RNA 3D Hub

JAR3D Query RF00468-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold 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, 50-55
  • Loop 2IL Column numbers: 21-26, 40-46
  • Loop 3HL Column numbers: 30-36

Loop 1 Internal loop

Column numbers: 16-17, 50-55 
    Scored sequences and counts

    
    GG*UUCAAC   21

    
    GG*UUUAAC    9

    
    AG*UUCAAC    5

    
    AG*UUUAAC    5

    
    GG*UUUAAU    5

    
    AG*UUCAAU    4

    
    AG*UUUAAU    2

    
    GG*UUCAAU    2

    
    UG*UUCAAU    2

    
    UG*UUCAAC    1

    
    Omitted sequenced and counts

    
    AG*UUYAAC    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_99380.1

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

82.14 19.02 4 3

2

Motif group IL_38186.6

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

37.50 -9.91 5 2

3

Motif group IL_61299.4

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

19.64 -28.29 5 3

4

Motif group IL_25573.1

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

16.07 -34.58 5 3

Loop 2 Internal loop

Column numbers: 21-26, 40-46 
    Scored sequences and counts

    
    GGAAAG*CAAGUAC    5

    
    GGAAAG*UAAGUAC    5

    
    GGAGGG*CAAGUAC    5

    
    GCAGGG*CAAGUAC    3

    
    GAAAGG*CCUUUAC    2

    
    GGAACG*CAAGUAC    2

    
    GGAAGG*CCUUUAU    2

    
    GGAGGG*CAAAUAC    2

    
    GGAGGG*CAGGUAC    2

    
    GGAGGG*CCGCUAC    2

    
    GUAGAG*CAUAUAC    2

    
    GAAAAG*CAAGUAC    1

    
    GAAAAG*CAGAUAC    1

    
    GAAAAG*CAGGUAC    1

    
    GAAAGG*CCUUUAU    1

    
    GAAGGG*CAAAUAC    1

    
    GCAGGG*UCUCUAC    1

    
    GGAAAG*AAAGUAC    1

    
    GGAAAG*CCGAUAU    1

    
    GGAAAG*UAGGUAC    1

    
    GGAAGG*CCUAUAC    1

    
    GGAAGG*UACGUAC    1

    
    GGAGAG*UCGAUAU    1

    
    GGAGGG*AAAGUAC    1

    
    GGAGGG*CCGCUAU    1

    
    GGAGGG*CCGGUAU    1

    
    GGAGGG*CCGUUAC    1

    
    GGAGGG*GAAGUAC    1

    
    GUAAAG*CAUAUAC    1

    
    GUAAAG*CCGCUAC    1

    
    GUAAGG*CAUCUAU    1

    
    GUAAGG*CUUAUAC    1

    
    GUAGGG*CAUCUAU    1

    
    GUAGGG*CCACUAC    1

    
    Omitted sequenced and counts

    
    GGAAAG*MAAAUAC    1

    
    GUAGRG*CAAAUAC    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_61286.1

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

58.18 3.59 3 3

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

2

Motif group IL_26307.2

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

43.64 5.97 5 3

7x6 Sarcin-Ricin; G-bulge

3

Motif group IL_24254.1

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

41.82 -1.74 6 4

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

4

Motif group IL_29198.2

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

36.36 -15.16 7 3

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

5

Motif group IL_16458.4

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

30.91 -22.14 4 4

Sarcin-Ricin target in LSU H95; G-bulge

6

Motif group IL_88269.4

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

27.27 -23.49 4 3

6x5 Sarcin-Ricin; G-bulge

7

Motif group IL_41756.4

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

25.45 -48.87 8 4

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

8

Motif group IL_04346.10

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

23.64 -44.75 5 4

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_47346.2

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

23.64 -57.52 8 4

tSH-tSH-tHH-tHS

10

Motif group IL_32016.1

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

12.73 -63.91 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: