RNA 3D Hub //

6S05 Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6S05_0011/A/31:53No text annotation
Not in a motif group
HL_6S05_0021/A/69:74No text annotation
Not in a motif group		homologous
HL_5TBW_002
HL_96776.3
HL_6S05_0031/A/90:96No text annotation
Not in a motif group		homologous
HL_5TBW_003
HL_67216.5
HL_6S05_0041/A/132:136No text annotation
Not in a motif group		homologous
HL_5TBW_004
HL_36982.3
HL_6S05_0051/A/194:201T-loop with 1 bulged base
Not in a motif group		homologous
HL_5TBW_005
HL_68493.6
HL_6S05_0061/A/208:212No text annotation
Not in a motif group		homologous
HL_5TBW_006
HL_98557.5
HL_6S05_0071/A/216:224No text annotation
Not in a motif group		homologous
HL_5TBW_007
HL_08002.6
HL_6S05_0081/A/278:287No text annotation
Not in a motif group		homologous
HL_5TBW_008
HL_54035.7
HL_6S05_0101/A/357:362Other HL
Not in a motif group		homologous
HL_5TBW_010
HL_43074.18
HL_6S05_0111/A/382:387GNRA
Not in a motif group		homologous
HL_5TBW_011
HL_43074.18
HL_6S05_0121/A/539:552No text annotation
Not in a motif group
HL_6S05_0131/A/599:604GNRA
Not in a motif group		homologous
HL_5TBW_013
HL_43074.18
HL_6S05_0141/A/639:650No text annotation
Not in a motif group		geometric
HL_4V9I_040
HL_32458.3
HL_6S05_0151/A/686:694No text annotation
Not in a motif group		homologous
HL_5TBW_015
HL_80105.3
HL_6S05_0171/A/732:737GNRA
Not in a motif group		homologous
HL_5TBW_017
HL_43074.18
HL_6S05_0221/A/958:963No text annotation
Not in a motif group		homologous
HL_5TBW_022
HL_15942.5
HL_6S05_0261/A/1148:1155No text annotation
Not in a motif group		homologous
HL_5TBW_026
HL_72451.5
HL_6S05_0291/A/1347:1357No text annotation
Not in a motif group
HL_6S05_0301/A/1403:1408GNRA
Not in a motif group		homologous
HL_5TBW_030
HL_43074.18
HL_6S05_0641/A/3025:3030No text annotation
Not in a motif group		geometric
HL_5J7L_179
HL_32527.3
HL_6S05_0651/A/3068:3073Ribsomal LSU H95
Not in a motif group		homologous
HL_5TBW_066
HL_67719.1
HL_6S05_0661/A/3110:3124No text annotation
Not in a motif group		homologous
HL_5TBW_067
HL_56677.5
HL_6S05_0671/A/3194:3197No text annotation
Not in a motif group		geometric
HL_5TBW_068
HL_46546.1
HL_6S05_0681/A/3300:3314No text annotation
Not in a motif group
HL_6S05_0701/x/36:41No text annotation
Not in a motif group		geometric
HL_5TBW_185
HL_02733.5
HL_6S05_0711/x/88:93GNRA
Not in a motif group		homologous
HL_5TBW_186
HL_43074.18
HL_6S05_0721/y/69:89No text annotation
Not in a motif group
HL_6S05_0731/y/108:114No text annotation
Not in a motif group		homologous
HL_5TBW_075
HL_06569.2
HL_6S05_0741/y/124:129No text annotation
Not in a motif group

Problematic loops

#loop idProblemSequence
HL_6S05_009No text annotation
HL_6S05_016GNRA
HL_6S05_018No text annotation
HL_6S05_019Other HL
HL_6S05_020No text annotation
HL_6S05_021No text annotation
HL_6S05_023No text annotation
HL_6S05_024No text annotation
HL_6S05_025No text annotation
HL_6S05_027No text annotation
HL_6S05_028No text annotation
HL_6S05_031T-loop with 2 stacked bulged bases
HL_6S05_032No text annotation
HL_6S05_033Other HL
HL_6S05_034No text annotation
HL_6S05_035No text annotation
HL_6S05_036GNRA
HL_6S05_037No text annotation
HL_6S05_038No text annotation
HL_6S05_039No text annotation
HL_6S05_040No text annotation
HL_6S05_041No text annotation
HL_6S05_042GNRA with one bulged base
HL_6S05_043UNCG
HL_6S05_044No text annotation
HL_6S05_045No text annotation
HL_6S05_046GNRA
HL_6S05_047Other HL
HL_6S05_048No text annotation
HL_6S05_049No text annotation
HL_6S05_050No text annotation
HL_6S05_051No text annotation
HL_6S05_052No text annotation
HL_6S05_053No text annotation
HL_6S05_054No text annotation
HL_6S05_055No text annotation
HL_6S05_056No text annotation
HL_6S05_057No text annotation
HL_6S05_058GNRA
HL_6S05_059No text annotation
HL_6S05_060No text annotation
HL_6S05_061No text annotation
HL_6S05_062No text annotation
HL_6S05_063GNRA
HL_6S05_069No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6S05_0011/A/7:8,
1/y/150:152		Single bulged C
Not in a motif group		homologous
IL_5TBW_002
IL_61258.10
IL_6S05_0021/A/13:15,
1/y/144:145		Single bulged U
Not in a motif group		homologous
IL_5TBW_003
IL_83039.11
IL_6S05_0031/A/27:28,
1/A/56:58		Single stack bend
Not in a motif group		homologous
IL_5TBW_004
IL_04038.4
IL_6S05_0041/A/81:89,
1/A/97:104		9x8 Sarcin-Ricin with GA cWW pair; G-bulge
Not in a motif group		geometric
IL_3DIL_003
IL_34470.1
IL_6S05_0051/A/123:124,
1/A/144:149		No text annotation
Not in a motif group		geometric
IL_5TBW_007
IL_19724.1
IL_6S05_0061/A/125:127,
1/A/141:143		No text annotation
Not in a motif group		homologous
IL_5TBW_008
IL_01312.13
IL_6S05_0081/A/169:173,
1/A/245:253		No text annotation
Not in a motif group
IL_6S05_0091/A/177:179,
1/A/237:241		Major groove platform with extra pair
Not in a motif group		homologous
IL_5TBW_011
IL_87630.5
IL_6S05_0101/A/189:192,
1/A/203:205		CC cWW
Not in a motif group		geometric
IL_4E59_001
IL_01312.13
IL_6S05_0111/A/337:339,
1/y/25:26		Single bulged A
Not in a motif group		homologous
IL_5TBW_013
IL_80007.16
IL_6S05_0121/A/376:379,
1/A/390:403		No text annotation
Not in a motif group		geometric
IL_5TBW_014
IL_60992.5
IL_6S05_0131/A/404:410,
1/y/13:19		Triple sheared with non-canonical cWW
Not in a motif group		homologous
IL_5TBW_015
IL_66414.5
IL_6S05_0141/A/412:414,
1/y/10:11		Single stack bend
Not in a motif group		geometric
IL_7A0S_054
IL_04038.4
IL_6S05_0151/A/414:415,
1/y/8:10		Single stack bend
Not in a motif group		geometric
IL_7A0S_054
IL_04038.4
IL_6S05_0161/A/429:431,
1/A/628:630		No text annotation
Not in a motif group		homologous
IL_5TBW_016
IL_01312.13
IL_6S05_0181/A/510:513,
1/A/577:581		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_1MFQ_004
IL_85877.10
IL_6S05_0191/A/517:525,
1/A/567:573		No text annotation
Not in a motif group		homologous
IL_5TBW_019
IL_41593.1
IL_6S05_0201/A/531:538,
1/A/553:561		No text annotation
Not in a motif group		homologous
IL_5TBW_020
IL_94501.1
IL_6S05_0211/A/667:670,
1/A/792:795		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_4K27_001
IL_85877.10
IL_6S05_0221/A/680:684,
1/A/696:700		No text annotation
Not in a motif group		homologous
IL_5TBW_022
IL_92343.1
IL_6S05_0231/A/725:728,
1/A/741:745		UAA/GAN
Not in a motif group		homologous
IL_5TBW_023
IL_53523.5
IL_6S05_0241/A/752:753,
1/A/779:781		Single bulged A
Not in a motif group		homologous
IL_5TBW_024
IL_80007.16
IL_6S05_0251/A/755:757,
1/A/774:777		Isolated non-canonical cWW with bulges
Not in a motif group		geometric
IL_5J7L_009
IL_55456.1
IL_6S05_0271/A/803:805,
1/A/938:940		No text annotation
Not in a motif group		homologous
IL_5TBW_027
IL_01312.13
IL_6S05_0281/A/805:809,
1/A/931:938		No text annotation
Not in a motif group		geometric
IL_5TBW_028
IL_17470.5
IL_6S05_0341/A/954:956,
1/A/965:967		No text annotation
Not in a motif group		homologous
IL_5TBW_034
IL_01312.13
IL_6S05_0351/A/969:970,
1/A/1111:1113		Single stack bend
Not in a motif group		homologous
IL_5TBW_035
IL_04038.4
IL_6S05_0361/A/977:981,
1/A/1102:1104		No text annotation
Not in a motif group		homologous
IL_5TBW_272
NA
IL_6S05_0371/A/983:985,
1/A/1099:1100		Single bulged G
Not in a motif group		homologous
IL_5TBW_037
IL_59137.10
IL_6S05_0411/A/1120:1122,
1/A/1136:1138		No text annotation
Not in a motif group		homologous
IL_5TBW_046
IL_01312.13
IL_6S05_0421/A/1167:1171,
1/A/1328:1332		UAA/GAN
Not in a motif group		homologous
IL_5TBW_048
IL_53523.5
IL_6S05_0431/A/1173:1180,
1/A/1325:1326		SSU/LSU pseudoknot
Not in a motif group		geometric
IL_5TBW_049
IL_15861.6
IL_6S05_0441/A/1180:1182,
1/A/1324:1325		Single bulged U
Not in a motif group		homologous
IL_5TBW_050
IL_83039.11
IL_6S05_0471/A/1207:1209,
1/A/1296:1297		Single bulged U
Not in a motif group		homologous
IL_5TBW_053
IL_83039.11
IL_6S05_0501/A/1376:1378,
1/A/1428:1431		Isolated cWS basepair
Not in a motif group		homologous
IL_5TBW_057
IL_01312.13
IL_6S05_0521/A/1388:1397,
1/A/1413:1419		No text annotation
Not in a motif group
IL_6S05_0541/A/1444:1450,
1/A/2354:2359		7x6 Sarcin-Ricin; G-bulge
Not in a motif group		homologous
IL_5TBW_061
IL_35110.5
IL_6S05_1041/A/3002:3007,
1/A/3139:3146		No text annotation
Not in a motif group
IL_6S05_1051/A/3012:3014,
1/A/3040:3042		No text annotation
Not in a motif group		homologous
IL_5TBW_115
IL_01312.13
IL_6S05_1061/A/3018:3025,
1/A/3030:3036		8x7 Sarcin-Ricin; G-bulge
Not in a motif group		homologous
IL_5TBW_116
IL_04346.5
IL_6S05_1071/A/3047:3051,
1/A/3091:3094		Major groove minor groove platform with tHH
Not in a motif group		homologous
IL_5TBW_117
IL_28060.3
IL_6S05_1081/A/3054:3059,
1/A/3084:3088		UAA/GAN related
Not in a motif group		homologous
IL_5TBW_118
IL_53523.5
IL_6S05_1101/A/3102:3107,
1/A/3127:3132		UAA/GAN with extra cWW
Not in a motif group		geometric
IL_5J7L_350
IL_49767.4
IL_6S05_1111/A/3162:3166,
1/A/3284:3288		No text annotation
Not in a motif group		geometric
IL_5TBW_121
IL_05867.1
IL_6S05_1131/A/3177:3179,
1/A/3210:3211		Single bulged A
Not in a motif group		geometric
IL_5TBW_123
IL_80007.16
IL_6S05_1141/A/3179:3188,
1/A/3204:3210		No text annotation
Not in a motif group		homologous
IL_5TBW_124
IL_56867.1
IL_6S05_1151/A/3193:3194,
1/A/3197:3199		Single bulged U
Not in a motif group		homologous
IL_5TBW_125
IL_83039.11
IL_6S05_1161/A/3318:3320,
1/A/3387:3388		Single bulged U
Not in a motif group		homologous
IL_5TBW_130
IL_83039.11
IL_6S05_1171/A/3324:3327,
1/A/3379:3383		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_3WBM_002
IL_85877.10
IL_6S05_1191/A/3332:3337,
1/A/3367:3371		No text annotation
Not in a motif group		homologous
IL_5TBW_133
IL_47002.1
IL_6S05_1211/x/15:16,
1/x/63:65		No text annotation
Not in a motif group
IL_6S05_1221/x/21:27,
1/x/53:58		No text annotation
Not in a motif group		homologous
IL_5TBW_373
IL_05523.1
IL_6S05_1231/x/28:29,
1/x/49:52		Minor groove platform
Not in a motif group		geometric
IL_5TBW_374
IL_94431.4
IL_6S05_1241/x/29:30,
1/x/47:49		Single stack bend
Not in a motif group		homologous
IL_5TBW_375
IL_04038.4
IL_6S05_1251/x/31:36,
1/x/41:46		No text annotation
Not in a motif group		homologous
IL_7A0S_105
IL_58346.1
IL_6S05_1261/x/83:85,
1/x/96:97		Single stack bend
Not in a motif group		geometric
IL_5J7L_269
IL_04038.4
IL_6S05_1271/y/44:64,
1/y/96:100		No text annotation
Not in a motif group		homologous
IL_5TBW_144
IL_23735.1
IL_6S05_1281/y/64:66,
1/y/93:96		Isolated non-canonical cWW with bulges
Not in a motif group		geometric
IL_5TBW_145
IL_55456.1
IL_6S05_1291/y/68:69,
1/y/89:91		Single bulged U
Not in a motif group		homologous
IL_5TBW_146
IL_83039.11

Problematic loops

#loop idProblemSequence
IL_6S05_007Single stack bend
IL_6S05_017No text annotation
IL_6S05_026No text annotation
IL_6S05_029Single bulged G
IL_6S05_030Triple sheared
IL_6S05_031Major groove platform with extra cWW
IL_6S05_032Single bulged U
IL_6S05_033No text annotation
IL_6S05_038No text annotation
IL_6S05_039No text annotation
IL_6S05_040No text annotation
IL_6S05_045No text annotation
IL_6S05_046No text annotation
IL_6S05_048No text annotation
IL_6S05_049No text annotation
IL_6S05_051Single bulged A
IL_6S05_053Single bulged A
IL_6S05_055No text annotation
IL_6S05_056UAA/GAN
IL_6S05_057Other IL
IL_6S05_058Major groove outside cWW, minor groove, intercalation pocket
IL_6S05_059No text annotation
IL_6S05_060Triple sheared
IL_6S05_061Single stack bend
IL_6S05_062Single stack bend
IL_6S05_063Single bulged C
IL_6S05_064Single stack bend
IL_6S05_065No text annotation
IL_6S05_066No text annotation
IL_6S05_067Kink-turn
IL_6S05_068No text annotation
IL_6S05_069Isolated tWW turn
IL_6S05_070Major groove platform; stack outside cWW
IL_6S05_071Intercalated tWH
IL_6S05_072No text annotation
IL_6S05_073No text annotation
IL_6S05_074No text annotation
IL_6S05_075No text annotation
IL_6S05_076Kink-turn related
IL_6S05_077No text annotation
IL_6S05_078No text annotation
IL_6S05_079No text annotation
IL_6S05_080Multiple bulged bases
IL_6S05_081No text annotation
IL_6S05_082Major groove platform with extra pair
IL_6S05_083Minor groove platform with intercalation
IL_6S05_084No text annotation
IL_6S05_085Minor groove platform
IL_6S05_086Double sheared
IL_6S05_087No text annotation
IL_6S05_088No text annotation
IL_6S05_089No text annotation
IL_6S05_090Single bulged A
IL_6S05_091Isolated tHS basepair with bulges
IL_6S05_092Single bulged A
IL_6S05_093Tandem non-canonical cWW pairs
IL_6S05_094No text annotation
IL_6S05_095No text annotation
IL_6S05_096No text annotation
IL_6S05_097No text annotation
IL_6S05_098Isolated non-canonical cWW with bulges
IL_6S05_099Multiple bulged bases
IL_6S05_100No text annotation
IL_6S05_101Minor groove platform with intercalation
IL_6S05_102No text annotation
IL_6S05_103Single bulged A
IL_6S05_109Multiple bulged bases
IL_6S05_112No text annotation
IL_6S05_118No text annotation
IL_6S05_120No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6S05_0021/A/369:376,
1/A/403:404,
1/y/19:20		No text annotation
Not in a motif group		homologous
J3_5TBW_002
NA
J3_6S05_0031/A/502:503,
1/A/588:597,
1/A/606:611		No text annotation
Not in a motif group		homologous
J3_5TBW_003
NA
J3_6S05_0061/A/986:987,
1/A/1062:1066,
1/A/1092:1098		No text annotation
Not in a motif group
J3_6S05_0151/A/3298:3300,
1/A/3314:3318,
1/A/3388:3390		No text annotation
Not in a motif group
J3_6S05_0161/x/9:14,
1/x/66:68,
1/x/110:112		No text annotation
Not in a motif group

Problematic loops

#loop idProblemSequence
J3_6S05_001No text annotation
J3_6S05_004No text annotation
J3_6S05_005No text annotation
J3_6S05_007No text annotation
J3_6S05_008No text annotation
J3_6S05_009No text annotation
J3_6S05_010No text annotation
J3_6S05_011No text annotation
J3_6S05_012No text annotation
J3_6S05_013No text annotation
J3_6S05_014No text annotation

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