RNA 3D Hub

JAR3D Query RF01714-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01714 Ocean-V RNA

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666667777
1234567890123456789012345678901234567890123456789012345678901234567890123
.........((((((........)))))).....(((.....((((................))))....)))
>ABEF01002814.1_681-753
AUAUUUUAUGACUUCAUUCAAUUGAAGUCCUCAAAGUGAGUACGUCGUAAGAUCGAAGCGCUGACGGAAAACU
>ABEF01002040.1_258-187
ACUCUUUUUGGUUUCAUUCAGUUGAAACCCUCA-AGCGAGUACGCCGUAAGACGCAAGCGCAGGCGGAAAACU
>ABEF01025170.1_751-680
ACUCUUUUUGAUUUCAUUCAGUUGAAAUCCUCA-CGCAAGUACGCCGUAAGACGCAAGCACAGGCGGAAAGCU

There are no chains in PDB that we map to Rfam family RF01714.

Jump to results for:

  • Loop 1HL Column numbers: 15-24
  • Loop 2IL Column numbers: 37-43, 66-71
  • Loop 3HL Column numbers: 46-63

Loop 1 Hairpin loop

Column numbers: 15-24 
    Scored sequences and counts

    
    CAUUCAGUUG    2

    
    CAUUCAAUUG    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_50779.4

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

100.00 9.41 6 4

2

Motif group HL_81545.2

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

100.00 5.56 5 3

3

Motif group HL_58224.1

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

66.67 12.40 3 3

4

Motif group HL_04642.1

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

66.67 8.77 3 3

tRNA D-loop

5

Motif group HL_69139.1

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

33.33 2.89 4 4

6

Motif group HL_67079.1

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

33.33 2.33 6 4

7

Motif group HL_28252.8

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

33.33 -31.82 4 2

T-loop with 2 stacked bulged bases

Loop 2 Internal loop

Column numbers: 37-43, 66-71 
    Scored sequences and counts

    
    CAAGUAC*GGAAAG    1

    
    CGAGUAC*GGAAAA    1

    
    UGAGUAC*GGAAAA    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 92.37 2 0

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

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

100.00 48.93 3 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

100.00 31.32 4 1

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

4

Motif group IL_47346.2

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

100.00 23.37 6 2

tSH-tSH-tHH-tHS

5

Motif group IL_61286.1

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

100.00 22.73 4 3

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

6

Motif group IL_02349.4

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

100.00 22.24 6 2

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

7

Motif group IL_29198.2

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

100.00 19.83 6 2

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

8

Motif group IL_04346.10

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

100.00 16.53 4 2

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_16458.4

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

100.00 10.13 4 3

Sarcin-Ricin target in LSU H95; G-bulge

10

Motif group IL_87284.1

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

33.33 -6.61 5 2

tSH-tHW-tWH-tHS

Loop 3 Hairpin loop

Column numbers: 46-63 
    Scored sequences and counts

    
    CGUAAGACGCAAGCACAG    1

    
    CGUAAGACGCAAGCGCAG    1

    
    CGUAAGAUCGAAGCGCUG    1
No Matches Found View All Results for this Loop

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