RNA 3D Hub

JAR3D Query RF02014-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF02014 mir-1178 microRNA precursor family

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901
..((((.((((((.....(((((((((....((((.(.(((((......))))).).))))....)))))))))....)))))).))))..
>URS000075A3D7_9598/1-90
GGGUUGGCUGGCAGAGGAAGGGAAGGGUCCGGGGUCGGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUG-
>URS0000CCB0D3_9600/1-89
--GUUGGCUGGCAGAGGAAGGGAAGGGUCCGGGGUCGGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUGU
>URS000075AF6E_9606/1-91
GCGUUGGCUGGCAGAGGAAGGGAAGGGUCCAGGGUCAGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUGU

There are no chains in PDB that we map to Rfam family RF02014.

Jump to results for:

  • Loop 1IL Column numbers: 6-8, 84-86
  • Loop 2IL Column numbers: 13-19, 74-79
  • Loop 3IL Column numbers: 27-32, 61-66
  • Loop 4IL Column numbers: 35-37, 56-58
  • Loop 5IL Column numbers: 37-39, 54-56
  • Loop 6HL Column numbers: 43-50

Loop 1 Internal loop

Column numbers: 6-8, 84-86 
    Scored sequences and counts

    
    GGC*GGU    3
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_44465.1

Basepair signature:
cWW-L-R-cWW

100.00 75.70 3 0

Isolated non-canonical cWW contact

2

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 71.44 1 0

Isolated cWH basepair

3

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 47.63 1 0

Isolated non-canonical cWW pair

4

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 14.72 3 1

Isolated cWS basepair

Loop 2 Internal loop

Column numbers: 13-19, 74-79 
    Scored sequences and counts

    
    AGAGGAA*UAGAAU    3
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 42.63 5 2

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_42778.1

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

100.00 8.50 7 3

3

Motif group IL_47346.2

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

100.00 1.75 7 3

tSH-tSH-tHH-tHS

Loop 3 Internal loop

Column numbers: 27-32, 61-66 
    Scored sequences and counts

    
    GUCCGG*CACUGU    2

    
    GUCCAG*CACUGU    1
No Matches Found View All Results for this Loop

Loop 4 Internal loop

Column numbers: 35-37, 56-58 
    Scored sequences and counts

    
    UCG*UUG    2

    
    UCA*UUG    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_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 75.90 4 0

Isolated non-canonical cWW pair

2

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 75.50 1 0

Isolated non-canonical cWW pair

3

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 58.76 3 0

4

Motif group IL_10796.1

Basepair signature:
cWW-L-R-cWW

100.00 52.04 1 1

5

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 37.31 2 0

Isolated non-canonical cWW pair

6

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 35.07 2 0

Isolated cWH basepair

7

Motif group IL_28037.2

Basepair signature:
cWW-cWW-cWW

100.00 28.13 2 0

Isolated non-canonical cWW pair

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 20.90 3 1

Stack and bulge

9

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 14.98 3 1

Multiple bulged bases

10

Motif group IL_85599.2

Basepair signature:
cWW-tHS-cWW

100.00 9.43 3 2

Isolated tHS basepair with bulges

Loop 5 Internal loop

Column numbers: 37-39, 54-56 
    Scored sequences and counts

    
    GGC*GGU    2

    
    AGC*GGU    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_44465.1

Basepair signature:
cWW-L-R-cWW

100.00 82.53 3 0

Isolated non-canonical cWW contact

2

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 77.74 1 0

Isolated cWH basepair

3

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 52.06 1 0

Isolated non-canonical cWW pair

4

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 21.94 3 1

Isolated cWS basepair

5

Motif group IL_99358.1

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

33.33 5.66 2 1

6

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

33.33 2.51 3 1

Isolated non-canonical cWW pair

7

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

33.33 2.18 5 2

8

Motif group IL_67095.2

Basepair signature:
cWW-tWW-cWW

33.33 1.30 5 2

Isolated tWW turn

Loop 6 Hairpin loop

Column numbers: 43-50 
    Scored sequences and counts

    
    GCAUGCCC    3
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_37344.1

Basepair signature:
cWW-F-F

100.00 11.69 4 2

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