RNA 3D Hub

JAR3D Query RF03393-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF03393 mir-2849 microRNA precursor family

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567
.....(((((.((((((((.((((((..((.((((((.((((((.....))))))...))))))))..))))))))...))))))..))))).....
>URS0000D54F43_7091/1-97
GUGGACGUUUAACUUUACGAUUAUGGACUCAGUUCCAAAAGAUAACUGGUGUUUUAUGUGGGACGAAACCGUGGCGGGUUGAGGUGGAAAUGAAAUG
>URS000075C6E5_7091/1-97
GUGGACGUUUAACUUUACGAUUAUGGACUCAGUUCCAAAAGAUAACUGAUGUUUUAUGUGGGACGAAACCAUGGCGGGUUGAGGUGGAAAUGAAAUG
>URS000075BC3C_7091/1-97
GUGGACGUUUAACUUUACGAUUAUGGACUCAGUUCCAAAAGAUAGCUGGUGUCUUAUGUGGGACGAAACCGUGGCGGGUUGAGGUGGAAAUGAAAUG

There are no chains in PDB that we map to Rfam family RF03393.

Jump to results for:

  • Loop 1IL Column numbers: 10-12, 85-88
  • Loop 2IL Column numbers: 17-18, 76-80
  • Loop 3IL Column numbers: 19-21, 74-75
  • Loop 4IL Column numbers: 26-29, 66-69
  • Loop 5IL Column numbers: 30-32, 64-65
  • Loop 6IL Column numbers: 37-39, 55-59
  • Loop 7HL Column numbers: 44-50

Loop 1 Internal loop

Column numbers: 10-12, 85-88 
    Scored sequences and counts

    
    UAA*UGGA    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_85599.2

Basepair signature:
cWW-tHS-cWW

100.00 88.18 2 0

Isolated tHS basepair with bulges

2

Motif group IL_96371.1

Basepair signature:
cWW-tHH-cWW

100.00 84.85 3 0

3

Motif group IL_55516.2

Basepair signature:
cWW-cWW-cSH-cWW

100.00 62.32 3 0

4

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

100.00 49.49 2 1

Isolated non-canonical cWW pair

5

Motif group IL_41344.1

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

100.00 23.70 4 2

6

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 16.04 1 1

Isolated non-canonical cWW pair

7

Motif group IL_61476.2

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

100.00 15.73 3 1

8

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 15.24 3 0

Isolated non-canonical cWW pair

9

Motif group IL_19668.1

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

100.00 12.49 5 2

Isolated non-canonical cWW pair

10

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 12.39 5 2

Isolated non-canonical cWW pair

Loop 2 Internal loop

Column numbers: 17-18, 76-80 
    Scored sequences and counts

    
    AC*GGGUU    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_20031.1

Basepair signature:
cWW-L-cWW-L

100.00 68.42 3 1

2

Motif group IL_29346.2

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

100.00 52.58 3 1

Left turn

3

Motif group IL_70376.1

Basepair signature:
cWW-L-cWW-L

100.00 40.27 5 1

4

Motif group IL_07171.1

Basepair signature:
cWW-L-cWW-L

100.00 39.08 5 1

Bulged stacked bases

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 25.40 2 1

Major groove intercalation

6

Motif group IL_94967.1

Basepair signature:
cWW-L-cWW-L

100.00 12.84 4 2

7

Motif group IL_92634.2

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

100.00 3.74 4 2

Loop 3 Internal loop

Column numbers: 19-21, 74-75 
    Scored sequences and counts

    
    GAU*GC    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_26793.1

Basepair signature:
cWW-L-cWW

100.00 76.63 2 0

Single stack bend

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 73.68 4 0

Multiple bulged bases

3

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 73.42 0 0

Single bulged A

4

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 71.97 1 0

Single stack bend

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 67.65 2 0

Major groove intercalation

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 66.02 2 0

7

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 62.86 3 0

Stack and bulge

8

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 58.45 3 0

Major groove platform

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 56.10 1 0

Major groove platform

10

Motif group IL_51454.3

Basepair signature:
cWW-cSH-cWW

100.00 49.74 1 0

Minor groove platform

Loop 4 Internal loop

Column numbers: 26-29, 66-69 
    Scored sequences and counts

    
    GACU*AAAC    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_80398.1

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

100.00 58.94 3 1

Minor groove platform

2

Motif group IL_09705.15

Basepair signature:
cWW-tSH-tHS-cWW

100.00 44.98 3 1

Double sheared

3

Motif group IL_85033.2

Basepair signature:
cWW-cWW-cWW-cWW

100.00 35.55 3 1

Tandem non-canonical cWW pairs

4

Motif group IL_64231.5

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

100.00 24.58 4 1

5

Motif group IL_51479.1

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

100.00 23.36 4 2

6

Motif group IL_68574.4

Basepair signature:
cWW-tHH-tHS-cWW

100.00 22.54 5 1

7

Motif group IL_84251.1

Basepair signature:
cWW-L-tHS-cWW

100.00 21.95 6 2

8

Motif group IL_48444.6

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

100.00 20.18 5 2

9

Motif group IL_91920.1

Basepair signature:
cWW-cWW-tHH-cWW

100.00 16.30 6 2

10

Motif group IL_62012.1

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

100.00 13.00 4 2

Decoding loop related

Loop 5 Internal loop

Column numbers: 30-32, 64-65 
    Scored sequences and counts

    
    CAG*CG    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_10569.1

Basepair signature:
cWW-L-cWW

100.00 100.00 0 0

2

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 100.00 1 0

Single stack bend

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 97.98 0 0

Multiple bulged bases

4

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 97.32 1 0

Single stack bend

5

Motif group IL_51454.3

Basepair signature:
cWW-cSH-cWW

100.00 96.97 0 0

Minor groove platform

6

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 96.33 0 0

Single bulged A

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 89.28 2 0

Major groove intercalation

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 87.46 2 0

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 86.02 2 0

Stack and bulge

10

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 85.21 0 0

Major groove platform

Loop 6 Internal loop

Column numbers: 37-39, 55-59 
    Scored sequences and counts

    
    AAA*UAUGU    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_90351.1

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

100.00 67.91 4 0

2

Motif group IL_19668.1

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

100.00 44.15 5 1

Isolated non-canonical cWW pair

3

Motif group IL_19102.1

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

100.00 39.84 3 2

4

Motif group IL_61476.2

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

100.00 35.33 4 1

5

Motif group IL_10389.1

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

100.00 25.21 6 2

6

Motif group IL_47972.1

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

100.00 20.09 5 2

7

Motif group IL_44325.1

Basepair signature:
cWW-cWH-cWW-L

100.00 18.28 6 2

8

Motif group IL_42314.1

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

100.00 13.72 5 3

9

Motif group IL_51191.1

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

100.00 8.93 4 2

10

Motif group IL_36516.3

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

100.00 8.89 4 2

Loop 7 Hairpin loop

Column numbers: 44-50 
    Scored sequences and counts

    
    AACUGAU    1

    
    AACUGGU    1

    
    AGCUGGU    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_30680.3

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

100.00 66.92 3 1

Pseudoknot geometry

2

Motif group HL_48417.5

Basepair signature:
cWW-F-F

66.67 3.53 3 2

3

Motif group HL_13963.3

Basepair signature:
cWW-F-F

33.33 -12.70 4 2

4

Motif group HL_20535.2

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

33.33 -12.90 5 3

5

Motif group HL_42046.2

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

33.33 -13.11 4 2

6

Motif group HL_56131.2

Basepair signature:
cWW-F-F

33.33 -15.45 4 2

7

Motif group HL_13189.1

Basepair signature:
cWW-F-F

33.33 -15.93 4 2

8

Motif group HL_37344.1

Basepair signature:
cWW-F-F

33.33 -18.22 5 3

9

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

33.33 -26.29 4 2

10

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

33.33 -27.66 3 2

Pseudoknot geometry with 3' bulge

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