RNA 3D Hub

JAR3D Query RF03081-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF03081 DUF805 RNA

Input Summary

      00000000011111111112222222222333333333344444444445555555555666666666677777
12345678901234567890123456789012345678901234567890123456789012345678901234
.....((((...........))))..............(((............)))..................
>URS0000D66257_12908/1-68
UGGAAGUAGAGACCAGU-AACUACUCAA--AUAAACG-GGUAUAACU-AAAAAACCUUAAGAGUA-AGGUGUAA
>URS0000D67100_12908/1-71
UAAUAGCUGAGUCCAGA-CACAUCUACAAAAAAAACGGGGCGUUACU-GCGAAGCCAUAUUAGUA-UUAUAAUA
>URS0000D6BCA4_525257/1-65
CUUUCAUGGAGUUAAGA-AACCACGU------AAACAAAGCGGAACC-GAAAAGCUAAACGAGUA-GGAAGAAU
>URS0000D69842_12908/1-69
UAAAAAAGGAGUCUAAG-AACCUUUCAA--AAAAAUAAGGCGGAACC-GAAAAGCCAAAUGAGUA-GGAUAUUU
>URS0000D67912_12908/1-69
AAAGUUUAGAGUCAAGAAAACUAAUUAA---AAAACAGGGAGUUUCC-GAAAAUCCAUAAGAGUA-GGAUAAAC
>URS0000D6965A_12908/1-69
UCUCCGUGAAGACCAGC-CCCCACGUA----AAAACGGGGCGUGACCCGAAAAGCCUGACGAGUAGGGACUUAA
>URS0000D6572A_12908/1-69
UAAUUGUAGAGACAAGG-AACUACAUGA--AAACACGGGGCGUUUCU-GAAAAGCCAAAUGAGUA-AGAGAAAA
>URS0000D6A9D5_12908/1-65
GGGCAAUGGAG--CAGA-UACCAUUUGA---AAAACG-GGCGAGUUC-GAAAAGCCAGAGGAGUA-GAGGAAAU
>URS0000D6BEA4_12908/1-67
GGGCAAUGGAAGACCGA-GACCAUUUU----AAAACGUGGCGAGUUC-GAAAAGCCUUAUGAGUA-GAGGAAAC
>URS0000D6A1C4_12908/1-69
AGAAAGUGGAGAAAAGA-AACCACAAA----AAAACUGGGUGUAUUCCGAAAGACCAUAAGAGUAGGAACAAAC
>URS0000D68C4F_12908/1-70
UUCACGUUGAGACCAGA-AACAACUUUA---AAAACUGAGAGUAUUCUGAAAAUCUUUAAGAGUAAGAACAAAA
>URS0000D6AB9B_12908/1-68
AAACAGUGGAGACCAGC-GACCACUUUA--A-AAGCGGGGUGACACU-GAAAUGCCAUAACAGUA-GGGGAAAU
>URS0000D65E8C_411154/1-66
CGUCUUUGGAGUCCAGU-GACCAUUUU-----AAACGGGGCGUAACC-GAAAAGCCUUAUGAGUA-GGAGUAUA
>URS0000D65AA5_12908/1-68
CUUAUGUGGAGUCCAGC-CACCACACCA---AAAACGGGGCGUCACC-GAAAAGCCAGAUGAGUA-GGACCAUC
>URS0000D6D1D2_382245/1-71
CCCCGGUGGAGACCGGA-AACCACUUGA--AUCAACGGGGCGGAACCCGAACAGCCAAACGAGUAGGGACAAGA
>URS0000D6CF98_12908/1-71
CCCCGGUGGAGUCCAGA-CACCACUUGA--AUAAACGGGGCGGAACCCGAACAGCCAAACGAGUAGGGACAAGA
>URS0000D67CC4_380703/1-71
CCCCGGUGGAGUCCGGA-CACCACUUGA--AUAAACGGGGCGGAACCCGAACAGCCAAACGAGUAGGGACAAGA
>URS0000D67946_12908/1-65
CAGAAAUGGAGUCCAGA-AACCAUUAC-----AAACGGGGUGAAACC-GAA-AACCUUCAGAGUA-GACAAUUA
>URS0000D6647C_12908/1-66
AAAAAGUGGAGACCAGA-AACCACUCGA---AAAACGG-GCGAUACA-AAAAAGU-AAAUUAUUA-UGAAAUUC
>URS0000D6BC0A_313606/1-68
AACCAAAGGAGACCAGA-AACCUUUAAA---CAAACGGGGCAGAACC-GAAAAGCCAUACGAGUA-GGAAAAUA
>URS0000D682DC_313595/1-68
ACAAAGUGGAGGCCAGA-ACCCAUUAGA---AAAACGGCACGGAACC-GAAAAGUGAUAUGAGUA-GGACAAAA
>URS0000D6B83B_12908/1-70
AAAAAAGGGAGACCAGU-ACCC-UAUUC--CAAAACGGGGCGAAUUCCGAAAAGCCAUACGAGUAAGAAAGAUU
>URS0000D66C0E_485917/1-65
UAAUGGUGGAG--CAGC-AACCACUUGU--AAAAACG-GGCGGG-CC-GAAAAGCCAAAAGAGUA-GGAACACA
>URS0000D6607A_485918/1-65
ACCAGGUGGAG--CAGC-GACCACUCAA---AAAACG-GGCGAAGCC-GAAAAGCCAGACGAGUA-GGAACAAA
>URS0000D68428_12908/1-68
AAAGAGUGGAGUUCAGC-GACCACUUAA--AAAAACGGGGCGACACC--AAAAGCCUUACGAGUA-GGAAAUUU
>URS0000D6C052_12908/1-71
UGAUAGUGGAGUUCAGA-UACCACUUUA--AUAAACGGGGCGCAAUCCGAAAAGCCUUAUGAGUAAGAAAAUUU
>URS0000D6C0C8_12908/1-66
UCAAAAUGGAGUCCAGA-AACUAUUAUA----AAACGGGGAGAAACC-GAA-AGCCAUACGAGUA-GGAAAUCU
>URS0000D66666_12908/1-68
AAAAUAUGGAGCCUAGA-AGCCAUCAU---AAAAACGAGGCGCAACU-GAAAAGCCAAAUGAGUA-AGAAAAAA
>URS0000D6D137_194439/1-67
AAAUAAUGGAGACCAGC-GACCAUUUC----AAAACGGGGCGACACC-GAAAAGCCAAACGAGUA-GGGACAUA
>URS0000D68925_12908/1-68
UAAGAGUGGAGUCCAGA-UCCCACUAUA---AAAACGGGGCGUCACC-GAAAAGCCAAAUGAGUA-GGUAUUAA
>URS0000D6A0A0_504472/1-67
AAAUAGUGGAGACCAGC-AACCACCUU----AAAACGGGGCGAAGCC-GAAAAGCCAAACGAGUA-GGAAAAAC
>URS0000D6A849_12908/1-70
AAAAAGUGGAGACCAGC-AACCAUUUUA---AAAACGGGGCGAAAACUGAAAAGCCAAACGAGUAAGAAUAAAA
>URS0000D6BFC2_313595/1-65
AAAAAGUGGAGUCCAGA-CACCAC-AU-----AAACGGGGCGCAACU-GAAAAGCCAAAUGAGUA-AGACAGAU
>URS0000D6CBA5_12908/1-68
AAAAAGUGGAGACCAGA-AACCACUAUA---AAAACGGGGCACCACC-GAAAAGCCAAAUGAGUA-GGACAAAA
>URS0000D6C9ED_12908/1-70
AAAAAGUGGAGACCAGA-AACCACUAAA--AAAAAGGGGGCGACACC-GAAAAGCCAAAUGAGUAAGGACAGCA
>URS0000D68500_12908/1-68
AAAAAGUAGAAACCAGA-AACUACUAAA---AAAACGGGGAUAAAUCCGAAAAUCCA-AAGAGUA-GGAAAUUU
>URS0000D65A1D_12908/1-68
AAAAAGUGGAGA-CAGU-GCCCACUAAA---AAAACGUGGCGGAAACCGAAAAGCC-UAUGAGUAGGUAAUCUU
>URS0000D669E5_269798/1-68
UUACCUUGGAGUCCAGA-AACCAUAUCA---AAAACGGGGCGAUACU-GAAAAGCCAUACGAGUA-GGAAUUAA
>URS0000D665DE_12908/1-71
AAUAAGUGGAGACUAGA-GACCACUAAA--AAAAACGGGACGGAUUCUGAAAAUCCUAAUGAGUAGGAAAAUUA
>URS0000D6BD45_376686/1-69
UAAAUGUGGAG--CAGA-ACCCACUAUA--AAAAACGAGGCGGAACCUGAAAAGCCUUAUGAGUAAGGAAAAUA
>URS0000D68734_376686/1-67
AAUAGGUGGAG--CAGA-ACCCACUAAA--AAAAACGAGGCGGAUCC-GAAAAGCCAUACGAGUA-GGAAACCA
>URS0000D6CE2A_12908/1-71
CAAAAGUUGAGACCAGA-AACAACUUUA--AAAAACGGGGCGAAAUCCGAAAAGCCAUAUGAGUAGGAAAAUAU
>URS0000D688A1_12908/1-71
AAAAAGUGGAGACCAGA-ACCCACUUUA--AAAAACGGGGCGUAUUCUGAAAAGCCUUAUGAGUAGGAAAAAUU
>URS0000D66BC4_12908/1-65
AUAAAGUGGAGACUAGA-ACCCACUUAA--AAAAAAAGGGCGUAUUCCGAAAAGCCUAAUGAGUAGGA------
>URS0000D68490_12908/1-68
AGAAUGUGGAGUCCAGA-UACCACCUAA---AAAACGGGGCGUAACC-GAAAAGCCAUACGAGUA-GGAAAACU
>URS0000D6C946_194439/1-68
UAAAUGUGGAGUCCAGA-AACCACAAGA---AAAACGGGGCGAUACC-GAAAAGCCUUACGAGUA-GGAAAACA

There are no chains in PDB that we map to Rfam family RF03081.

Rfam family RF03081 is part of clan CL00115, which includes Rfam families RF02914, RF03081 . However, there are no chains in PDB that we map to the Rfam families in that clan.

Jump to results for:

  • Loop 1HL Column numbers: 9-21
  • Loop 2HL Column numbers: 41-54

Loop 1 Hairpin loop

Column numbers: 9-21 
    Scored sequences and counts

    
    GAGACCAGA-AAC    6

    
    GAGUCCAGA-AAC    4

    
    GAGUCCAGA-CAC    3

    
    GAGACCAGC-AAC    2

    
    GAGACCAGC-GAC    2

    
    GAG--CAGA-ACC    2

    
    GAGUCAAGAAAAC    1

    
    AAGACCAGC-CCC    1

    
    GAAACCAGA-AAC    1

    
    GAAGACCGA-GAC    1

    
    GAGAAAAGA-AAC    1

    
    GAGACAAGG-AAC    1

    
    GAGACCAGA-ACC    1

    
    GAGACCAGU-AAC    1

    
    GAGACCAGU-ACC    1

    
    GAGACCGGA-AAC    1

    
    GAGACUAGA-ACC    1

    
    GAGACUAGA-GAC    1

    
    GAGCCUAGA-AGC    1

    
    GAGGCCAGA-ACC    1

    
    GAGUCCAGA-UAC    1

    
    GAGUCCAGA-UCC    1

    
    GAGUCCAGC-CAC    1

    
    GAGUCCAGU-GAC    1

    
    GAGUCCGGA-CAC    1

    
    GAGUCUAAG-AAC    1

    
    GAGUUAAGA-AAC    1

    
    GAGUUCAGA-UAC    1

    
    GAGUUCAGC-GAC    1

    
    GAGA-CAGU-GCC    1

    
    GAG--CAGA-UAC    1

    
    GAG--CAGC-AAC    1

    
    GAG--CAGC-GAC    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_01255.1

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

43.48 -3.88 6 4

2

Motif group HL_09260.2

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

36.96 -4.78 6 4

tRNA D-loop

3

Motif group HL_38649.1

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

23.91 -29.18 6 5

4

Motif group HL_80411.1

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

13.04 -19.69 6 4

tRNA D-loop

5

Motif group HL_31581.6

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

10.87 -37.79 7 5.5

6

Motif group HL_81312.1

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

10.87 -49.75 8 6

7

Motif group HL_07951.3

Basepair signature:
cWW-F-F

10.87 -75.11 6 4

tRNA D-loop

8

Motif group HL_02887.3

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

10.87 -100.98 8 6

T-loop with 3 stacked bulged bases

9

Motif group HL_93616.2

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

6.52 -22.37 5 3

tRNA D-loop

10

Motif group HL_67407.5

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

6.52 -46.50 4 4

Loop 2 Hairpin loop

Column numbers: 41-54 
    Scored sequences and counts

    
    CGGAACCCGAACAG    3

    
    CGGAACC-GAAAAG    3

    
    CGAAGCC-GAAAAG    2

    
    CGACACC-GAAAAG    2

    
    CGAGUUC-GAAAAG    2

    
    CGCAACU-GAAAAG    2

    
    CGUAACC-GAAAAG    2

    
    CGUCACC-GAAAAG    2

    
    AGUAUUCUGAAAAU    1

    
    AUAAAUCCGAAAAU    1

    
    CGAAAACUGAAAAG    1

    
    CGAAAUCCGAAAAG    1

    
    CGAAUUCCGAAAAG    1

    
    CGCAAUCCGAAAAG    1

    
    CGGAAACCGAAAAG    1

    
    CGGAACCUGAAAAG    1

    
    CGGAUUCUGAAAAU    1

    
    CGUAUUCCGAAAAG    1

    
    CGUAUUCUGAAAAG    1

    
    CGUGACCCGAAAAG    1

    
    UGUAUUCCGAAAGA    1

    
    AGUUUCC-GAAAAU    1

    
    CACCACC-GAAAAG    1

    
    CAGAACC-GAAAAG    1

    
    CGAUACA-AAAAAG    1

    
    CGAUACC-GAAAAG    1

    
    CGAUACU-GAAAAG    1

    
    CGGAUCC-GAAAAG    1

    
    CGUUACU-GCGAAG    1

    
    CGUUUCU-GAAAAG    1

    
    UAUAACU-AAAAAA    1

    
    UGACACU-GAAAUG    1

    
    AGAAACC-GAA-AG    1

    
    CGACACC--AAAAG    1

    
    CGGG-CC-GAAAAG    1

    
    UGAAACC-GAA-AA    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_88558.1

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

13.04 -35.07 5 4

2

Motif group HL_86109.1

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

6.52 -32.18 6 5

3

Motif group HL_11542.1

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

6.52 -42.08 6 6

4

Motif group HL_02483.1

Basepair signature:
cWW-tWH-F-cSH-F-F-F

6.52 -42.90 6 5

5

Motif group HL_38649.1

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

6.52 -58.49 6 5

6

Motif group HL_68257.1

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

2.17 -53.04 6 5

7

Motif group HL_70658.1

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

2.17 -58.00 8 6

8

Motif group HL_69139.1

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

2.17 -66.93 7 5

9

Motif group HL_60266.1

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

2.17 -69.13 7 5

Coloring options: