RNA 3D Hub //

5H4P Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5H4P_0011/1/38:45No text annotation
Not in a motif group		geometric
HL_5TBW_001
HL_06192.2
HL_5H4P_0021/1/69:74No text annotation
Not in a motif group		homologous
HL_8C3A_002
HL_02862.2
HL_5H4P_0031/1/90:96No text annotation
Not in a motif group		homologous
HL_8C3A_003
HL_67216.7
HL_5H4P_0041/1/132:136No text annotation
Not in a motif group		homologous
HL_8C3A_004
HL_98426.1
HL_5H4P_0051/1/194:201T-loop with 1 bulged base
Not in a motif group		homologous
HL_5TBW_005
HL_89380.2
HL_5H4P_0061/1/208:212No text annotation
Not in a motif group		homologous
HL_8C3A_006
HL_98984.2
HL_5H4P_0071/1/216:224No text annotation
Not in a motif group		homologous
HL_8C3A_007
HL_08002.8
HL_5H4P_0081/1/278:287No text annotation
Not in a motif group		homologous
HL_5TBW_008
HL_71554.2
HL_5H4P_0101/1/357:362No text annotation
Not in a motif group		homologous
HL_8C3A_010
HL_42097.1
HL_5H4P_0111/1/382:387No text annotation
Not in a motif group		homologous
HL_8C3A_011
HL_42097.1
HL_5H4P_0121/1/541:550No text annotation
Not in a motif group
HL_5H4P_0131/1/599:604GNRA
Not in a motif group		homologous
HL_5TBW_013
HL_42097.1
HL_5H4P_0141/1/640:649T-loop with 2 stacked bulged bases
Not in a motif group		homologous
HL_5TBW_014
HL_89380.2
HL_5H4P_0151/1/686:694No text annotation
Not in a motif group		homologous
HL_5TBW_015
HL_03345.1
HL_5H4P_0161/1/707:712No text annotation
Not in a motif group		homologous
HL_8C3A_016
HL_42097.1
HL_5H4P_0171/1/732:737GNRA
Not in a motif group		homologous
HL_5TBW_017
HL_42097.1
HL_5H4P_0221/1/957:964No text annotation
Not in a motif group
HL_5H4P_0251/1/1126:1132No text annotation
Not in a motif group		homologous
HL_8C3A_025
HL_42097.1
HL_5H4P_0261/1/1147:1156No text annotation
Not in a motif group
HL_5H4P_0291/1/1403:1408GNRA
Not in a motif group		homologous
HL_5TBW_030
HL_42097.1
HL_5H4P_0611/1/2835:2853No text annotation
Not in a motif group
HL_5H4P_0621/1/2897:2904No text annotation
Not in a motif group		homologous
HL_5TBW_062
HL_88526.2
HL_5H4P_0631/1/2920:2926No text annotation
Not in a motif group		geometric
HL_5TBW_063
HL_43656.2
HL_5H4P_0651/1/3025:3030GNRA
Not in a motif group		geometric
HL_5TBW_065
HL_42097.1
HL_5H4P_0661/1/3068:3073No text annotation
Not in a motif group		homologous
HL_8C3A_067
HL_46680.1
HL_5H4P_0671/1/3110:3124No text annotation
Not in a motif group		homologous
HL_5TBW_067
HL_56677.7
HL_5H4P_0681/1/3194:3197No text annotation
Not in a motif group		geometric
HL_6U8D_003
HL_89098.1
HL_5H4P_0691/1/3240:3247No text annotation
Not in a motif group		homologous
HL_5TBW_069
HL_14449.2
HL_5H4P_0701/1/3303:3311No text annotation
Not in a motif group		homologous
HL_5TBW_070
HL_27930.1
HL_5H4P_0711/1/3345:3360No text annotation
Not in a motif group
HL_5H4P_0721/3/36:41No text annotation
Not in a motif group		homologous
HL_5TBW_185
HL_87939.1
HL_5H4P_0731/3/88:93GNRA
Not in a motif group		homologous
HL_4V9F_072
HL_42097.1
HL_5H4P_0751/4/108:114No text annotation
Not in a motif group		homologous
HL_5TBW_075
HL_87939.1
HL_5H4P_0761/4/124:129No text annotation
Not in a motif group		homologous
HL_5TBW_076
HL_96851.2

Problematic loops

#loop idProblemSequence
HL_5H4P_009No text annotation
HL_5H4P_018No text annotation
HL_5H4P_019GNRA
HL_5H4P_020No text annotation
HL_5H4P_021No text annotation
HL_5H4P_023No text annotation
HL_5H4P_024No text annotation
HL_5H4P_027No text annotation
HL_5H4P_028No text annotation
HL_5H4P_030No text annotation
HL_5H4P_031No text annotation
HL_5H4P_032No text annotation
HL_5H4P_033No text annotation
HL_5H4P_034No text annotation
HL_5H4P_035No text annotation
HL_5H4P_036No text annotation
HL_5H4P_037No text annotation
HL_5H4P_038Other HL
HL_5H4P_039No text annotation
HL_5H4P_040No text annotation
HL_5H4P_041GNRA with one bulged base
HL_5H4P_042No text annotation
HL_5H4P_043No text annotation
HL_5H4P_044No text annotation
HL_5H4P_045No text annotation
HL_5H4P_046No text annotation
HL_5H4P_047Other HL
HL_5H4P_048No text annotation
HL_5H4P_049No text annotation
HL_5H4P_050No text annotation
HL_5H4P_051No text annotation
HL_5H4P_052No text annotation
HL_5H4P_053No text annotation
HL_5H4P_054No text annotation
HL_5H4P_055No text annotation
HL_5H4P_056No text annotation
HL_5H4P_057No text annotation
HL_5H4P_058No text annotation
HL_5H4P_059GNRA
HL_5H4P_060No text annotation
HL_5H4P_064GNRA
HL_5H4P_074No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5H4P_0011/1/3:4,
1/4/155:156		No text annotation
Not in a motif group
IL_5H4P_0021/1/7:8,
1/4/150:152		Single bulged C
Not in a motif group		homologous
IL_5TBW_002
IL_61258.12
IL_5H4P_0031/1/13:15,
1/4/144:145		Single bulged U
Not in a motif group		homologous
IL_5TBW_003
IL_83039.13
IL_5H4P_0041/1/27:28,
1/1/56:58		No text annotation
Not in a motif group		homologous
IL_8C3A_004
IL_76488.2
IL_5H4P_0051/1/31:38,
1/1/45:53		tSH-tHW-tHH-tHS
Not in a motif group		homologous
IL_5TBW_005
IL_35728.2
IL_5H4P_0061/1/82:89,
1/1/97:103		No text annotation
Not in a motif group		homologous
IL_8C3A_006
IL_88613.1
IL_5H4P_0071/1/123:124,
1/1/144:149		No text annotation
Not in a motif group		homologous
IL_5TBW_007
IL_19724.2
IL_5H4P_0081/1/125:127,
1/1/141:143		No text annotation
Not in a motif group		homologous
IL_5TBW_008
IL_95997.1
IL_5H4P_0091/1/163:167,
1/1/255:258		No text annotation
Not in a motif group		homologous
IL_8C3A_009
IL_80581.1
IL_5H4P_0101/1/169:170,
1/1/248:253		No text annotation
Not in a motif group		homologous
IL_5TBW_010
IL_74684.1
IL_5H4P_0111/1/177:179,
1/1/237:241		Major groove platform with extra pair
Not in a motif group		homologous
IL_5TBW_011
IL_63450.2
IL_5H4P_0121/1/189:191,
1/1/204:205		No text annotation
Not in a motif group		homologous
IL_8C3A_013
IL_83039.13
IL_5H4P_0131/1/337:339,
1/4/25:26		Single bulged A
Not in a motif group		homologous
IL_5TBW_013
IL_37497.2
IL_5H4P_0141/1/404:410,
1/4/13:19		Triple sheared with non-canonical cWW
Not in a motif group		homologous
IL_5TBW_015
IL_66414.6
IL_5H4P_0151/1/429:431,
1/1/628:630		No text annotation
Not in a motif group		homologous
IL_5TBW_016
IL_51629.2
IL_5H4P_0171/1/512:513,
1/1/577:579		No text annotation
Not in a motif group		homologous
IL_8C3A_020
IL_37497.2
IL_5H4P_0181/1/517:525,
1/1/567:573		No text annotation
Not in a motif group		homologous
IL_5TBW_019
IL_23992.1
IL_5H4P_0191/1/531:538,
1/1/553:561		No text annotation
Not in a motif group		homologous
IL_5TBW_020
IL_07703.1
IL_5H4P_0201/1/667:670,
1/1/792:795		No text annotation
Not in a motif group
IL_5H4P_0211/1/680:684,
1/1/696:700		No text annotation
Not in a motif group		homologous
IL_5TBW_022
IL_74284.1
IL_5H4P_0221/1/725:728,
1/1/741:745		No text annotation
Not in a motif group		homologous
IL_8C3A_025
IL_07235.1
IL_5H4P_0231/1/752:753,
1/1/779:781		Single bulged A
Not in a motif group		homologous
IL_5TBW_024
IL_37497.2
IL_5H4P_0241/1/755:756,
1/1/775:777		Single bulged U
Not in a motif group		homologous
IL_5TBW_025
IL_83039.13
IL_5H4P_0261/1/803:805,
1/1/938:940		No text annotation
Not in a motif group		homologous
IL_8C3A_029
IL_95997.1
IL_5H4P_0271/1/805:809,
1/1/931:938		No text annotation
Not in a motif group		geometric
IL_5TBW_028
IL_17470.6
IL_5H4P_0331/1/954:956,
1/1/965:967		No text annotation
Not in a motif group		homologous
IL_5TBW_034
IL_95997.1
IL_5H4P_0341/1/969:970,
1/1/1111:1113		Single stack bend
Not in a motif group		homologous
IL_5TBW_035
IL_76488.2
IL_5H4P_0351/1/977:982,
1/1/1101:1104		No text annotation
Not in a motif group		homologous
IL_8C3A_039
IL_59027.1
IL_5H4P_0361/1/983:985,
1/1/1099:1100		No text annotation
Not in a motif group		homologous
IL_8C3A_040
IL_00225.2
IL_5H4P_0391/1/1120:1122,
1/1/1136:1138		No text annotation
Not in a motif group		homologous
IL_8C3A_049
IL_95997.1
IL_5H4P_0401/1/1167:1171,
1/1/1328:1332		No text annotation
Not in a motif group		homologous
IL_8C3A_051
IL_89002.2
IL_5H4P_0411/1/1173:1180,
1/1/1325:1326		SSU/LSU pseudoknot
Not in a motif group		homologous
IL_5TBW_049
IL_15861.7
IL_5H4P_0421/1/1180:1182,
1/1/1324:1325		Single bulged U
Not in a motif group		geometric
IL_7A0S_035
IL_83039.13
IL_5H4P_0431/1/1187:1194,
1/1/1314:1319		No text annotation
Not in a motif group		homologous
IL_8C3A_054
IL_27086.1
IL_5H4P_0441/1/1194:1205,
1/1/1299:1314		No text annotation
Not in a motif group		geometric
IL_5TBW_052
IL_53762.1
IL_5H4P_0451/1/1207:1209,
1/1/1296:1297		No text annotation
Not in a motif group		homologous
IL_8C3A_056
IL_83039.13
IL_5H4P_0461/1/1218:1229,
1/1/1280:1287		No text annotation
Not in a motif group
IL_5H4P_0481/1/1376:1378,
1/1/1428:1431		Isolated cWS basepair
Not in a motif group		homologous
IL_5TBW_057
IL_52767.2
IL_5H4P_0491/1/1385:1387,
1/1/1420:1421		No text annotation
Not in a motif group		homologous
IL_8C3A_062
IL_37497.2
IL_5H4P_0501/1/1388:1395,
1/1/1415:1419		Kink-turn
Not in a motif group		homologous
IL_5TBW_059
IL_70923.2
IL_5H4P_0511/1/1397:1400,
1/1/1411:1413		No text annotation
Not in a motif group		homologous
IL_8C3A_064
IL_95997.1
IL_5H4P_0521/1/1443:1450,
1/1/2354:2360		8x7 Sarcin-Ricin; G-bulge
Not in a motif group		geometric
IL_5TBW_116
IL_04346.7
IL_5H4P_0791/1/2391:2394,
1/1/2986:2988		Major groove platform with extra pair
Not in a motif group		homologous
IL_5TBW_091
IL_63450.2
IL_5H4P_0901/1/2824:2826,
1/1/2863:2865		No text annotation
Not in a motif group		geometric
IL_5TBW_021
IL_95997.1
IL_5H4P_0911/1/2826:2831,
1/1/2857:2863		No text annotation
Not in a motif group
IL_5H4P_0921/1/2876:2877,
1/1/2949:2951		Major groove platform
Not in a motif group		homologous
IL_5TBW_107
IL_76223.2
IL_5H4P_0931/1/2879:2881,
1/1/2943:2947		Isolated non-canonical cWW with bulges
Not in a motif group		geometric
IL_5TBW_108
IL_90933.2
IL_5H4P_0941/1/2881:2882,
1/1/2940:2943		No text annotation
Not in a motif group		homologous
IL_8C3A_117
IL_71530.2
IL_5H4P_0951/1/2889:2891,
1/1/2912:2914		No text annotation
Not in a motif group		geometric
IL_5TBW_110
IL_51629.2
IL_5H4P_0961/1/2891:2892,
1/1/2909:2912		Minor groove platform with intercalation
Not in a motif group		homologous
IL_5TBW_111
IL_95601.3
IL_5H4P_0971/1/2918:2920,
1/1/2926:2928		No text annotation
Not in a motif group		homologous
IL_8C3A_120
IL_95997.1
IL_5H4P_0991/1/3004:3007,
1/1/3139:3144		Double sheared
Not in a motif group		homologous
IL_5TBW_114
IL_09705.9
IL_5H4P_1001/1/3012:3014,
1/1/3040:3042		No text annotation
Not in a motif group		homologous
IL_8C3A_124
IL_95997.1
IL_5H4P_1011/1/3018:3025,
1/1/3030:3036		8x7 Sarcin-Ricin; G-bulge
Not in a motif group		homologous
IL_5TBW_116
IL_04346.7
IL_5H4P_1021/1/3047:3051,
1/1/3091:3094		Major groove minor groove platform with tHH
Not in a motif group		homologous
IL_5TBW_117
IL_37712.2
IL_5H4P_1031/1/3054:3059,
1/1/3084:3088		UAA/GAN related
Not in a motif group		homologous
IL_5TBW_118
IL_17136.1
IL_5H4P_1041/1/3063:3064,
1/1/3077:3080		No text annotation
Not in a motif group		homologous
IL_8C3A_128
IL_71530.2
IL_5H4P_1051/1/3103:3107,
1/1/3127:3131		No text annotation
Not in a motif group		homologous
IL_8C3A_129
IL_89002.2
IL_5H4P_1061/1/3162:3166,
1/1/3284:3288		No text annotation
Not in a motif group		homologous
IL_5TBW_121
IL_05145.2
IL_5H4P_1071/1/3177:3179,
1/1/3210:3211		Single bulged A
Not in a motif group		homologous
IL_5TBW_123
IL_37497.2
IL_5H4P_1081/1/3179:3188,
1/1/3204:3210		No text annotation
Not in a motif group		geometric
IL_5TBW_124
IL_15174.1
IL_5H4P_1091/1/3193:3194,
1/1/3197:3199		Single bulged U
Not in a motif group		homologous
IL_5TBW_125
IL_83039.13
IL_5H4P_1101/1/3225:3229,
1/1/3258:3260		No text annotation
Not in a motif group		homologous
IL_5TBW_126
IL_19389.6
IL_5H4P_1111/1/3233:3235,
1/1/3252:3254		No text annotation
Not in a motif group		geometric
IL_4M4O_002
IL_95997.1
IL_5H4P_1121/1/3235:3238,
1/1/3249:3252		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_5TBW_128
IL_30621.2
IL_5H4P_1131/1/3300:3303,
1/1/3311:3314		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_5TBW_129
IL_30621.2
IL_5H4P_1141/1/3318:3320,
1/1/3387:3388		Single bulged U
Not in a motif group		geometric
IL_5TBW_130
IL_83039.13
IL_5H4P_1151/1/3324:3326,
1/1/3380:3383		Isolated non-canonical cWW with bulges
Not in a motif group		geometric
IL_4V9F_097
IL_82068.2
IL_5H4P_1161/1/3328:3330,
1/1/3373:3378		No text annotation
Not in a motif group		homologous
IL_8C3A_138
IL_90933.2
IL_5H4P_1171/1/3332:3337,
1/1/3367:3371		No text annotation
Not in a motif group		homologous
IL_8C3A_139
IL_83162.5
IL_5H4P_1181/1/3340:3342,
1/1/3363:3364		No text annotation
Not in a motif group		homologous
IL_8C3A_140
IL_83039.13
IL_5H4P_1191/1/3342:3345,
1/1/3360:3363		Double sheared
Not in a motif group		geometric
IL_4V9F_100
IL_09705.9
IL_5H4P_1201/3/15:16,
1/3/63:65		Single bulged A
Not in a motif group		homologous
IL_5TBW_372
IL_37497.2
IL_5H4P_1211/3/21:27,
1/3/53:58		No text annotation
Not in a motif group		homologous
IL_5TBW_373
IL_10207.2
IL_5H4P_1221/3/28:29,
1/3/49:52		Minor groove platform
Not in a motif group		geometric
IL_5TBW_374
IL_63797.2
IL_5H4P_1231/3/29:30,
1/3/47:49		Single stack bend
Not in a motif group		homologous
IL_5TBW_375
IL_76488.2
IL_5H4P_1241/3/32:36,
1/3/41:45		Symmetric double minor groove platform
Not in a motif group		geometric
IL_5TBW_376
IL_58103.6
IL_5H4P_1251/3/71:80,
1/3/100:107		9x8 Sarcin-Ricin with GA cWW pair; G-bulge
Not in a motif group		geometric
IL_3DIL_003
IL_34470.2
IL_5H4P_1261/3/84:87,
1/3/94:96		No text annotation
Not in a motif group		homologous
IL_5TBW_378
IL_95997.1
IL_5H4P_1271/4/44:64,
1/4/96:100		No text annotation
Not in a motif group		geometric
IL_5TBW_144
IL_44998.1
IL_5H4P_1281/4/64:66,
1/4/93:96		Isolated non-canonical cWW with bulges
Not in a motif group		homologous
IL_5TBW_145
IL_82068.2
IL_5H4P_1291/4/68:69,
1/4/89:91		Single bulged U
Not in a motif group		geometric
IL_5TBW_146
IL_83039.13

Problematic loops

#loop idProblemSequence
IL_5H4P_016No text annotation
IL_5H4P_025No text annotation
IL_5H4P_028No text annotation
IL_5H4P_029Triple sheared
IL_5H4P_030Major groove platform with extra cWW
IL_5H4P_031Single bulged U
IL_5H4P_032Multiple bulged bases
IL_5H4P_037Tandem non-canonical cWW pairs
IL_5H4P_038Single bulged A
IL_5H4P_047No text annotation
IL_5H4P_053Major groove minor groove platform with tHH
IL_5H4P_054No text annotation
IL_5H4P_055No text annotation
IL_5H4P_056No text annotation
IL_5H4P_057No text annotation
IL_5H4P_058No text annotation
IL_5H4P_059Single bulged C
IL_5H4P_060Single stack bend
IL_5H4P_061No text annotation
IL_5H4P_062No text annotation
IL_5H4P_063Kink-turn
IL_5H4P_064No text annotation
IL_5H4P_065No text annotation
IL_5H4P_066No text annotation
IL_5H4P_067Intercalated tWH
IL_5H4P_068No text annotation
IL_5H4P_069No text annotation
IL_5H4P_070No text annotation
IL_5H4P_071No text annotation
IL_5H4P_072Kink-turn related
IL_5H4P_073Major groove outside cWW, minor groove, intercalation pocket
IL_5H4P_074Major groove outside cWW, minor groove, intercalation pocket
IL_5H4P_075No text annotation
IL_5H4P_076No text annotation
IL_5H4P_077No text annotation
IL_5H4P_078No text annotation
IL_5H4P_080Minor groove platform with intercalation
IL_5H4P_081No text annotation
IL_5H4P_082Minor groove platform
IL_5H4P_083Isolated tHS basepair with bulges
IL_5H4P_084No text annotation
IL_5H4P_085Single bulged A
IL_5H4P_086No text annotation
IL_5H4P_087No text annotation
IL_5H4P_088No text annotation
IL_5H4P_089Major groove platform
IL_5H4P_098No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5H4P_0011/1/113:123,
1/1/149:158,
1/1/263:267		No text annotation
Not in a motif group
J3_5H4P_0021/1/501:503,
1/1/588:597,
1/1/606:612		No text annotation
Not in a motif group
J3_5H4P_0051/1/986:987,
1/1/1062:1066,
1/1/1092:1098		No text annotation
Not in a motif group		homologous
J3_5TBW_006
NA
J3_5H4P_0131/1/2886:2889,
1/1/2914:2916,
1/1/2930:2936		No text annotation
Not in a motif group
J3_5H4P_0141/1/3298:3300,
1/1/3314:3318,
1/1/3388:3390		No text annotation
Not in a motif group		homologous
J3_5TBW_015
NA
J3_5H4P_0151/3/9:15,
1/3/65:67,
1/3/111:112		No text annotation
Not in a motif group

Problematic loops

#loop idProblemSequence
J3_5H4P_003No text annotation
J3_5H4P_004No text annotation
J3_5H4P_006No text annotation
J3_5H4P_007No text annotation
J3_5H4P_008No text annotation
J3_5H4P_009No text annotation
J3_5H4P_010No text annotation
J3_5H4P_011No text annotation
J3_5H4P_012No text annotation

Coloring options:
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