RNA 3D Hub

JAR3D Query RF02032-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF02032 maps to these 73 chains: 9L0R|1|A, 9L0R|1|B, 9L0R|1|C, 9L0R|1|D, 9L0R|1|E, 9L0R|1|F, 9L0R|1|G, 9L0R|1|H, 9L0R|1|I, 9L0R|1|J, 9L0R|1|K, 9L0R|1|L, 9LEC|1|J, 9LEE|1|A, 9LEE|1|B, 9LEE|1|C, 9LEE|1|D, 9LEE|1|E, 9LEE|1|F, 9LEE|1|G, 9LEE|1|H, 9LEE|1|I, 9LEE|1|J, 9LEL|1|J, 9LEM|1|A, 9LEM|1|B, 9LEM|1|C, 9LEM|1|D, 9LEM|1|E, 9LEM|1|F, 9LEM|1|G, 9LEM|1|H, 9LEM|1|I, 9LEM|1|J, 9LHK|1|G, 9LHL|1|A, 9LHL|1|B, 9LHL|1|C, 9LHL|1|D, 9LHL|1|E, 9LHL|1|F, 9LHL|1|G, 9LHL|1|H, 9LHL|1|I, 9LHL|1|J, 9LHL|1|K, 9LHL|1|L, 9LHL|1|M, 9LHL|1|N, 9LMF|1|A, 9LMF|1|B, 9LMF|1|C, 9LMF|1|D, 9LMF|1|E, 9LMF|1|F, 9LMF|1|G, 9LMF|1|H, 9LMF|1|I, 9LMF|1|J, 9MEE|1|A, 9MEE|1|B, 9MEE|1|C, 9MEE|1|D, 9MEE|1|E, 9MEE|1|F, 9MEE|1|G, 9MEE|1|H, 9MEE|1|I, 9MEE|1|J, 9MEE|1|K, 9MEE|1|L, 9MEE|1|M, 9MEE|1|N See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 16 4-way junction loop

Column numbers: 319-325, 343-351, 367-371, 405-406 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GGCCGCC*UGAAUGGUG*--U-G*CA    1

    
    Omitted sequenced and counts

    
    UA-----*---------*GAG-U*AA    4

    
    -AGCUUA*U-------U*-C---*--    3

    
    GU-----*---------*UUAGA*UA    3

    
    UA-----*---------*GAA-U*AA    3

    
    GU-----*---------*UUAGG*CA    2

    
    CAC-GUU*---------*UAA-C*GG    1

    
    -AGCUUA*U-------U*-----*-C    1

    
    GU-----*---------*UUAGU*GA    1

    
    GU-----*---------*UUUGU*AA    1

    
    UA----A*UU------U*CU---*-U    1

    
    GU-----*---------*UAG-A*UA    1

    
    UA-----*---------*AAA-U*AA    1

    
    UA-----*---------*GAA-C*GA    1

    
    UA-----*---------*GAG-C*GA    1

    
    UA-----*---------*UAG-U*AA    1

    
    UA-----*---------*UCA-C*GA    1

    
    UA-----*---------*UCA-U*AA    1

    
    UA-----*GA-----AU*A----*-A    1

    
    AAC--CG*U--------*-----*-A    1

    
    ------G*CG------C*GA---*--    1

    
    ------G*UA------C*G----*-A    1

    
    G-----A*UA------G*-----*-A    1

    
    U------*---------*UAA-U*A-    1

    
    UA-----*---------*-----*-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 J4_91813.1

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

0.00 -189.18 11 6

2

Motif group J4_61885.6

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

0.00 -207.48 16 11

3

Motif group J4_59845.1

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

0.00 -223.40 13 8

4

Motif group J4_01665.1

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

0.00 -224.97 15 11

5

Motif group J4_94519.1

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

0.00 -248.00 11 10

tRNA junction

6

Motif group J4_45801.6

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

0.00 -253.56 11 9

7

Motif group J4_75852.1

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

0.00 -289.05 14 9

8

Motif group J4_65285.1

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

0.00 -308.79 16 11

tRNA junction

9

Motif group J4_12410.1

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

0.00 -309.98 15 9

10

Motif group J4_11418.1

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

0.00 -322.25 14 10

11

Motif group J4_47701.1

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

0.00 -330.14 16 11

12

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 -330.28 18 14

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 -341.27 18 14

14

Motif group J4_16596.1

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

0.00 -343.31 13 11

Cobalamin riboswitch junction

15

Motif group J4_80682.1

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

0.00 -346.42 14 11

tRNA junction

16

Motif group J4_44058.1

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

0.00 -349.62 13 11

17

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 -350.42 19 15

18

Motif group J4_88771.1

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

0.00 -357.49 16 11

19

Motif group J4_80390.1

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

0.00 -372.13 14 11

tRNA junction

20

Motif group J4_54165.1

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

0.00 -375.54 16 11

21

Motif group J4_10571.1

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

0.00 -376.13 14 12

22

Motif group J4_35578.3

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

0.00 -383.38 11 12

23

Motif group J4_36296.3

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

0.00 -391.27 15 11

tRNA junction

24

Motif group J4_71729.5

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

0.00 -399.14 14 10

25

Motif group J4_04930.6

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

0.00 -401.85 16 11

26

Motif group J4_40477.1

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

0.00 -402.49 15 12

tRNA junction

27

Motif group J4_59634.1

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

0.00 -405.09 15 13

28

Motif group J4_70449.28

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

0.00 -415.96 11 11

tRNA junction

29

Motif group J4_13620.1

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

0.00 -417.11 18 14

30

Motif group J4_36540.1

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

0.00 -419.57 16 13

31

Motif group J4_89787.1

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

0.00 -420.38 16 14

32

Motif group J4_61477.5

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

0.00 -422.89 17 15

33

Motif group J4_69051.6

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

0.00 -424.36 14 10

34

Motif group J4_48692.1

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

0.00 -425.55 14 11

35

Motif group J4_28426.1

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

0.00 -429.76 18 12

SAM-I/IV riboswitch junction

36

Motif group J4_07509.2

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

0.00 -452.45 18 15

37

Motif group J4_97085.2

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

0.00 -458.58 15 10

38

Motif group J4_77044.4

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

0.00 -470.61 15 12

39

Motif group J4_87855.1

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

0.00 -471.97 18 14

40

Motif group J4_10313.5

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

0.00 -472.94 16 13

41

Motif group J4_95838.1

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

0.00 -496.36 16 11

42

Motif group J4_15241.1

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

0.00 -513.54 22 16

43

Motif group J4_26776.1

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

0.00 -516.65 16 13

44

Motif group J4_63658.1

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

0.00 -519.92 15 13

45

Motif group J4_99897.1

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

0.00 -537.00 17 13

46

Motif group J4_47842.1

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

0.00 -550.15 15 12

47

Motif group J4_28473.1

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

0.00 -556.84 19 12

48

Motif group J4_40439.2

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

0.00 -566.70 15 13

SAM-I riboswitch junction

49

Motif group J4_24220.1

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

0.00 -598.46 17 14

50

Motif group J4_60168.1

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

0.00 -625.44 17 14

51

Motif group J4_72305.5

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

0.00 -625.88 13 12

tRNA junction

52

Motif group J4_65052.1

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

0.00 -629.69 15 11

53

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 -662.69 21 16

RNase P junction

54

Motif group J4_64571.5

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

0.00 -664.95 19 12

55

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 -680.20 19 19

RNase P junction

56

Motif group J4_93343.1

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

0.00 -723.60 15 13

57

Motif group J4_63076.1

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

0.00 -763.02 17 12

class I ligase product junction

58

Motif group J4_46448.1

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

0.00 -771.17 17 12

59

Motif group J4_07491.2

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

0.00 -778.81 12 9

Purine riboswitch junction

60

Motif group J4_69073.1

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

0.00 -817.55 14 12

61

Motif group J4_47478.1

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

0.00 -817.55 14 12

62

Motif group J4_57344.1

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

0.00 -830.44 15 12

63

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 -920.68 33 31

64

Motif group J4_43687.2

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

0.00 -922.20 14 11

65

Motif group J4_65356.1

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

0.00 -927.86 15 11

66

Motif group J4_45582.1

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

0.00 -937.32 16 11

67

Motif group J4_24280.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -984.31 15 12

68

Motif group J4_00691.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -1057.61 16 12

69

Motif group J4_76096.5

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -1204.71 14 13

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