RNA 3D Hub

JAR3D Query RF00468-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF00468 Hepatitis C virus stem-loop VII

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666667
1234567890123456789012345678901234567890123456789012345678901234567890
...(((((((((((((((((((...(((((.....)))))......))))))..)))))))))))))...
>NC_038882.1_9128-9197
UAGGCUUCUGUCCAGAGGAGGCAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGAACA
>NC_004102.1_9128-9197
UAGGCUUCUGUCCAGAGGAGGCAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGAACA
>EU234065.2_9023-9092
UAGGCUUCUGUCCAGAGGAGGCAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGAACA
>MN164851.1_8787-8856
UAAAUUGCUGUCCCAGGGGGGGAGGGCCGCUAUUUGCGGCAAGUACCUCUUCAACUGGGCAGUAAAGACC
>KJ439777.1_9128-9197
UAAGCUUCUGUCCAUGGGAGGAAAAGCCGCUAUAUGCGGCAGAUACCUCUUUAAUUGGGCAGUGAAGACC
>MN977327.1_9078-9147
CAGGCUACUGUCCCAAGGGGGAAAAGCCGCUAUUUGCGGCAAGUACCUCUUUAAUUGGGCAGUAAAAACC
>AY587845.1_9064-9133
CAAGCUACUGUCCCAGGGGGGGAGGGCUGCCACUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAGACC
>AJ851228.1_9101-9170
UAGGUUGCUGUCCCAGGGGGGGAGGGCUGCCACGUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAAACC
>KY348757.1_9088-9157
UAAGCUGCUAUCCCAGGGGGGGAGGGCCGCUAUAUGCGGAAAGUACCUCUUCAACUGGGCGGUGAAAACC
>KJ439768.1_9125-9194
UAAGUUGCUGUCCCAGGGGGGGAGGGCUGCUACCUGCGGCAAGUACCUCUUCAACUGGGCAGUAAGGACC
>MN164872.1_8787-8856
UAAGCUGAUAGCCCAAGGAGGGAAAGCCGCCAUAUGCGGCAAGUACCUCUUUAAUUGGGCUGUCAAAACC
>MW689980.1_8932-9001
UAGGCUGAUCGCCCGGGGGGGGAACGCCGCUAUAUGUGGCAAGUACCUCUUUAACUGGGCGGUCCGAACC
>MW689962.1_8932-9001
UAGGCUACUGUCCCAGGGAGGGAAAGCCGCUAUAUGCGGCAAGUACCUCUUCAACUGGGCAGUAAAAACC
>KX767023.1_9057-9126
UAAGCUGCUGUCCCAAGGGGGGAGGGCCGCCACUUGUGGCAGGUACCUCUUCAACUGGGCAGUAAGGACC
>EU234061.2_9073-9142
UAAGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGGACC
>AB677533.1_9137-9206
UAAGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAGGUACCUCUUCAACUGGGCAGUAAGGACC
>MW689975.1_9116-9185
UAAGUUGCUGUCCCAGGGGGGGAGGGCUGCCAUCUGUGGCAAAUACCUCUUCAAUUGGGCAGUAAAGACC
>MW689965.1_9132-9201
UAAGCUACUGUCCAGAGGAGGGAGGGCCGCCAUCUGCGGCCGUUACCUCUUCAACUGGGCGGUAAAAACC
>MW689971.1_9088-9157
UAAGCUACUGUCCCAGGGGGGGAGGGCCGCAAUUUGCGGGAAGUACCUCUUCAACUGGGCAGUAAAGACC
>MW690013.1_9111-9180
CGCCCUCUUACGUCAAGGAGGAAGGGCCGCUAUAUGCGGCAAAUACCUCUUUAACUGGGCAGUGAGGACC
>KC248199.1_9131-9200
UAAGCUACUGUCCCAGGGAGGGAGGGCCGCCGUGUGCGGCAAAUACCUCUUUAACUGGGCAGUAAAAACC
>MN164860.1_8805-8874
UAAGCUCCUGUCCCAAGGGGGGAAAGCUGCCAUAUGCGGCAAGUACCUCUUCAAUUGGGCAGUGAGAACA
>NC_009823.1_9193-9262
GUCCCUCAUCUCCCGUGGGGGGAGAGCGGCCGUUUGCGGUCGAUAUCUCUUCAAUUGGGCGGUGAAGACC
>AF169004.1_9193-9262
GUCCCUCAUCUCCCAUGGAGGGAGGGCGGCCGUUUGCGGCCGGUAUCUCUUCAACUGGGCGGUGAAGACC
>JX227965.1_9116-9185
UUCCCUCAUCAGCCGGGGGGGGAGGGCGGCCACAUGUGGCCGCUACCUCUUCAACUGGGCUGUGAAGACG
>KC197233.1_9166-9235
AUCCCUCAUCGCCCGGGGAGGGAGGGCAGGCAUAUGUGGCCGCUAUCUCUUCAACUGGGCAGUGAGGACC
>AB047639.1_9193-9262
GUCCCUCAUCUCCCGUGGAGGGAAAGCGGCCGUUUGCGGCCGAUAUCUCUUCAAUUGGGCGGUGAAGACC
>MK548369.1_9120-9189
UAGGCUKCUGUCCAGAGGGGGUAGRGCUGCYAUAUGCGGCAAAUACCUCUUYAACUGGGCAGUAAGAACA
>AY232740.1_9157-9226
CUCACUCAUCGCCCAGGGAGGGAGGGCGGCCAUUUGUGGCCGCUACCUCUUCAACUGGGCGGUGAAGACA
>KC197230.1_9169-9238
GUCCCUCCUCUCCCGGGGAGGUAAAGCGGCCAUAUGCGGCCGCUACCUCUUCAACUGGGCGGUGAGGACA
>NC_009824.1_9156-9225
CAAGCUUAUCGCCCAGGGAGGAAAGGCUAAAAUAUGCGGCCUUUAUCUCUUUAAUUGGGCGGUACGCACC
>KY620603.1_9155-9224
CAAGCUUAUCGCCCAGGGAGGGAAGGCCAAAAUAUGCGGCCUUUAUCUCUUUAAUUGGGCGGUACGCACC
>KJ470619.1_9157-9226
UAAGCUUAUAGCUCAGGGGGGAAAGGCCAAAAUCUGUGGCCUUUACCUCUUUAACUGGGCUGUACGCACC
>JF735124.1_9156-9225
UAAGCUUAUAGCUCAAGGGGGUAAGGCCGCUAUAUGCGGCUUAUACCUCUUCAAUUGGGCUGUACGCACA
>MN628597.1_9159-9228
UAAGCUUAUCGCCCAGGGAGGGAAGGCCAAGAUAUGUGGCCUUUAUCUCUUUAAUUGGGCGGUACGCACC
>KY620874.1_9167-9236
CAAACUCAUUGCCCAGGGAGGGAAGGCCAGGAUAUGCGGCCUAUACCUCUUUAACUGGGCAGUGCGUACC
>JF735122.1_9150-9219
AAAGCUCAUUUCCCAAGGAGGAAAGGCCAAAAUUUGCGGCCUUUACCUCUUCAAUUGGGCAGUGCGCACA
>NC_009825.1_9057-9126
UAAGCUUAUCGCCCAGGGAGGUAGAGCCAAAAUAUGUGGCAUAUACCUCUUUAACUGGGCGGUAAAAACC
>KM043284.1_9118-9187
UAAGCUUAUCGCUCAGGGAGGUAAAGCCAAAAUCUGUGGCAUAUACCUCUUUAACUGGGCGGUAAAAACC
>FJ462437.1_9112-9181
UAAGCUCAUCGCUCAGGGGGGUAGAGCCAGAAUCUGUGGCAUAUACCUCUUUAACUGGGCGGUAAAAACC
>NC_009826.1_9075-9144
UAAGCUCAUCGCCCAGGGAGGUAGGGCCGCCAUCUGCGGCAUCUAUCUCUUCAACUGGGCGGUGAAGACA
>MH427311.1_9135-9204
UAAGCUCAUCGCUCAGGGAGGUAAGGCCGCCAUCUGCGGCAUCUAUCUCUUCAACUGGGCGGUGAAAACA
>DQ278891.1_9139-9208
GAAGCUUAUCGCCCAGGGAGGGAACGCAGCGAUUUGCGGCAAGUACCUCUUUAAUUGGGCGGUAAGGACU
>LC435023.1_9090-9159
AAAGCUCAUCGCCCAGGGGGGGAAAGCUGCUAUUUGCGGUAAGUACCUCUUCAACUGGGCGGUGAAGACC
>MK327987.1_9137-9206
UAAGCUUAUCGCCCAGGGUGGGAAGGCCGCUGUAUGCGGUACGUACCUCUUCAACUGGGCCGUAAAAACU
>MG878999.1_8808-8877
CAAAUUGAUCGCUCAGGGGGGAAAAGCUGCAUUAUGCGGCAGGUACCUCUUCAAUUGGGCGGUUAAAACU
>KC844040.1_9143-9212
CAAGUUAAUUGCUCAAGGGGGGAAAGCCGCUAUAUGCGGAAAGUACCUCUUCAAUUGGGCAGUUAAAACG
>MG717928.1_9156-9225
CAAACUCAUUGCCCAAGGGGGGAAAGCGGCCAUAUGCGGUAAGUACCUCUUUAACUGGGCAGUGAAGACC
>KJ678751.1_9110-9179
CAAACUCAUCGCCCAAGGGGGGAAAGCUGCUAUAUGCGGUAGGUACCUCUUUAACUGGGCGGUGAAGACC
>MG717925.1_9096-9165
CAAACUCAUUGCCCAAGGGGGGAAAGCGGCCAUAUGCGGUAAGUACCUCUUUAACUGGGCGGUGAAGACC
>NC_009827.1_9153-9222
CAAACUCAUUGCCCAAGGUGGGAAAGCAGCGAUAUGCGGCAAGUACCUCUUUAACUGGGCAGUGAAGACC
>AY878652.1_9107-9176
AAARCUCAUCGCCCAGGGGGGGAAAGCCGCUAUAUGCGGCAAGUACCUCUUUAACUGGGCGGUAAGAACC
>KM504115.1_9141-9210
UAAACUCGUCGCCCAGGGGGGGAAAGCCGCUGAAUGCGGUAAGUACCUCUUCAACUGGGCGGUGAGGACA
>EU158186.1_9109-9178
AAAGCUCAUUGCUCAGGGGGGGAAAGCUGCUAUCUGCGGUAAGUACCUCUUCAACUGGGCUGUUAAGACC
>MK139017.1_9140-9209
GAAGCUCAUUGCCCAGGGGGGGAAAGCCGCAAUAUGCGGMAAAUACCUCUUCAACUGGGCUGUGAGAACC
>NC_030791.1_9132-9201
GGGGCUGAUAGGCCAGGGGGGCAGGGCUCGCAUAUGCGGUCUCUACCUCUUCAACUGGGCUGUCAGGACC
>MH590700.1_9141-9210
CAGGCUCAUAGCCCAGGGUGGUAGGGCGGCCAUAUGUGGCCACUACCUCUUUAACUGGGCUGUGAAAACA

There are no chains in PDB that we map to Rfam family RF00468.

Jump to results for:

  • Loop 1IL Column numbers: 16-17, 52-55
  • Loop 2IL Column numbers: 22-26, 40-47
  • Loop 3HL Column numbers: 30-36

Loop 1 Internal loop

Column numbers: 16-17, 52-55 
    Scored sequences and counts

    
    GG*CAAC   21

    
    GG*UAAC    9

    
    AG*CAAC    5

    
    AG*UAAC    5

    
    GG*UAAU    5

    
    AG*CAAU    4

    
    AG*UAAU    2

    
    GG*CAAU    2

    
    UG*CAAU    2

    
    UG*CAAC    1

    
    Omitted sequenced and counts

    
    AG*YAAC    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_82107.4

Basepair signature:
cWW-cWW

100.00 89.17 1 0

Multiple bulged bases

2

Motif group IL_76709.2

Basepair signature:
cWW-L-cWW-L

100.00 82.97 2 0

3

Motif group IL_73355.1

Basepair signature:
cWW-L-cWW-L

100.00 82.32 1 0

4

Motif group IL_15052.4

Basepair signature:
cWW-L-cWW-L

100.00 78.95 1 0

Minor groove platform

5

Motif group IL_00881.1

Basepair signature:
cWW-L-cWW-L

100.00 78.70 2 0

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 75.85 4 0

Intercalated cWS

7

Motif group IL_95583.2

Basepair signature:
cWW-L-cWW

100.00 74.26 1 0

Minor groove platform, major groove intercalation

8

Motif group IL_68140.4

Basepair signature:
cWW-cSH-cWW

100.00 71.29 2 0

Major groove minor groove platform; mini C-loop

9

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 50.05 3 1

10

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 47.36 1 0

Major groove platform

Loop 2 Internal loop

Column numbers: 22-26, 40-47 
    Scored sequences and counts

    
    GAAAG*CAAGUACC    5

    
    GAAAG*UAAGUACC    5

    
    GAGGG*CAAGUACC    5

    
    CAGGG*CAAGUACC    3

    
    AAAGG*CCUUUACC    2

    
    GAACG*CAAGUACC    2

    
    GAAGG*CCUUUAUC    2

    
    GAGGG*CAAAUACC    2

    
    GAGGG*CAGGUACC    2

    
    GAGGG*CCGCUACC    2

    
    UAGAG*CAUAUACC    2

    
    AAAAG*CAAGUACC    1

    
    AAAAG*CAGAUACC    1

    
    AAAAG*CAGGUACC    1

    
    AAAGG*CCUUUAUC    1

    
    AAGGG*CAAAUACC    1

    
    CAGGG*UCUCUACC    1

    
    GAAAG*AAAGUACC    1

    
    GAAAG*CCGAUAUC    1

    
    GAAAG*UAGGUACC    1

    
    GAAGG*CCUAUACC    1

    
    GAAGG*UACGUACC    1

    
    GAGAG*UCGAUAUC    1

    
    GAGGG*AAAGUACC    1

    
    GAGGG*CCGCUAUC    1

    
    GAGGG*CCGGUAUC    1

    
    GAGGG*CCGUUACC    1

    
    GAGGG*GAAGUACC    1

    
    UAAAG*CAUAUACC    1

    
    UAAAG*CCGCUACC    1

    
    UAAGG*CAUCUAUC    1

    
    UAAGG*CUUAUACC    1

    
    UAGGG*CAUCUAUC    1

    
    UAGGG*CCACUACC    1

    
    Omitted sequenced and counts

    
    GAAAG*MAAAUACC    1

    
    UAGRG*CAAAUACC    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_54041.2

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

40.00 -0.94 5 4

tHW-tHW cross-strand stack

2

Motif group IL_77045.1

Basepair signature:
cWW-L-tSW-L-tHW-cWW-L

14.55 -24.35 9 5

Kink-turn

3

Motif group IL_01488.3

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

3.64 -25.55 5 4

Kink-turn

4

Motif group IL_59258.1

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

3.64 -44.47 9 5

5

Motif group IL_77870.1

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

1.82 -47.37 6 6

6

Motif group IL_69229.3

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

1.82 -51.58 7 5

Kink-turn

Loop 3 Hairpin loop

Column numbers: 30-36 
    Scored sequences and counts

    
    CCAUAUG    9

    
    CUAUAUG    9

    
    CCACUUG    4

    
    CCAUCUG    4

    
    AAAUAUG    3

    
    CCGUUUG    3

    
    CUAUUUG    3

    
    AAAUCUG    2

    
    GCAUAUG    2

    
    AAAUUUG    1

    
    AGAUAUG    1

    
    CAAUAUG    1

    
    CAAUUUG    1

    
    CAUUAUG    1

    
    CCACAUG    1

    
    CCACGUG    1

    
    CCAUUUG    1

    
    CCGUGUG    1

    
    CGAUAUG    1

    
    CGAUUUG    1

    
    CUACCUG    1

    
    CUAUCUG    1

    
    CUGAAUG    1

    
    CUGUAUG    1

    
    GAAUCUG    1

    
    GGAUAUG    1

    
    Omitted sequenced and counts

    
    CYAUAUG    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_53890.2

Basepair signature:
cWW-F-F-F

69.64 8.11 2 2

2

Motif group HL_59735.5

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

51.79 -4.21 2.5 2

3

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

48.21 -9.42 3 3

Other HL

4

Motif group HL_39243.1

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

48.21 -10.07 4 2

5

Motif group HL_57875.1

Basepair signature:
cWW-F-F

44.64 -10.83 3 2

6

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

42.86 -17.37 3 3

7

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

42.86 -24.58 2 2

8

Motif group HL_20535.2

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

35.71 -18.55 4.5 3

9

Motif group HL_25967.2

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

32.14 -7.32 3 2

10

Motif group HL_48417.5

Basepair signature:
cWW-F-F

30.36 -3.09 2 2

Coloring options: