RNA 3D Hub

JAR3D Query RF02686-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF02686 RAGATH-6 RNA

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012
.........((.(.....(........)....))).............(((((....)))))...............(((((((((((((((.((((((.....)))........(((((......)))))))))))))))))))))))...
>BABB01003568.1/701-850
AUCUGUUUAGCCAUAGCAA-UAUCGU-UGAAAUGCAAAUCAUCUACUUAUGUCGUGAGACAUUAUUUAACCACGUUAAAGUAUAAUAAUAUAAGUUAGGUAUGCCCUUAUAAAGACUUAGGUAACGCUAAGGACUAUAUUAUUAUACUUCUU
>BAAZ01000382.1/2451-2601
AAUUCAUUCGC-AAAGUAAUUAUUCUAUGAAAUGCAAAUUAUCUUCAUAUGUUGUGAAACAUAGCUUAACCACGUUAAAGUAUAAUAAUAUAAGUUAGGUAUGCCCUUAUAAAGACUUAGGUAGCGCUAAGGACUAUAUUAUUAUACUUCUU

There are no chains in PDB that we map to Rfam family RF02686.

Jump to results for:

  • Loop 1IL Column numbers: 11-13, 33-34
  • Loop 2IL Column numbers: 13-19, 28-33
  • Loop 3HL Column numbers: 19-28
  • Loop 4HL Column numbers: 53-58
  • Loop 5IL Column numbers: 92-94, 134-135
  • Loop 6J3 Column numbers: 96-97, 107-116, 131-132
  • Loop 7HL Column numbers: 99-105
  • Loop 8HL Column numbers: 120-127

Loop 1 Internal loop

Column numbers: 11-13, 33-34 
    Scored sequences and counts

    
    CCA*UG    1

    
    C-A*UG    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 52.39 2.5 0.5

Single stack bend

2

Motif group IL_61258.15

Basepair signature:
cWW-L-cWW

100.00 47.43 0.5 0.5

Single bulged C

3

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 43.60 1 0.5

Single stack bend

4

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 39.79 2 0.5

Major groove platform

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 39.35 3 1

Intercalated cWS

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 37.74 3 1

7

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 37.33 1 1

Multiple bulged bases

8

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

100.00 28.31 3 1

9

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 26.44 3 1

Major groove intercalation

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 22.98 2.5 1

Loop 2 Internal loop

Column numbers: 13-19, 28-33 
    Scored sequences and counts

    
    AAAGUAA*UGAAAU    1

    
    AUAGCAA*UGAAAU    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 62.68 3 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

100.00 27.30 6 2.5

8x6 Sarcin-Ricin with inserted A; G-bulge

3

Motif group IL_24254.1

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

100.00 26.17 6 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

4

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

100.00 25.86 6.5 2.5

tSH-tSH-tHH-tHS

5

Motif group IL_32016.1

Basepair signature:
cWW-tSH-tSH-tSS-tHS-L-R-cWW

100.00 7.52 6 3.5

Kink-turn

6

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

50.00 3.14 5.5 2.5

8x6 Sarcin-Ricin with inserted Y; G-bulge

7

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

50.00 -7.34 2.5 2.5

8x7 Sarcin-Ricin; G-bulge

8

Motif group IL_16458.4

Basepair signature:
cWW-L-R-L-R-cSH-tWH-tHS-cWW

50.00 -9.26 5.5 3

Sarcin-Ricin target in LSU H95; G-bulge

9

Motif group IL_88116.2

Basepair signature:
cWW-tSH-L-R-L-R-L-R-cWW-cWW

50.00 -12.27 5.5 3.5

10

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

50.00 -15.79 5 3.5

7x7 Sarcin-Ricin with intercalated A; G-bulge

Loop 3 Hairpin loop

Column numbers: 19-28 
    Scored sequences and counts

    
    AUUAUUCUAU    1

    
    A-UAUCGU-U    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_28075.1

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

50.00 1.06 3 2

2

Motif group HL_78197.1

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

50.00 -1.81 3.5 2

3

Motif group HL_98252.1

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

50.00 -14.58 4 4

4

Motif group HL_85434.1

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

50.00 -18.12 5.5 3.5

5

Motif group HL_26934.1

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

50.00 -22.36 5 3

6

Motif group HL_83808.4

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

50.00 -24.80 6 4

Pseudoknot

7

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

50.00 -24.92 3.5 1.5

T-loop with unstacked turn

8

Motif group HL_93135.1

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

50.00 -43.74 5 4

Pseudoknot

9

Motif group HL_50006.2

Basepair signature:
cWW-F-F

50.00 -48.37 5 3

10

Motif group HL_66103.1

Basepair signature:
cWW-F-F

50.00 -103.61 5 3

Loop 4 Hairpin loop

Column numbers: 53-58 
    Scored sequences and counts

    
    CGUGAG    1

    
    UGUGAA    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_52953.3

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

100.00 89.10 1 0

2

Motif group HL_13963.3

Basepair signature:
cWW-F-F

100.00 66.20 3 1

3

Motif group HL_37824.7

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

100.00 59.84 0 0

GNRA

4

Motif group HL_93535.1

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

100.00 58.84 1.5 1

5

Motif group HL_59843.1

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

100.00 51.48 2 1

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

100.00 48.79 2 1

7

Motif group HL_56676.1

Basepair signature:
cWW-F-F

100.00 45.93 2 1

8

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

100.00 44.40 1 0

UNCG

9

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

100.00 43.71 1.5 1

10

Motif group HL_75660.5

Basepair signature:
cWW-F

100.00 39.30 2.5 1

Loop 5 Internal loop

Column numbers: 92-94, 134-135 
    Scored sequences and counts

    
    AAG*CU    2
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

100.00 99.99 2 0

2

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 99.95 0 0

Single stack bend

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 97.40 2 0

Multiple bulged bases

4

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 96.04 0 0

Single stack bend

5

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 91.71 0 0

Single bulged A

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 89.14 1 0

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 86.40 4 0

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 84.50 0 0

Stack and bulge

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 77.56 2 0

Major groove platform

10

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 75.31 3 0

Major groove platform

Loop 6 3-way junction loop

Column numbers: 96-97, 107-116, 131-132 
    Scored sequences and counts

    
    UA*UUAUAAAGAC*GG    2
No Matches Found View All Results for this Loop

Loop 7 Hairpin loop

Column numbers: 99-105 
    Scored sequences and counts

    
    GUAUGCC    2
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

100.00 23.71 3 1

2

Motif group HL_67667.2

Basepair signature:
cWW-F-F

100.00 5.88 4 2

3

Motif group HL_50006.2

Basepair signature:
cWW-F-F

100.00 2.52 4 3

4

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

100.00 2.27 3 2

5

Motif group HL_30068.2

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

100.00 1.64 4 2

Loop 8 Hairpin loop

Column numbers: 120-127 
    Scored sequences and counts

    
    GGUAACGC    1

    
    GGUAGCGC    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_81538.2

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

100.00 58.01 1 1

GNRA with tandem sheared

2

Motif group HL_84299.4

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

100.00 51.61 1.5 1.5

3

Motif group HL_93324.4

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

100.00 42.70 2.5 1.5

Pseudoknot geometry

4

Motif group HL_25061.1

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

50.00 10.67 4.5 2.5

5

Motif group HL_77436.5

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

50.00 9.19 1.5 1.5

T-loop related

6

Motif group HL_78197.1

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

50.00 6.19 2.5 2.5

7

Motif group HL_20167.2

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

50.00 -1.31 2 2

8

Motif group HL_77600.2

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

50.00 -9.78 2.5 1.5

9

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

50.00 -11.88 4.5 3.5

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