RNA 3D Hub //

8I9W Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8I9W_0011/C1/38:45GNRA with extra cWW
geometric
HL_7A0S_056
HL_87268.2
HL_8I9W_0021/C1/69:74No text annotation
homologous
HL_8C3A_002
NA
HL_8I9W_0031/C1/90:96No text annotation
homologous
HL_8C3A_003
NA
HL_8I9W_0041/C1/129:134UNCG
geometric
HL_4U7U_001
HL_61337.3
HL_8I9W_0051/C1/187:194T-loop with 2 stacked bulged bases
homologous
HL_8C3A_005
NA
HL_8I9W_0061/C1/201:205No text annotation
homologous
HL_5TBW_006
NA
HL_8I9W_0071/C1/209:217T-loop with unstacked turn
homologous
HL_5TBW_007
NA
HL_8I9W_0081/C1/270:279No text annotation
homologous
HL_5TBW_008
NA
HL_8I9W_0091/C1/295:304tRNA D-loop
geometric
HL_4V9K_033
HL_20490.1
HL_8I9W_0101/C1/349:354GNRA
homologous
HL_8C3A_010
NA
HL_8I9W_0111/C1/374:379GNRA
homologous
HL_5TBW_011
NA
HL_8I9W_0121/C1/455:460No text annotation
geometric
HL_5TBW_018
NA
HL_8I9W_0131/C1/532:539No text annotation
homologous
HL_5TBW_012
NA
HL_8I9W_0141/C1/588:592Mini UNCG
geometric
HL_4V88_192
NA
HL_8I9W_0151/C1/627:636No text annotation
geometric
HL_5J7L_015
NA
HL_8I9W_0161/C1/674:680No text annotation
geometric
HL_5J7L_151
NA
HL_8I9W_0171/C1/716:721UNCG
geometric
HL_5J7L_030
NA
HL_8I9W_0181/C1/744:749No text annotation
homologous
HL_8P9A_130
HL_44506.2
HL_8I9W_0191/C1/892:897GNRA
geometric
HL_3E5C_002
HL_34789.4
HL_8I9W_0201/C1/939:944No text annotation
geometric
HL_2Y9H_003
HL_75660.7
HL_8I9W_0221/C1/1058:1065T-loop related
geometric
HL_4LFB_025
HL_63894.2
HL_8I9W_0231/C1/1108:1114Other HL
geometric
HL_4V9F_039
HL_67772.1
HL_8I9W_0241/C1/1130:1137No text annotation
homologous
HL_5TBW_026
NA
HL_8I9W_0251/C1/1221:1231No text annotation
homologous
HL_8C3A_027
NA
HL_8I9W_0261/C1/1249:1256GNRA wlth tandem sheared
homologous
HL_8C3A_028
NA
HL_8I9W_0271/C1/1329:1339Mini UNCG
geometric
HL_4OOG_001
HL_12626.2
HL_8I9W_0281/C1/1385:1390GNRA
homologous
HL_8C3A_030
NA
HL_8I9W_0301/C1/2331:2340No text annotation
geometric
HL_5J7L_143
NA
HL_8I9W_0511/C1/2433:2436No text annotation
HL_8I9W_0331/C1/2736:2740No text annotation
geometric
HL_5TBW_006
NA
HL_8I9W_0351/C1/2855:2862No text annotation
homologous
HL_5TBW_062
NA
HL_8I9W_0361/C1/2876:2886No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_8I9W_0371/C1/2921:2926No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_8I9W_0381/C1/2982:2987GNRA
geometric
HL_5B2P_001
HL_34789.4
HL_8I9W_0391/C1/3025:3030Ribsomal LSU H95
homologous
HL_8C3A_067
NA
HL_8I9W_0401/C1/3067:3081No text annotation
homologous
HL_8C3A_068
NA
HL_8I9W_0411/C1/3142:3147UNCG
geometric
HL_5Y85_004
HL_61337.3
HL_8I9W_0421/C1/3181:3189No text annotation
geometric
HL_2Y9H_005
HL_44506.2
HL_8I9W_0431/C1/3243:3251No text annotation
homologous
HL_8C3A_071
NA
HL_8I9W_0441/C1/3289:3296No text annotation
geometric
HL_361D_002
NA
HL_8I9W_0451/C2/47:56Pseudoknot with intercalation
geometric
HL_7A0S_001
HL_17803.1
HL_8I9W_0461/C2/69:89No text annotation
geometric
HL_3HJW_001
HL_18423.1
HL_8I9W_0471/C2/108:114No text annotation
homologous
HL_5TBW_075
NA
HL_8I9W_0481/C2/124:129No text annotation
homologous
HL_5TBW_076
NA
HL_8I9W_0491/C2/171:175No text annotation
geometric
HL_2Y8Y_001
HL_40612.1
HL_8I9W_0501/C2/196:201GNRA
geometric
HL_4V9F_072
HL_34789.4

Problematic loops

#loop idProblemSequence
HL_8I9W_021No text annotation
HL_8I9W_029No text annotation
HL_8I9W_031No text annotation
HL_8I9W_032No text annotation
HL_8I9W_034No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8I9W_0011/C1/7:8,
1/C2/150:152		Single bulged C
homologous
IL_8C3A_002
NA
IL_8I9W_0021/C1/13:15,
1/C2/144:145		Single bulged U
homologous
IL_8C3A_003
NA
IL_8I9W_0031/C1/27:28,
1/C1/56:58		No text annotation
homologous
IL_8C3A_004
NA
IL_8I9W_0041/C1/31:38,
1/C1/45:53		tSH-tHW-tHH-tHS
geometric
IL_5TBW_005
NA
IL_8I9W_0051/C1/82:89,
1/C1/97:103		No text annotation
homologous
IL_8C3A_006
NA
IL_8I9W_0061/C1/123:124,
1/C1/139:144		No text annotation
geometric
IL_5TBW_007
NA
IL_8I9W_0071/C1/125:127,
1/C1/136:138		Isolated non-canonical cWW pair
homologous
IL_8C3A_008
NA
IL_8I9W_0081/C1/154:155,
1/C1/252:254		Single bulged U
geometric
IL_6MWN_006
IL_97561.3
IL_8I9W_0091/C1/157:159,
1/C1/249:250		Single stack bend
homologous
IL_5TBW_009
NA
IL_8I9W_0101/C1/163:164,
1/C1/240:245		No text annotation
IL_8I9W_0111/C1/167:170,
1/C1/234:237		Double sheared
geometric
IL_4KZD_002
IL_58355.2
IL_8I9W_0121/C1/172:173,
1/C1/230:232		Single stack bend
homologous
IL_8C3A_012
NA
IL_8I9W_0131/C1/175:178,
1/C1/225:228		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.2
IL_8I9W_0141/C1/182:184,
1/C1/197:198		Single bulged U
homologous
IL_5TBW_012
NA
IL_8I9W_0151/C1/329:331,
1/C2/25:26		Single bulged A
homologous
IL_5TBW_013
NA
IL_8I9W_0161/C1/368:371,
1/C1/382:395		No text annotation
homologous
IL_8C3A_015
NA
IL_8I9W_0171/C1/396:402,
1/C2/13:19		Triple sheared with non-canonical cWW
homologous
IL_8C3A_016
NA
IL_8I9W_0181/C1/420:422,
1/C1/616:618		Isolated non-canonical cWW pair
homologous
IL_5TBW_016
NA
IL_8I9W_0191/C1/434:436,
1/C1/480:482		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_01003.3
IL_8I9W_0201/C1/445:450,
1/C1/465:471		No text annotation
IL_8I9W_0211/C1/507:515,
1/C1/557:564		No text annotation
homologous
IL_5TBW_019
NA
IL_8I9W_0221/C1/522:529,
1/C1/542:550		No text annotation
IL_8I9W_0231/C1/657:659,
1/C1/771:773		Isolated non-canonical cWW pair
homologous
IL_8C3A_023
NA
IL_8I9W_0241/C1/667:671,
1/C1/683:687		No text annotation
homologous
IL_5TBW_022
NA
IL_8I9W_0251/C1/712:715,
1/C1/722:726		No text annotation
homologous
IL_8C3A_025
NA
IL_8I9W_0261/C1/733:734,
1/C1/760:762		Single bulged A
homologous
IL_5TBW_024
NA
IL_8I9W_0271/C1/736:737,
1/C1/756:758		Single bulged U
homologous
IL_8C3A_027
NA
IL_8I9W_0281/C1/739:744,
1/C1/749:754		No text annotation
homologous
IL_8C3A_028
NA
IL_8I9W_0291/C1/784:786,
1/C1/919:921		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_01003.3
IL_8I9W_0301/C1/786:790,
1/C1/912:919		tHW-tHW cross-strand stack
homologous
IL_5TBW_028
NA
IL_8I9W_1021/C1/799:801,
1/C1/886:887		Single bulged U
geometric
IL_8C3A_056
NA
IL_8I9W_0321/C1/890:892,
1/C1/897:899		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_01003.3
IL_8I9W_0331/C1/935:937,
1/C1/946:948		Isolated non-canonical cWW pair
homologous
IL_5TBW_034
NA
IL_8I9W_0341/C1/950:951,
1/C1/1093:1095		No text annotation
homologous
IL_8C3A_038
NA
IL_8I9W_0351/C1/958:963,
1/C1/1083:1086		No text annotation
IL_8I9W_0361/C1/964:966,
1/C1/1081:1082		Single bulged G
homologous
IL_8C3A_040
NA
IL_8I9W_0371/C1/972:974,
1/C1/1038:1040		Isolated non-canonical cWW pair
geometric
IL_4LFB_006
IL_01003.3
IL_8I9W_1041/C1/972:978,
1/C1/1034:1040		No text annotation
homologous
IL_8C3A_041
NA
IL_8I9W_0381/C1/974:978,
1/C1/1034:1038		No text annotation
IL_8I9W_0391/C1/978:979,
1/C1/1032:1034		Minor groove platform
homologous
IL_8C3A_042
NA
IL_8I9W_0401/C1/1051:1053,
1/C1/1069:1071		Isolated non-canonical cWW pair
homologous
IL_8C3A_047
NA
IL_8I9W_0411/C1/1056:1058,
1/C1/1065:1066		Single bulged G
homologous
IL_8C3A_048
NA
IL_8I9W_0421/C1/1102:1104,
1/C1/1118:1120		Isolated non-canonical cWW pair
homologous
IL_8C3A_049
NA
IL_8I9W_0431/C1/1149:1153,
1/C1/1310:1314		UAA/GAN
homologous
IL_8C3A_051
NA
IL_8I9W_0441/C1/1155:1162,
1/C1/1307:1308		SSU/LSU pseudoknot
homologous
IL_8C3A_052
NA
IL_8I9W_0451/C1/1162:1164,
1/C1/1306:1307		Single bulged U
geometric
IL_7RQB_038
NA
IL_8I9W_0461/C1/1169:1176,
1/C1/1296:1301		No text annotation
homologous
IL_8C3A_054
NA
IL_8I9W_0471/C1/1176:1187,
1/C1/1281:1296		No text annotation
IL_8I9W_0481/C1/1189:1191,
1/C1/1278:1279		Single bulged U
homologous
IL_5TBW_053
NA
IL_8I9W_0491/C1/1200:1208,
1/C1/1265:1269		Kink-turn
homologous
IL_8C3A_057
NA
IL_8I9W_0501/C1/1216:1220,
1/C1/1232:1236		No text annotation
homologous
IL_8C3A_058
NA
IL_8I9W_0511/C1/1244:1248,
1/C1/1257:1259		Major groove platform with extra cWW
homologous
IL_8C3A_059
NA
IL_8I9W_0521/C1/1358:1360,
1/C1/1410:1413		No text annotation
homologous
IL_8C3A_061
NA
IL_8I9W_0531/C1/1367:1369,
1/C1/1402:1403		Single bulged A
homologous
IL_8C3A_062
NA
IL_8I9W_0541/C1/1370:1377,
1/C1/1397:1401		Kink-turn
homologous
IL_8C3A_063
NA
IL_8I9W_0551/C1/1380:1382,
1/C1/1393:1394		Single bulged A
homologous
IL_5TBW_060
NA
IL_8I9W_0561/C1/1426:1432,
1/C1/2316:2321		No text annotation
homologous
IL_8C3A_065
NA
IL_8I9W_0581/C1/1862:1868,
1/C1/2308:2311		No text annotation
IL_8I9W_0591/C1/1873:1875,
1/C1/2302:2303		No text annotation
IL_8I9W_0601/C1/1879:1880,
1/C1/2296:2298		Single bulged G
geometric
IL_4C7O_004
IL_28408.2
IL_8I9W_0611/C1/1900:1902,
1/C1/2072:2074		Isolated non-canonical cWW pair
geometric
IL_5ED1_002
IL_01003.3
IL_8I9W_0621/C1/2090:2091,
1/C1/2285:2287		No text annotation
IL_8I9W_0631/C1/2353:2356,
1/C1/2944:2946		Isolated non-canonical cWW with bulges
geometric
IL_7ELQ_002
NA
IL_8I9W_0641/C1/2372:2374,
1/C1/2767:2769		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_8I9W_0651/C1/2374:2375,
1/C1/2765:2767		Single bulged A
geometric
IL_4V88_409
NA
IL_8I9W_0661/C1/2385:2387,
1/C1/2562:2565		Isolated tHS basepair with bulges
homologous
IL_5TBW_095
NA
IL_8I9W_0671/C1/2406:2407,
1/C1/2463:2465		No text annotation
IL_8I9W_0681/C1/2413:2425,
1/C1/2454:2457		No text annotation
IL_8I9W_0691/C1/2428:2431,
1/C1/2438:2451		No text annotation
geometric
IL_3U4M_003
IL_75283.2
IL_8I9W_0701/C1/2728:2731,
1/C1/2745:2746		Single stack bend
homologous
IL_5TBW_101
NA
IL_8I9W_0711/C1/2793:2797,
1/C1/2807:2811		No text annotation
homologous
IL_8C3A_114
NA
IL_8I9W_0721/C1/2839:2840,
1/C1/2898:2903		Multiple bulged bases
homologous
IL_5TBW_109
NA
IL_8I9W_0731/C1/2847:2849,
1/C1/2870:2872		Isolated non-canonical cWW pair
geometric
IL_5TBW_110
NA
IL_8I9W_1061/C1/2847:2850,
1/C1/2867:2872		No text annotation
homologous
IL_8P9A_338
IL_07469.3
IL_8I9W_0741/C1/2849:2850,
1/C1/2867:2870		Major groove platform with intercalation
geometric
IL_4V9F_089
IL_94991.2
IL_8I9W_0751/C1/2918:2919,
1/C1/2928:2930		Single bulged A
geometric
IL_2QUX_002
IL_14190.2
IL_8I9W_0761/C1/2961:2964,
1/C1/3096:3101		Double sheared
homologous
IL_5TBW_114
NA
IL_8I9W_0771/C1/2969:2971,
1/C1/2997:2999		Isolated non-canonical cWW pair
homologous
IL_8C3A_124
NA
IL_8I9W_0781/C1/2975:2982,
1/C1/2987:2993		8x7 Sarcin-Ricin; G-bulge
homologous
IL_8C3A_125
NA
IL_8I9W_0791/C1/3004:3008,
1/C1/3048:3051		Major groove minor groove platform with tHH
homologous
IL_5TBW_117
NA
IL_8I9W_0801/C1/3011:3016,
1/C1/3041:3045		UAA/GAN related
homologous
IL_8C3A_127
NA
IL_8I9W_0811/C1/3020:3021,
1/C1/3034:3037		Multiple bulged bases
homologous
IL_5TBW_119
NA
IL_8I9W_0821/C1/3060:3064,
1/C1/3084:3088		UAA/GAN
homologous
IL_8C3A_129
NA
IL_8I9W_0831/C1/3117:3119,
1/C1/3224:3226		Isolated non-canonical cWW pair
homologous
IL_8C3A_130
NA
IL_8I9W_0841/C1/3120:3122,
1/C1/3222:3223		Single bulged U
geometric
IL_2PJP_001
IL_97561.3
IL_8I9W_0851/C1/3129:3131,
1/C1/3155:3156		Single bulged U
geometric
IL_5J7L_017
NA
IL_8I9W_0861/C1/3132:3140,
1/C1/3149:3154		No text annotation
IL_8I9W_0871/C1/3167:3173,
1/C1/3197:3202		No text annotation
IL_8I9W_0881/C1/3175:3177,
1/C1/3193:3195		Isolated non-canonical cWW pair
homologous
IL_5TBW_127
NA
IL_8I9W_0891/C1/3240:3243,
1/C1/3251:3254		Tandem non-canonical cWW pairs
geometric
IL_1JID_002
IL_15225.2
IL_8I9W_0901/C1/3258:3260,
1/C1/3328:3329		Single bulged U
homologous
IL_8C3A_136
NA
IL_8I9W_0911/C1/3264:3265,
1/C1/3321:3324		Multiple bulged bases
geometric
IL_7OS0_002
IL_71421.2
IL_8I9W_0921/C1/3268:3270,
1/C1/3313:3318		No text annotation
homologous
IL_8C3A_138
NA
IL_8I9W_0931/C1/3272:3277,
1/C1/3307:3311		No text annotation
homologous
IL_8C3A_139
NA
IL_8I9W_0941/C1/3280:3282,
1/C1/3303:3304		No text annotation
IL_8I9W_0951/C1/3282:3285,
1/C1/3300:3303		Double sheared; A in syn
homologous
IL_8C3A_141
NA
IL_8I9W_0961/C2/64:66,
1/C2/93:96		Isolated non-canonical cWW pair
homologous
IL_5TBW_145
NA
IL_8I9W_0971/C2/68:69,
1/C2/89:91		Single bulged U
geometric
IL_5TBW_146
NA
IL_8I9W_0981/C2/184:185,
1/C2/211:214		Multiple bulged bases
geometric
IL_4V88_392
NA
IL_8I9W_0991/C2/188:190,
1/C2/207:208		Single bulged A
geometric
IL_1U63_004
IL_14190.2
IL_8I9W_1001/C2/224:225,
1/C2/293:295		Single bulged A
geometric
IL_1CSL_002
IL_14190.2
IL_8I9W_1011/C2/226:227,
1/C2/290:292		No text annotation

Problematic loops

#loop idProblemSequence
IL_8I9W_031Single stack bend
IL_8I9W_103No text annotation
IL_8I9W_057No text annotation
IL_8I9W_105No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8I9W_0011/C1/113:123,
1/C1/144:153,
1/C1/255:259		No text annotation
homologous
J3_8P9A_042
J3_69230.1
J3_8I9W_0071/C1/113:124,
1/C1/139:153,
1/C1/255:259		No text annotation
J3_8I9W_0081/C1/179:182,
1/C1/198:207,
1/C1/219:224		No text annotation
J3_8I9W_0091/C1/332:348,
1/C1/355:360,
1/C2/21:24		No text annotation
homologous
J3_8P9A_045
J3_07616.1
J3_8I9W_0101/C1/361:368,
1/C1/395:396,
1/C2/19:20		No text annotation
geometric
J3_8C3A_048
NA
J3_8I9W_0111/C1/361:371,
1/C1/382:396,
1/C2/19:20		No text annotation
homologous
J3_8C3A_049
NA
J3_8I9W_0021/C1/427:433,
1/C1/483:485,
1/C1/605:611		No text annotation
J3_8I9W_0121/C1/492:493,
1/C1/578:587,
1/C1/593:598		No text annotation
homologous
J3_8P9A_048
J3_86133.1
J3_8I9W_0131/C1/967:968,
1/C1/1044:1048,
1/C1/1074:1080		No text annotation
homologous
J3_8P9A_051
J3_84137.1
J3_8I9W_0031/C1/1212:1214,
1/C1/1238:1244,
1/C1/1259:1261		No text annotation
homologous
J3_5TBW_007
NA
J3_8I9W_0051/C1/2394:2397,
1/C1/2474:2478,
1/C1/2549:2555		No text annotation
geometric
J3_4V9F_007
J3_86017.1
J3_8I9W_0061/C1/2844:2847,
1/C1/2872:2874,
1/C1/2888:2894		No text annotation
homologous
J3_8C3A_011
NA
J3_8I9W_0141/C1/3124:3129,
1/C1/3156:3164,
1/C1/3205:3220		No text annotation
J3_8I9W_0151/C1/3238:3239,
1/C1/3255:3258,
1/C1/3329:3332		No text annotation
J3_8I9W_0161/C2/44:45,
1/C2/58:64,
1/C2/96:100		No text annotation
homologous
J3_8P9A_067
J3_01004.1
J4_8I9W_0011/C1/112:113,
1/C1/259:264,
1/C1/285:291,
1/C1/308:311		No text annotation
homologous
J4_8P9A_012
J4_94698.1
J4_8I9W_0021/C1/179:182,
1/C1/198:201,
1/C1/205:207,
1/C1/219:224		No text annotation
J4_8I9W_0031/C1/2966:2969,
1/C1/2999:3000,
1/C1/3055:3057,
1/C1/3091:3094		No text annotation
J5_8I9W_0011/C1/20:22,
1/C2/35:42,
1/C2/102:107,
1/C2/115:116,
1/C2/137:139		No text annotation
homologous
J5_8P9A_010
J5_27223.1
J5_8I9W_0021/C1/645:650,
1/C1/780:783,
1/C1/922:926,
1/C1/1356:1358,
1/C1/1413:1419		No text annotation
J6_8I9W_0011/C1/22:27,
1/C1/58:68,
1/C1/75:79,
1/C1/106:110,
1/C1/313:323,
1/C2/32:35		No text annotation
J7_8I9W_0011/C1/930:935,
1/C1/948:949,
1/C1/1096:1099,
1/C1/1123:1128,
1/C1/1139:1143,
1/C1/1320:1321,
1/C1/1347:1352		No text annotation

Problematic loops

#loop idProblemSequence
J3_8I9W_004No text annotation

Coloring options:
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