

107

Motif group J3_46299.2

Basepair signature:
19

0.00 -224.54 11 10

108

Motif group J3_59914.1

Basepair signature:
9

0.00 -227.16 10 5

109

Motif group J3_44163.2

Basepair signature:
18

0.00 -227.76 13 10

110

Motif group J3_58525.1

Basepair signature:
20

0.00 -229.12 16 11

111

Motif group J3_44792.1

Basepair signature:
19

0.00 -230.19 14 11

112

Motif group J3_71753.1

Basepair signature:
17

0.00 -230.30 12 11

113

Motif group J3_21426.1

Basepair signature:
19

0.00 -230.53 16 11

114

Motif group J3_28315.1

Basepair signature:
12

0.00 -230.99 9 7

115

Motif group J3_75408.1

Basepair signature:
20

0.00 -236.74 13 12

116

Motif group J3_83592.1

Basepair signature:
19

0.00 -237.88 15 12

117

Motif group J3_08394.3

Basepair signature:
20

0.00 -239.19 13 11

118

Motif group J3_07845.1

Basepair signature:
7

0.00 -242.21 8 4

119

Motif group J3_00458.1

Basepair signature:
20

0.00 -247.93 15 12

120

Motif group J3_22899.1

Basepair signature:
20

0.00 -263.03 17 12

121

Motif group J3_97280.1

Basepair signature:
19

0.00 -263.45 14 10

122

Motif group J3_88233.1

Basepair signature:
15

0.00 -264.11 14 10

123

Motif group J3_64189.2

Basepair signature:
11

0.00 -269.87 9 6

124

Motif group J3_41339.1

Basepair signature:
20

0.00 -277.64 14 13

125

Motif group J3_39320.1

Basepair signature:
21

0.00 -277.77 15 13

126

Motif group J3_68440.1

Basepair signature:
19

0.00 -289.15 14 12

127

Motif group J3_46317.4

Basepair signature:
19

0.00 -290.29 14 11

128

Motif group J3_01596.1

Basepair signature:
23

0.00 -295.13 18 13

129

Motif group J3_59706.1

Basepair signature:
21

0.00 -296.35 15 13

130

Motif group J3_65403.1

Basepair signature:
21

0.00 -300.28 17 14

131

Motif group J3_32601.5

Basepair signature:
12

0.00 -314.13 14 9

132

Motif group J3_77951.1

Basepair signature:
20

0.00 -320.97 16 12

133

Motif group J3_33494.1

Basepair signature:
12

0.00 -325.14 12 6

134

Motif group J3_61367.1

Basepair signature:
23

0.00 -329.18 17 15

135

Motif group J3_83516.4

Basepair signature:
22

0.00 -331.50 19 15

136

Motif group J3_17791.2

Basepair signature:
19

0.00 -337.90 13 11

137

Motif group J3_28621.5

Basepair signature:
13

0.00 -345.82 13 8

138

Motif group J3_63687.1

Basepair signature:
17

0.00 -350.58 16 15

139

Motif group J3_70599.1

Basepair signature:
11

0.00 -352.69 8 5

140

Motif group J3_90186.1

Basepair signature:
20

0.00 -373.24 17 14

141

Motif group J3_36821.1

Basepair signature:
11

0.00 -373.32 7 7

142

Motif group J3_19664.1

Basepair signature:
22

0.00 -373.49 19 16

143

Motif group J3_38098.1

Basepair signature:
25

0.00 -395.73 20 17

144

Motif group J3_51249.1

Basepair signature:
13

0.00 -423.78 12 10

145

Motif group J3_93261.1

Basepair signature:
25

0.00 -428.90 20 18

146

Motif group J3_46124.1

Basepair signature:
26

0.00 -444.47 22 19

147

Motif group J3_03190.1

Basepair signature:
17

0.00 -450.69 21 20

148

Motif group J3_69466.1

Basepair signature:
27

0.00 -451.08 20 19

149

Motif group J3_74474.1

Basepair signature:
23

0.00 -451.28 17 15

150

Motif group J3_30040.2

Basepair signature:
24

0.00 -458.90 17 16

151

Motif group J3_09667.1

Basepair signature:
11

0.00 -470.02 8 6

152

Motif group J3_65214.1

Basepair signature:
28

0.00 -481.71 21 18

153

Motif group J3_93059.1

Basepair signature:
13

0.00 -519.81 15 11

154

Motif group J3_08040.1

Basepair signature:
29

0.00 -537.20 24 21

155

Motif group J3_10708.1

Basepair signature:
22

0.00 -538.46 21 19

156

Motif group J3_58429.1

Basepair signature:
27

0.00 -560.22 23 22

157

Motif group J3_60031.2

Basepair signature:
12

0.00 -574.88 7 6

158

Motif group J3_28460.1

Basepair signature:
28

0.00 -622.46 28 25

159

Motif group J3_33327.1

Basepair signature:
26

0.00 -652.61 26 24

160

Motif group J3_24879.1

Basepair signature:
28

0.00 -655.54 23 19

161

Motif group J3_75076.1

Basepair signature:
34

0.00 -670.90 26 25

162

Motif group J3_92134.2

Basepair signature:
26

0.00 -735.51 22 21

163

Motif group J3_08158.1

Basepair signature:
36

0.00 -803.11 31 31

164

Motif group J3_13378.1

Basepair signature:
38

0.00 -831.23 31 31

165

Motif group J3_28639.1

Basepair signature:
18

0.00 -9999.00 16 14

Coloring options: