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 9 4-way junction loop

Column numbers: 182-183, 218-219, 229-232, 244-245 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    GC*GG*CACG*CC   85

    
    GC*GG*CAUG*CC    2

    
    GG*UG*CCAG*CC    2

    
    GC*GG*CAAG*CC    1

    
    GC*GG*CGCG*CC    1

    
    Omitted sequenced and counts

    
    -C*GG*CAAG*CC    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 J4_47478.1

Basepair signature:
cWW-F-cWW-cWS-cHW-cWW-cWW

100.00 55.62 10 2

2

Motif group J4_69073.1

Basepair signature:
cWW-cHS-cWW-cWS-cHW-cWW-cWW

100.00 55.62 10 2

3

Motif group J4_63076.1

Basepair signature:
cWW-tSS-cWW-cWW-cWW

100.00 18.52 5 2

class I ligase product junction

4

Motif group J4_24280.2

Basepair signature:
cWW-cWW-cWW-cWW

1.10 -4.78 6 1

5

Motif group J4_28473.1

Basepair signature:
cWW-F-F-F-cWW-cWW-F-cWW-F

0.00 -41.87 3 3

6

Motif group J4_10571.1

Basepair signature:
cWW-F-F-F-cWW-F-F-cWW-F

0.00 -43.64 9 4

7

Motif group J4_00691.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -48.52 2 2

8

Motif group J4_72305.5

Basepair signature:
cWW-F-cWW-cWW-cHS-F-cWW

0.00 -68.18 7 3

tRNA junction

9

Motif group J4_97085.2

Basepair signature:
cWW-cWW-F-cWW-tHS-cWW-F-F

0.00 -68.84 5 4

10

Motif group J4_07491.2

Basepair signature:
cWW-F-F-tWS-F-F-cWW-cWW-cWW

0.00 -70.86 9 3

Purine riboswitch junction

11

Motif group J4_28426.1

Basepair signature:
cWW-F-cWW-F-F-F-F-F-cWW-cWW

0.00 -75.30 6 4

SAM-I/IV riboswitch junction

12

Motif group J4_48692.1

Basepair signature:
cWW-tHW-F-F-cWW-cWW-cWW

0.00 -78.70 10 4

13

Motif group J4_65052.1

Basepair signature:
cWW-cWW-cWW-F-cWW-tWS-cWW

0.00 -84.44 7 4

14

Motif group J4_76096.5

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -98.95 2 2

15

Motif group J4_43687.2

Basepair signature:
cWW-cWW-cWW-cWW-cWW

0.00 -104.14 2 1

16

Motif group J4_77044.4

Basepair signature:
cWW-F-tHS-F-cWW-cWW-cWW-F-cWW

0.00 -110.64 7 5

17

Motif group J4_36296.3

Basepair signature:
cWW-F-cWW-cWW-F-F-F-cWW

0.00 -113.98 7 6

tRNA junction

18

Motif group J4_95838.1

Basepair signature:
cWW-F-F-cWW-F-F-cWW-cWW-F

0.00 -122.50 7 4

19

Motif group J4_87855.1

Basepair signature:
cWW-F-cWW-F-F-F-cWW-F-cWW

0.00 -129.94 11 6

20

Motif group J4_40477.1

Basepair signature:
cWW-F-cWW-F-cWW-cHW-F-F-F-cWW-F

0.00 -131.40 11 6

tRNA junction

21

Motif group J4_80390.1

Basepair signature:
cWW-cWW-cWW-F-F-cWW-F-F

0.00 -134.46 8 6

tRNA junction

22

Motif group J4_64571.5

Basepair signature:
cWW-F-cWW-tSS-cWW-F-cWW

0.00 -134.93 5 5

23

Motif group J4_57344.1

Basepair signature:
cWW-F-cWW-F-cWW-cSH-cWW

0.00 -137.41 5 4

24

Motif group J4_26776.1

Basepair signature:
cWW-tSH-F-cWW-cWW-F-tHS-cWW

0.00 -140.22 11 6

25

Motif group J4_36540.1

Basepair signature:
cWW-cWW-F-F-F-cWW-F-cWW-F-F

0.00 -142.77 11 7

26

Motif group J4_24220.1

Basepair signature:
cWW-F-F-tWS-F-F-cWW-tHS-cWW-cWW

0.00 -148.36 11 5

27

Motif group J4_35578.3

Basepair signature:
cWW-F-cWW-F-F-F-tHW-F-cWW-cWW

0.00 -152.83 11 6

28

Motif group J4_99897.1

Basepair signature:
cWW-F-cWW-cWW-cWW-cWW-F-cWW

0.00 -153.02 9 6

29

Motif group J4_70449.28

Basepair signature:
cWW-F-cWW-cWW-cHS-F-cWW-cWW

0.00 -155.56 7 5

tRNA junction

30

Motif group J4_40439.2

Basepair signature:
cWW-F-cWW-F-F-F-F-F-cWW-F-cWW

0.00 -157.24 10 6

SAM-I riboswitch junction

31

Motif group J4_46448.1

Basepair signature:
cWW-cWS-tSH-cWW-cWW-cWW

0.00 -159.48 8 3

32

Motif group J4_75852.1

Basepair signature:
cWW-tSW-cSS-cWW-F-cSH-cWW-cWW-F-F

0.00 -168.85 13 7

33

Motif group J4_45582.1

Basepair signature:
cWW-F-cWW-cWW-cWW-cWW

0.00 -176.57 9 4

34

Motif group J4_54165.1

Basepair signature:
cWW-F-F-F-cWW-cWW-cWW-cWW-cWW-F-F

0.00 -177.31 11 7

35

Motif group J4_47842.1

Basepair signature:
cWW-F-F-tWS-F-cWH-cWW-cWW-cWW-cWW

0.00 -178.26 12 6

36

Motif group J4_04930.6

Basepair signature:
cWW-F-F-tWW-tHH-cWW-cWW-cHW-cWW

0.00 -179.24 8 7

37

Motif group J4_89787.1

Basepair signature:
cWW-F-cWW-F-F-F-F-F-F-F-cWW-cWW

0.00 -180.53 9 8

38

Motif group J4_10313.5

Basepair signature:
cWW-cWW-tHW-F-F-F-F-F-F-cWW-cWW

0.00 -183.71 12 7

39

Motif group J4_71729.5

Basepair signature:
cWW-tSH-cHH-F-F-tHS-cWW-cWW-F-F-cWW

0.00 -191.22 9 7

40

Motif group J4_65285.1

Basepair signature:
cWW-F-F-F-F-F-cWW-cWW-F-cWW-F

0.00 -195.92 11 8

tRNA junction

41

Motif group J4_65356.1

Basepair signature:
cWW-tSS-cWW-cWW-cWW-cWW

0.00 -197.98 7 3

42

Motif group J4_59845.1

Basepair signature:
cWW-tSW-F-cWW-F-F-cWW-F-F-cWW-F-F

0.00 -203.89 15 8

43

Motif group J4_91813.1

Basepair signature:
cWW-cWW-F-tSH-cWW-F-F-F-cWW-F

0.00 -206.35 11 7

44

Motif group J4_94519.1

Basepair signature:
cWW-F-F-F-F-F-cWW-F-F-F-F-cWW-cWW

0.00 -211.09 14 8

tRNA junction

45

Motif group J4_80682.1

Basepair signature:
cWW-F-F-F-F-F-cWW-cWW-F-cWW-F

0.00 -215.76 11 8

tRNA junction

46

Motif group J4_88771.1

Basepair signature:
cWW-tSS-cWW-tSS-cWW-cWW-tWH-tWH-cSH-cWW

0.00 -215.95 9 8

47

Motif group J4_59634.1

Basepair signature:
cWW-F-F-F-cHS-F-F-F-F-F-F-F-F

0.00 -216.27 11 9

48

Motif group J4_01665.1

Basepair signature:
cWW-tWH-F-tWH-cWW-tSS-F-tHW-tSS-cWW-cWW

0.00 -228.88 9 9

49

Motif group J4_47701.1

Basepair signature:
cWW-F-F-cWW-F-cWW-cWW-cWW-F-F-F-F

0.00 -230.03 12 9

50

Motif group J4_44058.1

Basepair signature:
cWW-cWW-F-cWW-F-cWW-cWW-F-cWW-F

0.00 -240.08 15 9

51

Motif group J4_12410.1

Basepair signature:
cWW-cWW-F-F-cSS-F-cWW-tHS-cWW-F-cWW

0.00 -241.52 10 9

52

Motif group J4_11418.1

Basepair signature:
cWW-F-F-tSH-cHH-F-F-tHS-cWW-cWW-F-F-cWW

0.00 -249.26 13 9

53

Motif group J4_13620.1

Basepair signature:
cWW-F-F-F-F-F-cWW-cWW-cHS-F-F-F-cWW-F

0.00 -259.79 15 10

54

Motif group J4_57327.1

Basepair signature:
cWW-F-F-F-F-F-F-F-F-cWW-F-cWW-F-F-F

0.00 -265.60 14 12

55

Motif group J4_16596.1

Basepair signature:
cWW-F-F-F-cWW-F-cWW-F-cWW-cWW-F-F

0.00 -275.98 16 10

Cobalamin riboswitch junction

56

Motif group J4_15241.1

Basepair signature:
cWW-cSH-tHS-cWW-F-F-tHW-F-cWW-F-F-F-cWW

0.00 -276.45 11 10

57

Motif group J4_61477.5

Basepair signature:
cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

0.00 -286.99 15 10

58

Motif group J4_45801.6

Basepair signature:
cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

0.00 -292.24 13 10

59

Motif group J4_61885.6

Basepair signature:
cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F

0.00 -299.54 13 13

60

Motif group J4_07509.2

Basepair signature:
cWW-tSW-F-F-tHS-F-cWW-F-cWW-F-F-tHS-F-cWW

0.00 -355.10 18 12

61

Motif group J4_69051.6

Basepair signature:
cWW-F-cWW-F-tHW-F-cWW-F-F-F-F-F-cWW-cWW

0.00 -355.92 16 11

62

Motif group J4_70672.1

Basepair signature:
cWW-tSH-F-F-F-F-F-F-cSW-F-tHS-cWW-cWW-cWW-F-cWW-F

0.00 -367.00 18 15

63

Motif group J4_63658.1

Basepair signature:
cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tSW-F-cSH-F-F

0.00 -408.04 16 12

64

Motif group J4_98739.1

Basepair signature:
cWW-F-F-F-F-cWW-F-F-F-F-F-F-F-F-cWW-cWW-F-F-F

0.00 -409.02 18 16

65

Motif group J4_12209.1

Basepair signature:
cWW-F-F-F-cWW-tWH-F-cWW-F-F-F-tWS-tWH-F-F-F-F-F-cSH-cWW-F

0.00 -502.07 22 19

RNase P junction

66

Motif group J4_60168.1

Basepair signature:
cWW-F-F-F-F-F-cWW-F-F-F-cWW-F-tSS-F-cWW

0.00 -518.22 13 11

67

Motif group J4_93343.1

Basepair signature:
cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

0.00 -549.18 15 12

68

Motif group J4_04237.1

Basepair signature:
cWW-F-F-F-cWH-F-F-F-F-cWW-F-F-F-F-cWW-F-F-F-F-F-F-F-F-F-F

0.00 -576.09 25 23

69

Motif group J4_19572.1

Basepair signature:
cWW-F-cSW-F-F-tWH-cWW-F-cHW-F-cWW-F-tWS-F-cWW-F-F-F-cSH-tWH-cWW-F-F-F

0.00 -615.65 23 22

RNase P junction

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