RNA 3D Hub

JAR3D Query RF03081-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam 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 2IL Column numbers: 48-53, 60-66
  • Loop 3HL Column numbers: 53-60

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 Internal loop

Column numbers: 48-53, 60-66 
    Scored sequences and counts

    
    -GAAAA*UGAGUA-   10

    
    -GAAAA*CGAGUA-    9

    
    CGAAAA*UGAGUAG    3

    
    CGAACA*CGAGUAG    3

    
    UGAAAA*UGAGUAG    2

    
    -GAAAA*AGAGUA-    2

    
    CGAAAA*CGAGUAA    1

    
    CGAAAA*CGAGUAG    1

    
    CGAAAA*UGAGUAA    1

    
    CGAAAG*AGAGUAG    1

    
    UGAAAA*AGAGUAA    1

    
    UGAAAA*CGAGUAA    1

    
    UGAAAA*UGAGUAA    1

    
    -GAAAA*UGAGUAA    1

    
    CGAAAA*AGAGUA-    1

    
    -AAAAA*AGAGUA-    1

    
    -AAAAA*UUAUUA-    1

    
    -GAAAA*GGAGUA-    1

    
    -GAAAU*ACAGUA-    1

    
    -GCGAA*UUAGUA-    1

    
    --AAAA*CGAGUA-    1

    
    -GAA-A*AGAGUA-    1

    
    -GAA-A*CGAGUA-    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_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

89.13 48.42 3 0

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

56.52 -0.58 5 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

3

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

50.00 0.75 5 1

8x6 Sarcin-Ricin with inserted Y; G-bulge

4

Motif group IL_61286.1

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

30.43 -22.43 6 3

8x6 Sarcin-Ricin with inserted A; G-bulge

5

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

26.09 -12.21 6 2

8x6 Sarcin-Ricin with bulged A; G-bulge

6

Motif group IL_29198.2

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

26.09 -20.87 6 2

7x7 Sarcin-Ricin with intercalated A; G-bulge

7

Motif group IL_47346.2

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

26.09 -23.02 6 2

tSH-tSH-tHH-tHS

8

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

23.91 -30.21 5 2

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_87284.1

Basepair signature:
cWW-tSH-tHW-tWH-tHS-cWW

17.39 -44.68 5 2

tSH-tHW-tWH-tHS

10

Motif group IL_16458.4

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

15.22 -29.36 6 3

Sarcin-Ricin target in LSU H95; G-bulge

Loop 3 Hairpin loop

Column numbers: 53-60 
    Scored sequences and counts

    
    AGCCAAAU    7

    
    AGCCAAAC    6

    
    AGCCAUAC    6

    
    AGCCUUAU    5

    
    AGCCAUAU    2

    
    AGCCUUAC    2

    
    AACCUUAA    1

    
    AACCUUCA    1

    
    AGCCAAAA    1

    
    AGCCAGAC    1

    
    AGCCAGAG    1

    
    AGCCAGAU    1

    
    AGCCUAAU    1

    
    AGCCUGAC    1

    
    AGCUAAAC    1

    
    AGUGAUAU    1

    
    AUCCAUAA    1

    
    AUCCUAAU    1

    
    AUCUUUAA    1

    
    GACCAUAA    1

    
    UGCCAUAA    1

    
    AGCC-UAU    1

    
    AGU-AAAU    1

    
    AUCCA-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_00914.1

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

63.04 0.85 3.5 2

2

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

52.17 3.51 4 2

3

Motif group HL_72628.1

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

39.13 -14.70 4 2

4

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

39.13 -22.02 4 2

5

Motif group HL_85993.1

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

32.61 -20.12 4 3

6

Motif group HL_93324.4

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

28.26 -27.88 4 2

Pseudoknot geometry

7

Motif group HL_10540.1

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

21.74 -22.58 5 3

8

Motif group HL_42046.2

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

17.39 -57.35 5 3

9

Motif group HL_73266.9

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

15.22 -29.92 3 3

10

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

13.04 -35.65 5 4

Other HL

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