RNA 3D Hub

JAR3D Query RF01122-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01122 Small nucleolar RNA sR39

Input Summary

      000000000111111111122222222223333333333444444444455555555556
123456789012345678901234567890123456789012345678901234567890
.((((.(((....(((.............(.).....))).....)))))))........
>AJ248284.1_236815-236761
GGCGAUGAAGAAAAUUUCGCUAGCUGAAAAGU-----GAUGAGUACCCUCGCAACUGAGC
>BA000001.2_1411664-1411723
GGUGAUGAGGAAAAUUUCGCUAGCUGAAGUGAAAGAUGAUGAAUACCCUCGCAACCGAGC
>AP006878.1_832424-832370
GGCGAUGACGACAAUUUCGCUAGCUGACCGGU-----GAUGACUACCCUCGCAACCGAGC
>DQ516907.1_5418-5363
GGCGAUGAUGACAAUUUCGCUAUCUGAUUCUG----UGAUGACUACUCCCGCAGCUGAGC
>M97860.2_1902-1843
GGCGAUGAAGAUAAUUUCGCUAGCCGAAAAAUAAGAUGAGGAGUACCCUCGCAACUGAGC

There are no chains in PDB that we map to Rfam family RF01122.

Jump to results for:

  • Loop 1IL Column numbers: 5-7, 48-49
  • Loop 2IL Column numbers: 9-14, 40-46
  • Loop 3IL Column numbers: 16-30, 32-38
  • Loop 4HL Column numbers: 30-32

Loop 1 Internal loop

Column numbers: 5-7, 48-49 
    Scored sequences and counts

    
    AUG*CU    4

    
    AUG*CC    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_81831.1

Basepair signature:
cWW-L-cWW

100.00 94.40 3 0

Intercalated cWS

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 92.24 3 0

3

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 86.91 0 0

Single stack bend

4

Motif group IL_89505.4

Basepair signature:
cWW-L-cWW

100.00 85.47 0 0

Single bulged U

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 76.52 4 0

6

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 74.16 1 0

Single stack bend

7

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 67.22 3 0

Major groove platform

8

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 60.68 3 1

Multiple bulged bases

9

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 55.54 1 1

Major groove intercalation

10

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 45.32 3 0

Major groove platform

Loop 2 Internal loop

Column numbers: 9-14, 40-46 
    Scored sequences and counts

    
    AGAAAA*UGAGUAC    1

    
    AGAUAA*GGAGUAC    1

    
    CGACAA*UGACUAC    1

    
    GGAAAA*UGAAUAC    1

    
    UGACAA*UGACUAC    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 53.81 3 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

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

40.00 10.91 5 3

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

3

Motif group IL_41756.4

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

40.00 5.64 5 2

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

4

Motif group IL_02349.4

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

40.00 -5.28 6 3

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

5

Motif group IL_29198.2

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

40.00 -6.25 7 3

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

6

Motif group IL_47346.2

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

40.00 -20.76 7 3

tSH-tSH-tHH-tHS

7

Motif group IL_09044.1

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

20.00 -9.95 4 3

8

Motif group IL_04736.1

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

20.00 -12.42 7 4

9

Motif group IL_87284.1

Basepair signature:
cWW-tSH-tHW-tWH-tHS-cWW

20.00 -13.49 6 3

tSH-tHW-tWH-tHS

10

Motif group IL_61286.1

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

20.00 -22.61 7 4

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

Loop 3 Internal loop

Column numbers: 16-30, 32-38 
    Scored sequences and counts

    
    UUCGCUAGCCGAAAA*UAAGAUG    1

    
    UUCGCUAGCUGAAGU*AAAGAUG    1

    
    UUCGCUAUCUGAUUC*G----UG    1

    
    UUCGCUAGCUGAAAA*U-----G    1

    
    UUCGCUAGCUGACCG*U-----G    1
No Matches Found View All Results for this Loop

Loop 4 Hairpin loop

Column numbers: 30-32 
    Scored sequences and counts

    
    AAU    1

    
    AGU    1

    
    CUG    1

    
    GGU    1

    
    UGA    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_32346.4

Basepair signature:
cWW-F

20.00 -5.70 2 1

2

Motif group HL_78677.1

Basepair signature:
cWW-F-F

20.00 -6.88 3 2

3

Motif group HL_70782.2

Basepair signature:
cWW-F

20.00 -18.37 3 3

4

Motif group HL_48778.2

Basepair signature:
cWW-F

20.00 -19.23 2 1

Mini UNCG

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