RNA 3D Hub

JAR3D Query RF03125-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

There are no chains in PDB that we map to Rfam family RF03125.

Rfam family RF03125 is part of clan CL00117, which includes Rfam families RF03121, RF03123, RF03125, RF03122, RF00164, RF03124, RF00165 .
There is 1 chain in PDB that we map to these Rfam families: 1XJR|1|A . See it at RNA 3D Hub by filtering on Rfam family, clan, or chain.

Loop 15 4-way junction loop

Column numbers: 192-193, 211-214, 263-265, 280-292 
    Scored sequences and counts

    
    GG*CCAC*GCU*AUAUGGAAGAGCC   11
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_35578.3

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

0.00 -245.49 13 8

2

Motif group J4_89787.1

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

0.00 -250.21 14 11

3

Motif group J4_65285.1

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

0.00 -260.45 14 10

tRNA junction

4

Motif group J4_80390.1

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

0.00 -268.88 16 10

tRNA junction

5

Motif group J4_80682.1

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

0.00 -282.31 14 10

tRNA junction

6

Motif group J4_61885.6

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

0.00 -286.20 19 12

7

Motif group J4_36296.3

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

0.00 -291.02 16 9

tRNA junction

8

Motif group J4_87855.1

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

0.00 -303.94 16 9

9

Motif group J4_40477.1

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

0.00 -310.54 14 10

tRNA junction

10

Motif group J4_15241.1

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

0.00 -312.80 14 10

11

Motif group J4_94519.1

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

0.00 -315.48 16 10

tRNA junction

12

Motif group J4_28426.1

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

0.00 -318.12 13 9

SAM-I/IV riboswitch junction

13

Motif group J4_57327.1

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

0.00 -332.39 17 15

14

Motif group J4_70449.28

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

0.00 -339.20 13 8

tRNA junction

15

Motif group J4_13620.1

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

0.00 -366.69 20 13

16

Motif group J4_47701.1

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

0.00 -366.75 16 10

17

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 -369.46 16 14

18

Motif group J4_59634.1

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

0.00 -387.53 16 11

19

Motif group J4_10571.1

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

0.00 -402.36 18 12

20

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 -410.88 17 15

21

Motif group J4_40439.2

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

0.00 -424.31 15 10

SAM-I riboswitch junction

22

Motif group J4_16596.1

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

0.00 -432.83 15 13

Cobalamin riboswitch junction

23

Motif group J4_10313.5

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

0.00 -433.19 16 12

24

Motif group J4_59845.1

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

0.00 -455.17 17 11

25

Motif group J4_36540.1

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

0.00 -467.60 14 13

26

Motif group J4_54165.1

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

0.00 -472.56 18 12

27

Motif group J4_77044.4

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

0.00 -481.73 15 12

28

Motif group J4_28473.1

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

0.00 -483.30 14 12

29

Motif group J4_44058.1

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

0.00 -498.92 18 14

30

Motif group J4_63658.1

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

0.00 -505.46 17 13

31

Motif group J4_26776.1

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

0.00 -509.01 20 13

32

Motif group J4_01665.1

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

0.00 -510.50 18 13

33

Motif group J4_69051.6

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

0.00 -514.85 16 14

34

Motif group J4_99897.1

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

0.00 -530.75 17 12

35

Motif group J4_48692.1

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

0.00 -532.14 14 12

36

Motif group J4_97085.2

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

0.00 -539.80 16 12

37

Motif group J4_91813.1

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

0.00 -540.00 19 13

38

Motif group J4_64571.5

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

0.00 -565.52 14 9

39

Motif group J4_11418.1

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

0.00 -570.01 21 17

40

Motif group J4_72305.5

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

0.00 -575.49 15 11

tRNA junction

41

Motif group J4_71729.5

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

0.00 -577.80 18 15

42

Motif group J4_04930.6

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

0.00 -592.43 17 14

43

Motif group J4_95838.1

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

0.00 -594.39 16 12

44

Motif group J4_12410.1

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

0.00 -598.99 20 18

45

Motif group J4_61477.5

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

0.00 -601.67 17 14

46

Motif group J4_45801.6

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

0.00 -602.90 16 14

47

Motif group J4_88771.1

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

0.00 -610.86 17 14

48

Motif group J4_07509.2

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

0.00 -622.96 16 15

49

Motif group J4_47842.1

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

0.00 -635.12 14 12

50

Motif group J4_65052.1

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

0.00 -655.59 17 12

51

Motif group J4_93343.1

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

0.00 -661.95 17 13

52

Motif group J4_75852.1

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

0.00 -676.33 20 16

53

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 -677.62 23 18

RNase P junction

54

Motif group J4_57344.1

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

0.00 -750.81 15 12

55

Motif group J4_60168.1

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

0.00 -774.19 21 18

56

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 -802.96 25 19

RNase P junction

57

Motif group J4_69073.1

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

0.00 -825.65 16 12

58

Motif group J4_47478.1

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

0.00 -825.65 16 12

59

Motif group J4_24220.1

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

0.00 -883.67 20 16

60

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 -924.30 33 28

61

Motif group J4_63076.1

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

0.00 -1143.17 18 13

class I ligase product junction

62

Motif group J4_07491.2

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

0.00 -1159.48 20 15

Purine riboswitch junction

63

Motif group J4_24280.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -1188.20 16 13

64

Motif group J4_45582.1

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

0.00 -1194.68 18 14

65

Motif group J4_00691.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -1209.56 16 13

66

Motif group J4_65356.1

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

0.00 -1209.57 20 15

67

Motif group J4_46448.1

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

0.00 -9040.05 17 13

68

Motif group J4_76096.5

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -9999.00 16 14

69

Motif group J4_43687.2

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

0.00 -9999.00 15 13

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