RNA 3D Hub

JAR3D Query RF02265-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF02265 MAT2A 3'UTR stem loop F

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666
1234567890123456789012345678901234567890123456789012345678901234567
(((((((.((.((.(((..(((((((((...))......))))))).))).....)))).)))))))
>AY603043.1/620-685
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>ABRT010239600.1/5971-6036
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAAAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAIY01292066.1/5286-5350
CAUGGAG-AG-GCUGACUUGGCCGGUGUGCUACAGAGAAGCCAGCUUGUUGACAUGCUCCUCCAUUG
>BC001686.2/2616-2681
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAYZ01081944.1/5969-6034
CAUGGAGGAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC062394.1/3163-3228
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BT030708.1/2625-2690
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAPN01391386.1/6556-6622
CGUGGGGAGACGCUGACUUGGCUGGUGUUGUACAGAGAAGCCAGCUUGUUUACAGGCUCAUCCCAUG
>AALT01193755.1/758-823
CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC016753.9/112052-112117
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC116115.11/197073-197008
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AANN01466464.1/6628-6693
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUGCUCCAUG
>AAFR03050370.1/29132-29197
CAUGGAGGAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCCUACUCCAUG
>AC190303.9/101604-101539
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC001854.2/2616-2681
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC154002.8/25257-25192
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC058360.1/3179-3244
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AK054569.1/1861-1796
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC207174.3/18990-19055
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAQQ01101557.1/1002-938
CGUGGAGAGA-GCGGACUUGGCUGGCGUGGUACAGAGAAGCCAGCUUGUUUACAUGC-UACUCCAUG
>ABBA01166058.1/319-254
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>L43509.1/2508-2573
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AB168627.1/1740-1805
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>ABRP01178872.1/23996-23931
CAUGGAAAAA-GCAGACCUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUUCAUG
>AAGW02007302.1/51363-51428
CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUCAUCCAUG
>AAWZ02030028.1/3579-3514
CCUGGGAGGG-GCUGACUUGGCCGGUGUGGUACAGAGAAGCCGGCUUGUUUACUUACCCGUCCCACG

There are no chains in PDB that we map to Rfam family RF02265.

Jump to results for:

  • Loop 1IL Column numbers: 7-9, 59-61
  • Loop 2IL Column numbers: 10-12, 57-58
  • Loop 3IL Column numbers: 13-15, 50-56
  • Loop 4IL Column numbers: 17-20, 46-48
  • Loop 5IL Column numbers: 26-27, 33-40
  • Loop 6HL Column numbers: 28-32

Loop 1 Internal loop

Column numbers: 7-9, 59-61 
    Scored sequences and counts

    
    GAA*UAU   17

    
    AAA*UAU    1

    
    AGG*CGU    1

    
    GAA*UCA    1

    
    GAA*UGC    1

    
    GAG*CAU    1

    
    GAG*UAC    1

    
    GGA*UAC    1

    
    GGA*UAU    1

    
    G-A*CCU    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_57744.1

Basepair signature:
cWW-cWW-cWW

96.15 56.82 1 0

Isolated non-canonical cWW pair

2

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

96.15 53.52 3 0

Isolated cWS basepair

3

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

96.15 48.12 2 0

Isolated non-canonical cWW pair

4

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

92.31 69.87 2 0

Stack and bulge

5

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

92.31 45.81 3 1

6

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

92.31 42.74 3 1

Isolated non-canonical cWW pair

7

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

92.31 30.32 3 0

Isolated cWH basepair

8

Motif group IL_44465.1

Basepair signature:
cWW-L-R-cWW

92.31 10.61 3 1

Isolated non-canonical cWW contact

9

Motif group IL_67095.2

Basepair signature:
cWW-tWW-cWW

88.46 23.53 2 1

Isolated tWW turn

10

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

88.46 6.75 3 1

Isolated non-canonical cWW pair

Loop 2 Internal loop

Column numbers: 10-12, 57-58 
    Scored sequences and counts

    
    A-G*CU   21

    
    ACG*CU    1

    
    A-G*CC    1

    
    G-G*CC    1

    
    G-G*CU    1

    
    Omitted sequenced and counts

    
    A-G*C-    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_07039.3

Basepair signature:
cWW-L-cWW

100.00 18.21 3 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

96.00 29.95 2 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

96.00 23.08 2 1

Multiple bulged bases

4

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

96.00 22.02 3 1

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

96.00 21.89 3 1

Intercalated cWS

6

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

96.00 4.23 1 1

Single bulged G

7

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

92.00 19.41 1 1

Single stack bend

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

92.00 16.96 2 1

Major groove intercalation

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

92.00 16.34 1 1

Single stack bend

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

92.00 12.65 3 1

Loop 3 Internal loop

Column numbers: 13-15, 50-56 
    Scored sequences and counts

    
    CUG*UUACAUG   18

    
    CGG*UUACAUG    4

    
    CAG*UUACAUG    1

    
    CUG*UGACAUG    1

    
    CUG*UUACAGG    1

    
    CUG*UUACUUA    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_43622.1

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

3.85 -18.19 5 2

2

Motif group IL_74957.1

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

3.85 -20.46 6 4

cWH basepair with bulged bases

Loop 4 Internal loop

Column numbers: 17-20, 46-48 
    Scored sequences and counts

    
    CUUG*UUG   25

    
    CCUG*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_51387.2

Basepair signature:
cWW-cSH-cWW-cWW

100.00 65.10 3 0

2

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 54.67 1 0

Isolated non-canonical cWW pair

3

Motif group IL_99358.1

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

100.00 43.10 3 1

4

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 10.01 3 1

Stack and bulge

5

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

96.15 11.16 3 1

Isolated non-canonical cWW pair

6

Motif group IL_92446.2

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

96.15 3.01 4 1

7

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

3.85 -3.48 5 2

Isolated non-canonical cWW pair

8

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

3.85 -18.37 3 2

9

Motif group IL_41344.1

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

3.85 -29.27 4 2

Loop 5 Internal loop

Column numbers: 26-27, 33-40 
    Scored sequences and counts

    
    UG*CAGAGAAG   24

    
    CG*CAGAGAAG    1

    
    UG*CAGAAAAG    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_38394.1

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

100.00 46.04 2 1

2

Motif group IL_46086.1

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

96.15 5.21 2 2

3

Motif group IL_82968.1

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

3.85 -12.98 5 3

Loop 6 Hairpin loop

Column numbers: 28-32 
    Scored sequences and counts

    
    UGGUA   24

    
    UGCUA    1

    
    UUGUA    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_56334.1

Basepair signature:
cWW-F

100.00 60.27 2 1

Mini UNCG

2

Motif group HL_56131.2

Basepair signature:
cWW-F-F

100.00 54.71 2 1

3

Motif group HL_48417.5

Basepair signature:
cWW-F-F

100.00 50.47 2 1

4

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

100.00 48.28 3 1

5

Motif group HL_75660.5

Basepair signature:
cWW-F

100.00 48.20 2 1

6

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

100.00 41.86 1 1

tRNA D-loop

7

Motif group HL_32346.4

Basepair signature:
cWW-F

100.00 39.63 2 1

8

Motif group HL_81100.2

Basepair signature:
cWW

100.00 37.15 3 1

9

Motif group HL_13189.1

Basepair signature:
cWW-F-F

100.00 32.44 2 2

10

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

100.00 19.97 3 2

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