RNA 3D Hub

JAR3D Query RF02014-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam 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: 3-8, 32-36
  • Loop 2HL Column numbers: 11-29
  • Loop 3HL Column numbers: 43-50
  • Loop 4IL Column numbers: 60-64, 80-84
  • Loop 5HL Column numbers: 69-75

Loop 1 Internal loop

Column numbers: 3-8, 32-36 
    Scored sequences and counts

    
    GUUGGC*GGGUC    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_94351.1

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

100.00 20.03 6 2

2

Motif group IL_73759.1

Basepair signature:
cWW-cSH-tHS-cWH-cHW-cWW

100.00 14.57 4 2

Part of G-quadruplex

Loop 2 Hairpin loop

Column numbers: 11-29 
    Scored sequences and counts

    
    GCAGAGGAAGGGAAGGGUC    3
No Matches Found View All Results for this Loop

Loop 3 Hairpin loop

Column numbers: 43-50 
    Scored sequences and counts

    
    GCAUGCCC    3
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# 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

Loop 4 Internal loop

Column numbers: 60-64, 80-84 
    Scored sequences and counts

    
    UCACU*GUCAG    3
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# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_70411.2

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

100.00 25.25 3 1

Loop 5 Hairpin loop

Column numbers: 69-75 
    Scored sequences and counts

    
    UUCCCUA    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_30680.3

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

100.00 35.05 3 1

Pseudoknot geometry

2

Motif group HL_66103.1

Basepair signature:
cWW-F-F

100.00 29.32 4 2

3

Motif group HL_13529.1

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

100.00 17.45 3 2

4

Motif group HL_65794.5

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

100.00 12.21 2 1

Pseudoknot geometry

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