RNA 3D Hub

JAR3D Query RF02686-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam 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 1HL Column numbers: 8-14
  • Loop 2IL Column numbers: 29-33, 56-60
  • Loop 3HL Column numbers: 37-52
  • Loop 4J3 Column numbers: 92-97, 107-116, 131-135
  • Loop 5HL Column numbers: 99-105
  • Loop 6HL Column numbers: 120-127

Loop 1 Hairpin loop

Column numbers: 8-14 
    Scored sequences and counts

    
    UAGCCAU    1

    
    UCGC-AA    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_93535.1

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

100.00 15.76 3 1.5

2

Motif group HL_13963.3

Basepair signature:
cWW-F-F

50.00 -0.13 4 2

3

Motif group HL_70782.2

Basepair signature:
cWW-F

50.00 -9.56 4 2

4

Motif group HL_56131.2

Basepair signature:
cWW-F-F

50.00 -10.44 3 2.5

5

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

50.00 -34.49 4.5 2.5

6

Motif group HL_13189.1

Basepair signature:
cWW-F-F

50.00 -37.75 3 2.5

7

Motif group HL_22135.1

Basepair signature:
cWW-F-F

50.00 -39.03 2 1.5

8

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

50.00 -40.63 3.5 2.5

9

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

50.00 -45.70 2.5 2

10

Motif group HL_99040.1

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

50.00 -45.89 3.5 2.5

Loop 2 Internal loop

Column numbers: 29-33, 56-60 
    Scored sequences and counts

    
    GAAAU*GAAAC    1

    
    GAAAU*GAGAC    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_63519.1

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

100.00 0.64 4 3

2

Motif group IL_17948.2

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

50.00 6.06 2.5 1.5

Double sheared with non-canonical cWW

3

Motif group IL_61440.1

Basepair signature:
cWW-tSH-tHS-tWS-cWW

50.00 3.08 6.5 2.5

Triple sheared

4

Motif group IL_21667.1

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

50.00 1.99 5.5 2.5

5

Motif group IL_01038.1

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

50.00 -7.00 3.5 2.5

UAA/GAN with extra stack

6

Motif group IL_62654.1

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

50.00 -11.42 5 3.5

tSH-tHH-tHS

7

Motif group IL_66798.2

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

50.00 -25.15 5.5 2.5

AAA cross-strand stack

Loop 3 Hairpin loop

Column numbers: 37-52 
    Scored sequences and counts

    
    AAUCAUCUACUUAUGU    1

    
    AAUUAUCUUCAUAUGU    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_88364.2

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

50.00 -17.61 6.5 4.5

Loop 4 3-way junction loop

Column numbers: 92-97, 107-116, 131-135 
    Scored sequences and counts

    
    AAGUUA*UUAUAAAGAC*GGACU    2
No Matches Found View All Results for this Loop

Loop 5 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 6 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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