RNA 3D Hub

JAR3D Query RF01446-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01446 small nucleolar RNA snR95

Input Summary

      000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222222222222
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012
........((((((.((((((......(((..(((((....((((((((........)))))))))))))..)))(((((...(((((((........)))))))......))))).............((((............................))))))))))))))))(((((((.........)))))))......................
>AB004535.1_423-644
UUUAACAACCAUGUUCACUUUCCACUUGAGAAGACACAAAAAUUGUCUUGUCGCUUUAGGAUAAUGUGUUGACUCGCAGGAACUAGUUGCAAUGAACGGCGAUUAAAUUGGUCUGUUUUUUUGUUGGUUAAGCAUGGUAGAUAACGUUUGUUCAAACAAUAGCUUAAAGUGACAUGGUUUUGCCUAUGUUUAUGGUAAAAGCAUCGAUAGAGCUGUACAUUU
>AB004534.1_35594-35815
UUUAACAACCAUGUUCACUUUCCACUUGAGAAGACACAAAAAUUGUCUUGUCGCUUUAGGAUAAUGUGUUGACUCGCAGGAACUAGUUGCAAUGAACGGCGAUUAAAUUGGUCUGUUUUUUUGUUGGUUAAGCAUGGUAGAUAACGUUUGUUCAAACAAUAGCUUAAAGUGACAUGGUUUUGCCUAUGUUUAUGGUAAAAGCAUCGAUAGAGCUGUACAUUU

There are no chains in PDB that we map to Rfam family RF01446.

Jump to results for:

  • Loop 1IL Column numbers: 14-16, 171-172
  • Loop 2J4 Column numbers: 21-28, 75-76, 116-130, 165-166
  • Loop 3IL Column numbers: 30-33, 70-73
  • Loop 4IL Column numbers: 37-42, 65-66
  • Loop 5HL Column numbers: 49-58
  • Loop 6IL Column numbers: 80-84, 105-112
  • Loop 7HL Column numbers: 90-99
  • Loop 8HL Column numbers: 133-162
  • Loop 9HL Column numbers: 184-194

Loop 1 Internal loop

Column numbers: 14-16, 171-172 
    Scored sequences and counts

    
    UUC*GA    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_81831.1

Basepair signature:
cWW-L-cWW

100.00 99.28 4 0

Intercalated cWS

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 96.58 2 0

3

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 94.68 2 0

4

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 89.16 1 0

Major groove platform

5

Motif group IL_89505.4

Basepair signature:
cWW-L-cWW

100.00 86.58 0 0

Single bulged U

6

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 84.11 2 0

Single stack bend

7

Motif group IL_51454.3

Basepair signature:
cWW-cSH-cWW

100.00 78.42 1 0

Minor groove platform

8

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 74.72 3 0

Single stack bend

9

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 72.82 3 0

Major groove platform

10

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 66.26 3 1

Multiple bulged bases

Loop 2 4-way junction loop

Column numbers: 21-28, 75-76, 116-130, 165-166 
    Scored sequences and counts

    
    UCCACUUG*CG*UUUUUUUGUUGGUUA*UA    2
No Matches Found View All Results for this Loop

Loop 3 Internal loop

Column numbers: 30-33, 70-73 
    Scored sequences and counts

    
    GAAG*UGAC    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_09705.15

Basepair signature:
cWW-tSH-tHS-cWW

100.00 83.87 0 0

Double sheared

2

Motif group IL_10484.1

Basepair signature:
cWW-tSH-tHS-cWW

100.00 57.78 3 1

Double sheared

3

Motif group IL_84251.1

Basepair signature:
cWW-L-tHS-cWW

100.00 55.65 4 1

4

Motif group IL_80398.1

Basepair signature:
cWW-L-cSW-L-R-cWW

100.00 46.80 2 1

Minor groove platform

5

Motif group IL_48444.6

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

100.00 41.15 3 1

6

Motif group IL_68574.4

Basepair signature:
cWW-tHH-tHS-cWW

100.00 39.04 3 1

7

Motif group IL_85033.2

Basepair signature:
cWW-cWW-cWW-cWW

100.00 30.00 3 1

Tandem non-canonical cWW pairs

8

Motif group IL_25872.4

Basepair signature:
cWW-cWW-cWH-cWW

100.00 24.79 4 1

9

Motif group IL_41344.1

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

100.00 18.54 5 2

10

Motif group IL_23774.1

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

100.00 16.85 3 1

UAA/GAN variation

Loop 4 Internal loop

Column numbers: 37-42, 65-66 
    Scored sequences and counts

    
    CAAAAA*UG    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_46086.1

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

100.00 51.56 2 1

2

Motif group IL_98347.1

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

100.00 38.07 3 1

3

Motif group IL_87211.1

Basepair signature:
cWW-cSW-L-cWW-L

100.00 16.73 3 2

4

Motif group IL_59302.1

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

100.00 7.02 5 2

5

Motif group IL_49714.1

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

100.00 2.14 6 2

Major groove intercalation

Loop 5 Hairpin loop

Column numbers: 49-58 
    Scored sequences and counts

    
    UGUCGCUUUA    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_24792.1

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

100.00 11.91 6 4

2

Motif group HL_08510.1

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

100.00 10.11 3 3

3

Motif group HL_99867.1

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

100.00 7.58 5 3

4

Motif group HL_87463.1

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

100.00 3.00 6 4

5

Motif group HL_73255.1

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

100.00 2.66 5 3

Loop 6 Internal loop

Column numbers: 80-84, 105-112 
    Scored sequences and counts

    
    GAACU*AAAUUGGU    2
No Matches Found View All Results for this Loop

Loop 7 Hairpin loop

Column numbers: 90-99 
    Scored sequences and counts

    
    CAAUGAACGG    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_50779.4

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

100.00 44.39 4 2

2

Motif group HL_93438.2

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

100.00 22.13 4 3

3

Motif group HL_36335.1

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

100.00 10.51 3 3

4

Motif group HL_75293.5

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

100.00 9.86 4 4

Loop 8 Hairpin loop

Column numbers: 133-162 
    Scored sequences and counts

    
    CAUGGUAGAUAACGUUUGUUCAAACAAUAG    2
No Matches Found View All Results for this Loop

Loop 9 Hairpin loop

Column numbers: 184-194 
    Scored sequences and counts

    
    CUAUGUUUAUG    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_93135.1

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

100.00 50.65 2 2

Pseudoknot

2

Motif group HL_99769.3

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

100.00 27.87 5 3

3

Motif group HL_34964.1

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

100.00 17.33 6 4

4

Motif group HL_67079.1

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

100.00 16.24 5 3

5

Motif group HL_98252.1

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

100.00 4.75 5 3

6

Motif group HL_87463.1

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

100.00 4.17 5 3

7

Motif group HL_29762.1

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

100.00 0.05 5 4

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