RNA 3D Hub

JAR3D Query RF03073-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF03073 RT-19 RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901
....((((((((............))).)))))..........................................(((((.....(((..................)))....)))))...
>URS0000D665BD_12908/1-112
AUUACCGUCGGCCACGA--UCUAAGCCAGACGGC-A-UGCCACGGCCAGAU---CCGAAAAUGCAACACGAGCACGCGGCCGGUAGAU--GAACCCAUCCAGCCACAUCGACAGCCGCGCA
>URS0000D65871_12908/1-94
ACUACCUCCCGCA--CG---GGAAGCGAGGAGGC-ACAGCCCCGGCCAGUU---CCGAAAAUCAAA-CCGAGAAGGCGGCCGGUAGA---------------CGCA-UCGAAAGCCGC-CA
>URS0000D6A46D_12908/1-94
ACUACCUCCCGCGU-----GGGAAGCGAGGAGGCCC-AGCCCCGGCCAGUU---CCGAAAAUCAAA-CCGAGAAGGCGGCCGGUAGA---------------CGCA-UCGAAAGCCGC-CA
>URS0000D6B60E_1203540/1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B60E_205913/1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B60E_12908/1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D66F8F_12908/1-107
ACUGCCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_12908/1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_411481/1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_1263059/1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D67BFC_12908/1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGGCAGCCGG-CA
>URS0000D665C9_12908/1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUACCC--GAACCCCUCCAGCAACAGGGAACGCCGG-CA
>URS0000D693BF_12908/1-106
ACUACCCUCCGUCA-----UGCCAACGAGAGGGC-A-CGCCUCGGCCCAG----CCGAAAAUCAAA-CCGAGCACGCGGCCGGUAGAC--GACCCACGCCAGCACCGUCGAACGCCGC-CA
>URS0000D6C28D_12908/1-100
ACUACCCUCCGCU-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGGC----------CAAGAUGAGCCGAACGCCGC-CA
>URS0000D6B350_12908/1-97
ACUACCCUCCGCC-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGAC------------CCCAA-GUCGAACGCCGC-CA
>URS0000D658F7_12908/1-98
ACUACCCUCCGCC-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGGC------------CCCAUGGCCGAACGCCGC-CA
>URS0000D685C7_12908/1-97
ACUACCCUCCGCCUUGG-GGAUAUGCGAGAGGGC-U-UGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGAACGCGACCGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D69B86_565040/1-98
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGGCUGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D6B4A9_12908/1-98
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGGCUGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D67B95_12908/1-101
ACUACCCUCCGCUUUCGGGGACACGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAAAGCCGC-CA
>URS0000D6C904_12908/1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAACGCCGC-CA
>URS0000D6BD80_12908/1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAACGCCGC-CA
>URS0000D676AC_12908/1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGACCGGUAGGC------------CACAUGGCCGAACGCCGC-CA

There are no chains in PDB that we map to Rfam family RF03073.

Jump to results for:

  • Loop 1IL Column numbers: 9-10, 27-29
  • Loop 2HL Column numbers: 12-25
  • Loop 3IL Column numbers: 80-86, 109-114
  • Loop 4HL Column numbers: 88-107

Loop 1 Internal loop

Column numbers: 9-10, 27-29 
    Scored sequences and counts

    
    CC*GAG   22

    
    CG*CAG    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_26793.1

Basepair signature:
cWW-L-cWW

100.00 100.00 0 0

Single stack bend

2

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 99.88 0 0

Single stack bend

3

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 99.84 0 0

Single bulged A

4

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

100.00 99.44 2 0

5

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 96.90 2 0

Multiple bulged bases

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 93.60 1 0

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 87.35 3 0

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 86.50 1 0

Stack and bulge

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 81.15 2 0

Major groove platform

10

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 75.32 3 0

Major groove platform

Loop 2 Hairpin loop

Column numbers: 12-25 
    Scored sequences and counts

    
    CG-CCA---GCCAG    9

    
    CUUUCGGGGAUAUG    5

    
    CC-------GCCCG    2

    
    CUUUCGGGGACACG    1

    
    CCUUGG-GGAUAUG    1

    
    CCACGA--UCUAAG    1

    
    CA--CG---GGAAG    1

    
    CGU-----GGGAAG    1

    
    UCA-----UGCCAA    1

    
    CU-------GCCCG    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_93438.2

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

39.13 -90.27 5 4

2

Motif group HL_85434.1

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

39.13 -96.97 7 5

3

Motif group HL_67407.5

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

39.13 -730.48 5 5

4

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

13.04 -97.39 5 5

5

Motif group HL_65794.5

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

13.04 -3356.93 3 3

Pseudoknot geometry

6

Motif group HL_50860.2

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

8.70 -125.65 5 4

7

Motif group HL_87553.1

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

8.70 -171.51 3 3

8

Motif group HL_37369.2

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

8.70 -254.71 4 4

9

Motif group HL_07951.3

Basepair signature:
cWW-F-F

8.70 -1201.84 5 5

tRNA D-loop

10

Motif group HL_58224.1

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

4.35 -76.03 6 5

Loop 3 Internal loop

Column numbers: 80-86, 109-114 
    Scored sequences and counts

    
    CCGGUAG*CGAACG   12

    
    CCAGUAG*CGAACG    3

    
    CCGGUAG*CGAAAG    3

    
    CUGGUAG*CGAACG    2

    
    CCAGUAG*CGGCAG    1

    
    CCGGUAC*GGAACG    1

    
    CCGGUAG*CGACAG    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

100.00 57.00 1 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

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

95.65 10.48 7 3

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

3

Motif group IL_16458.4

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

86.96 24.47 4 2

Sarcin-Ricin target in LSU H95; G-bulge

4

Motif group IL_04346.10

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

69.57 -0.48 4 3

8x7 Sarcin-Ricin; G-bulge

5

Motif group IL_88269.4

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

69.57 -1.22 4 2

6x5 Sarcin-Ricin; G-bulge

6

Motif group IL_61286.1

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

21.74 -12.73 6 4

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

7

Motif group IL_47346.2

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

17.39 -24.23 6 4

tSH-tSH-tHH-tHS

8

Motif group IL_29198.2

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

13.04 -12.90 4 3

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

9

Motif group IL_06136.2

Basepair signature:
cWW-tHS-cWW-tHS-tSH-tSH-cWW

13.04 -14.14 5 2

Quadruple sheared

10

Motif group IL_65594.1

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

13.04 -14.50 4 3

8x7 Sarcin-Ricin; G-bulge

Loop 4 Hairpin loop

Column numbers: 88-107 
    Scored sequences and counts

    
    CCCGAACCCAUCCAGCACCG    4

    
    C--GAACCCAUCCAGCACCG    4

    
    C------------CAUAAGG    3

    
    A--------------CAU-U    3

    
    ---------------CGCA-    2

    
    C--GAACCCCUCCAGCAACA    1

    
    C--GACCCACGCCAGCACCG    1

    
    U--GAACCCAUCCAGCCACA    1

    
    C----------CAAGAUGAG    1

    
    C------------CACAUGG    1

    
    C------------CCCAUGG    1

    
    C------------CCCAA-G    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_56131.2

Basepair signature:
cWW-F-F

26.09 -5164.29 5 5

2

Motif group HL_70782.2

Basepair signature:
cWW-F

26.09 -5203.56 5 5

3

Motif group HL_87553.1

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

21.74 -404.96 5 3

4

Motif group HL_93324.4

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

21.74 -7395.73 5 3

Pseudoknot geometry

5

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

17.39 -3876.77 5 4

Other HL

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

17.39 -5181.57 4 4

7

Motif group HL_20743.5

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

13.04 -336.70 7 6

8

Motif group HL_10540.1

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

13.04 -1981.21 5 4

9

Motif group HL_48417.5

Basepair signature:
cWW-F-F

13.04 -2182.83 4 4

10

Motif group HL_37344.1

Basepair signature:
cWW-F-F

13.04 -4647.24 5 4

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