RNA 3D Hub

JAR3D Query RF01460-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01460 Listeria sRNA rliH

Input Summary

      000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222223333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333444444444444444444444444444444
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
......((..))..................................(((((((((............(((((((.(((.....(((.........)))....)))...............(((((....(((((((..(((.((((((...((((((.............))))))....)))))).))))))))))...))))).........((((...((((.((((((....((((((((............................))))))))........))))))..)))).....))))..)))))))..................)))))))))((((..........)))).....................((((((((..(((((((......))))))).))))))))......
>AADQ01000003.1_73707-73279
CUUCCAGUCCACCAAACAUAUCACAUUUUUGGCAAAGGGAGCGAUAUUUGGGAUUGGAGCGAAUAAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUAGAAACUUCGGUACCGUGUAUAUCUACAACAACUGAGGCUAAACUGGUUGCGGCUGAGAACUCAUCCAUCACUUUUUCAAUGAGCAUUUCGUUGCUUUUGGACUGUAGUAACAUAGCUAUUCCCCUUUCGGCGAGACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGAGUAAUUUCAUAAGAGAAUGCCCAAACCAUGCAUUACUGGAUGGCUUUUUGUCAUUAUUUUUUUUGAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU
>AL596167.1_168444-168872
CUUCCAACCCGCCAAACAUAUCACAUUUUUGGCAAAGCGAGCGAUAUUUUGGGUUAGAACGAAUGAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUUGAAACUUCGGUACCGUGUAUAUCUACAACAACUGAGGCUAGACUAGUAGCGGCUGAGAACUCAUCCAUGACUUUUUCAAGAAGCAUUUCAUUGCUUUUGGUUUGUAGUAACAUAGCUAUUCCCCUUUCGGCAAUACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGACUAAUUUCAUAAGAGAAAGCCCAAACCAUGCUCUACUGGAUGGCUUUUUGUCGUUUAUUUUUUUGAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU
>AM263198.1_1123866-1124294
CUUCAAGGCCCCCAAACAUAUCACAUUUUUGACAAAGUGAGCGAUAUUUUGGGUUGGAACGAAUGAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUAGAAACUUCGGUACCGUGUAUAUCUACAACAACGGAGGCUAGACUCGUUGCGGCUGAAAACUCAUCCAUGACUUUUUCAAUGAGCAAUUCGUUGCUUUUGGACUGUAGUAACAUAGUUAUUCCCCUUUCGGCAAUACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGACCAAUUUCAUAGUAAAAGCCCCAAACCAUGCAUGACUGGAUGGCUUUUUGUAUAUAAUUUUUUAAAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU

There are no chains in PDB that we map to Rfam family RF01460.

Jump to results for:

  • Loop 1HL Column numbers: 8-11
  • Loop 2IL Column numbers: 55-68, 318-337
  • Loop 3J4 Column numbers: 74-76, 105-121, 205-215, 309-312
  • Loop 4IL Column numbers: 78-84, 98-103
  • Loop 5HL Column numbers: 86-96
  • Loop 6IL Column numbers: 125-130, 197-201
  • Loop 7IL Column numbers: 136-139, 190-191
  • Loop 8IL Column numbers: 141-143, 186-188
  • Loop 9IL Column numbers: 148-152, 176-181
  • Loop 10HL Column numbers: 157-171
  • Loop 11IL Column numbers: 218-222, 300-306
  • Loop 12IL Column numbers: 225-227, 294-297
  • Loop 13IL Column numbers: 232-237, 280-289
  • Loop 14HL Column numbers: 244-273
  • Loop 15HL Column numbers: 349-360
  • Loop 16IL Column numbers: 392-395, 414-416
  • Loop 17HL Column numbers: 401-408

Loop 1 Hairpin loop

Column numbers: 8-11 
    Scored sequences and counts

    
    CCCG    1

    
    GCCC    1

    
    UCCA    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_78677.1

Basepair signature:
cWW-F-F

100.00 47.86 2 1

2

Motif group HL_70782.2

Basepair signature:
cWW-F

100.00 47.39 3 2

3

Motif group HL_13189.1

Basepair signature:
cWW-F-F

100.00 41.62 3 2

4

Motif group HL_48778.2

Basepair signature:
cWW-F

100.00 40.86 2 1

Mini UNCG

5

Motif group HL_56131.2

Basepair signature:
cWW-F-F

100.00 36.72 3 2

6

Motif group HL_32346.4

Basepair signature:
cWW-F

100.00 35.59 1 1

7

Motif group HL_27483.1

Basepair signature:
cWW-F

100.00 25.90 4 2

8

Motif group HL_22135.1

Basepair signature:
cWW-F-F

100.00 15.04 3 1

9

Motif group HL_94980.1

Basepair signature:
cWW-F-F

100.00 13.16 4 2

10

Motif group HL_35941.1

Basepair signature:
cWW-F

100.00 0.49 3 2

Loop 2 Internal loop

Column numbers: 55-68, 318-337 
    Scored sequences and counts

    
    UAGAACGAAUGAGU*AGACUAAUUUCAUAAGAGAA    1

    
    UGGAACGAAUGAGU*AGACCAAUUUCAUAGUAAAA    1

    
    UGGAGCGAAUAAGU*AGAGUAAUUUCAUAAGAGAA    1
No Matches Found View All Results for this Loop

Loop 3 4-way junction loop

Column numbers: 74-76, 105-121, 205-215, 309-312 
    Scored sequences and counts

    
    AAA*UCGGUACCGUGUAUAUC*GUAACAUAGCU*AUAU    2

    
    AAA*UCGGUACCGUGUAUAUC*GUAACAUAGUU*AUAU    1
No Matches Found View All Results for this Loop

Loop 4 Internal loop

Column numbers: 78-84, 98-103 
    Scored sequences and counts

    
    GGAGUAA*AGAAAC    2

    
    GGAGUAA*UGAAAC    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 88.98 3 0

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_41756.4

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

100.00 50.03 3 1

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

3

Motif group IL_02349.4

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

100.00 35.06 4 2

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

4

Motif group IL_24254.1

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

100.00 31.96 6 2

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

5

Motif group IL_47346.2

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

100.00 28.84 4 2

tSH-tSH-tHH-tHS

6

Motif group IL_29198.2

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

100.00 18.50 4 2

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

7

Motif group IL_04346.10

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

100.00 10.29 4 2

8x7 Sarcin-Ricin; G-bulge

8

Motif group IL_61286.1

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

100.00 9.25 7 3

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

9

Motif group IL_16458.4

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

33.33 -7.03 6 3

Sarcin-Ricin target in LSU H95; G-bulge

Loop 5 Hairpin loop

Column numbers: 86-96 
    Scored sequences and counts

    
    GUUACAUAAUC    3
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_98252.1

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

100.00 27.19 5 3

2

Motif group HL_34964.1

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

100.00 23.13 3 3

3

Motif group HL_29762.1

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

100.00 22.86 5 3

4

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

100.00 22.54 5 3

5

Motif group HL_60266.1

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

100.00 15.08 3 3

6

Motif group HL_04725.1

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

100.00 12.41 3 3

7

Motif group HL_87463.1

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

100.00 11.22 3 3

8

Motif group HL_45785.1

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

100.00 10.53 4 4

9

Motif group HL_81545.2

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

100.00 2.49 2 2

Loop 6 Internal loop

Column numbers: 125-130, 197-201 
    Scored sequences and counts

    
    AACAAC*GGACU    2

    
    AACAAC*GGUUU    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_25186.4

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

100.00 34.79 4 2

2

Motif group IL_21667.1

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

100.00 23.20 6 2

3

Motif group IL_97631.1

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

66.67 23.03 4 2

Triple sheared related

4

Motif group IL_09044.1

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

66.67 7.41 4 2

5

Motif group IL_80231.1

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

66.67 1.52 4 2

Other IL

6

Motif group IL_59258.1

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

66.67 -5.32 7 3

7

Motif group IL_62654.1

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

66.67 -5.89 7 3

tSH-tHH-tHS

8

Motif group IL_80926.1

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

66.67 -6.48 7 3

9

Motif group IL_88269.4

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

66.67 -9.66 5 3

6x5 Sarcin-Ricin; G-bulge

10

Motif group IL_17948.2

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

66.67 -25.23 5 1

Double sheared with non-canonical cWW

Loop 7 Internal loop

Column numbers: 136-139, 190-191 
    Scored sequences and counts

    
    CUAG*UG    2

    
    CUAA*UG    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_42626.2

Basepair signature:
cWW-cWW

100.00 84.36 2 0

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 84.29 1 0

3

Motif group IL_56987.1

Basepair signature:
cWW-L-cWW

100.00 81.34 2 0

4

Motif group IL_82107.4

Basepair signature:
cWW-cWW

100.00 71.68 1 0

Multiple bulged bases

5

Motif group IL_68140.4

Basepair signature:
cWW-cSH-cWW

100.00 67.31 2 0

Major groove minor groove platform; mini C-loop

6

Motif group IL_84476.1

Basepair signature:
cWW-cWW

100.00 66.50 1 0

Multiple bulged bases

7

Motif group IL_14368.1

Basepair signature:
cWW-L-cWW-cSH

100.00 66.32 1 0

Major groove platform with intercalated tWH

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 61.92 2 0

Major groove intercalation

9

Motif group IL_00881.1

Basepair signature:
cWW-L-cWW-L

100.00 50.59 1 1

10

Motif group IL_15052.4

Basepair signature:
cWW-L-cWW-L

100.00 50.26 3 0

Minor groove platform

Loop 8 Internal loop

Column numbers: 141-143, 186-188 
    Scored sequences and counts

    
    CUA*UCA    1

    
    CUC*UCG    1

    
    CUG*UCG    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_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 77.32 4 0

Isolated non-canonical cWW pair

2

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 72.70 3 0

Isolated non-canonical cWW pair

3

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 70.04 3 0

4

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 48.60 1 0

Isolated non-canonical cWW pair

5

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 32.83 2 0

Isolated cWH basepair

6

Motif group IL_28037.2

Basepair signature:
cWW-cWW-cWW

100.00 32.02 2 0

Isolated non-canonical cWW pair

7

Motif group IL_10796.1

Basepair signature:
cWW-L-R-cWW

100.00 25.96 2 1

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 23.68 3 1

Stack and bulge

9

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 19.07 2 1

Multiple bulged bases

10

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 7.91 2 1

Isolated cWS basepair

Loop 9 Internal loop

Column numbers: 148-152, 176-181 
    Scored sequences and counts

    
    CGGCU*AAUGAG    2

    
    CGGCU*AAGAAG    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_94351.1

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

100.00 63.19 5 1

2

Motif group IL_73759.1

Basepair signature:
cWW-cSH-tHS-cWH-cHW-cWW

100.00 11.79 5 3

Part of G-quadruplex

3

Motif group IL_59258.1

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

100.00 10.77 7 3

4

Motif group IL_42778.1

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

33.33 1.35 6 4

5

Motif group IL_80231.1

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

33.33 1.12 4 3

Other IL

6

Motif group IL_21667.1

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

33.33 -0.01 6 3

7

Motif group IL_97631.1

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

33.33 -3.91 6 4

Triple sheared related

8

Motif group IL_88269.4

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

33.33 -4.97 6 3

6x5 Sarcin-Ricin; G-bulge

9

Motif group IL_70411.2

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

33.33 -6.74 6 4

10

Motif group IL_25186.4

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

33.33 -7.83 6 4

Loop 10 Hairpin loop

Column numbers: 157-171 
    Scored sequences and counts

    
    ACUCAUCCAUGACUU    2

    
    ACUCAUCCAUCACUU    1
No Matches Found View All Results for this Loop

Loop 11 Internal loop

Column numbers: 218-222, 300-306 
    Scored sequences and counts

    
    UCCCC*GAUAACA    3
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_80231.1

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

100.00 33.01 4 3

Other IL

2

Motif group IL_59258.1

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

100.00 6.18 4 4

Loop 12 Internal loop

Column numbers: 225-227, 294-297 
    Scored sequences and counts

    
    UCG*CAUG    3
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_99358.1

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

100.00 74.48 3 0

2

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 33.25 4 1

Isolated non-canonical cWW pair

3

Motif group IL_61438.4

Basepair signature:
cWW-L-cWW

100.00 29.98 2 1

4

Motif group IL_15698.3

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

100.00 21.62 1 1

5

Motif group IL_90351.1

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

100.00 17.51 4 1

6

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

100.00 14.30 2 1

Isolated non-canonical cWW pair

7

Motif group IL_83389.2

Basepair signature:
cWW-cWW

100.00 9.04 3 2

8

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 5.62 3 1

Isolated non-canonical cWW pair

Loop 13 Internal loop

Column numbers: 232-237, 280-289 
    Scored sequences and counts

    
    UACUUG*UUACAUUUUC    2

    
    GACUUG*UUACAUUUUC    1
No Matches Found View All Results for this Loop

Loop 14 Hairpin loop

Column numbers: 244-273 
    Scored sequences and counts

    
    UUCUGUCGUUCUUAGUAUAGCAUAUUUAUA    3
No Matches Found View All Results for this Loop

Loop 15 Hairpin loop

Column numbers: 349-360 
    Scored sequences and counts

    
    UGCAUGACUGGA    1

    
    UGCAUUACUGGA    1

    
    UGCUCUACUGGA    1
No Matches Found View All Results for this Loop

Loop 16 Internal loop

Column numbers: 392-395, 414-416 
    Scored sequences and counts

    
    CAAA*UCG    3
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_61438.4

Basepair signature:
cWW-L-cWW

100.00 98.03 2 0

2

Motif group IL_90351.1

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

100.00 84.28 4 0

3

Motif group IL_51387.2

Basepair signature:
cWW-cSH-cWW-cWW

100.00 74.99 2 0

4

Motif group IL_83389.2

Basepair signature:
cWW-cWW

100.00 67.90 3 1

5

Motif group IL_99358.1

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

100.00 61.04 2 1

6

Motif group IL_41344.1

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

100.00 44.92 5 1

7

Motif group IL_09990.4

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

100.00 43.67 5 1

8

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 42.62 4 1

9

Motif group IL_55516.2

Basepair signature:
cWW-cWW-cSH-cWW

100.00 34.54 4 1

10

Motif group IL_15698.3

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

100.00 33.74 3 1

Loop 17 Hairpin loop

Column numbers: 401-408 
    Scored sequences and counts

    
    GUUAAAAC    3
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_81538.2

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

100.00 94.19 0 0

GNRA with tandem sheared

2

Motif group HL_77436.5

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

100.00 76.27 0 0

T-loop related

3

Motif group HL_41464.2

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

100.00 74.52 1 1

4

Motif group HL_04259.3

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

100.00 67.30 2 1

GNRA with extra cWW

5

Motif group HL_31585.4

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

100.00 43.94 1 1

Purine riboswitch

6

Motif group HL_00914.1

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

100.00 36.60 2 2

7

Motif group HL_97917.2

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

100.00 35.32 4 2

8

Motif group HL_84299.4

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

100.00 34.87 2 2

9

Motif group HL_77082.1

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

100.00 34.34 3 2

Pseudoknot geometry

10

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

100.00 31.93 3 1

Coloring options: