RNA 3D Hub //

8C8X Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8C8X_0011/A/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_8C8X_0021/A/87:95No text annotation
homologous
HL_5J7L_135
NA
HL_8C8X_0031/A/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.6
HL_8C8X_0051/A/158:168No text annotation
homologous
HL_5J7L_138
NA
HL_8C8X_0071/A/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_8C8X_0081/A/246:252No text annotation
homologous
HL_5J7L_141
NA
HL_8C8X_0091/A/305:312T-loop with 2 stacked bulged bases
homologous
HL_4WF9_010
HL_13999.1
HL_8C8X_0101/A/319:323No text annotation
homologous
HL_7RQB_011
NA
HL_8C8X_0111/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_8C8X_0121/A/382:392No text annotation
homologous
HL_5J7L_145
NA
HL_8C8X_0131/A/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.4
HL_8C8X_0141/A/462:467GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_8C8X_0151/A/487:493GNRA
homologous
HL_5J7L_148
NA
HL_8C8X_0171/A/566:575No text annotation
homologous
HL_7RQB_018
NA
HL_8C8X_0181/A/611:617No text annotation
homologous
HL_5J7L_151
NA
HL_8C8X_0191/A/629:634GNRA
homologous
HL_5J7L_152
NA
HL_8C8X_0221/A/744:753No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_8C8X_0231/A/779:785UNCG variation
homologous
HL_7A0S_023
HL_51020.1
HL_8C8X_0241/A/826:831No text annotation
homologous
HL_7RQB_025
NA
HL_8C8X_0271/A/978:985No text annotation
homologous
HL_7A0S_027
HL_47171.1
HL_8C8X_0301/A/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_8C8X_0311/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_8C8X_0321/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_8C8X_0331/A/1363:1368GNRA
homologous
HL_7RQB_035
NA
HL_8C8X_0341/A/1389:1398No text annotation
homologous
HL_7RQB_036
NA
HL_8C8X_0351/A/1451:1459Mini UNCG
geometric
HL_4L8H_001
HL_90436.1
HL_8C8X_0361/A/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_8C8X_0381/A/1565:1568No text annotation
homologous
HL_7RQB_039
NA
HL_8C8X_0391/A/1612:1619No text annotation
homologous
HL_4WF9_038
HL_28592.1
HL_8C8X_0691/A/1630:1636GNRA
homologous
HL_5J7L_174
NA
HL_8C8X_0411/A/1691:1696UNCG
geometric
HL_4PMI_004
NA
HL_8C8X_0431/A/1752:1756No text annotation
homologous
HL_7RQB_044
NA
HL_8C8X_0441/A/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_8C8X_0451/A/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_8C8X_0491/A/2027:2036No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_8C8X_0511/A/2209:2215No text annotation
homologous
HL_5J7L_185
NA
HL_8C8X_0531/A/2264:2276No text annotation
homologous
HL_4WF9_050
HL_02042.1
HL_8C8X_0611/A/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_8C8X_0641/A/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_8C8X_0651/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_34789.1

Problematic loops

#loop idProblemSequence
HL_8C8X_004Mini UNCG
HL_8C8X_006No text annotation
HL_8C8X_016No text annotation
HL_8C8X_020No text annotation
HL_8C8X_021No text annotation
HL_8C8X_025No text annotation
HL_8C8X_026GNRA
HL_8C8X_028No text annotation
HL_8C8X_068No text annotation
HL_8C8X_029No text annotation
HL_8C8X_037UNCG
HL_8C8X_040GNRA with extra cWW
HL_8C8X_042No text annotation
HL_8C8X_046GNRA variation
HL_8C8X_047No text annotation
HL_8C8X_048No text annotation
HL_8C8X_050No text annotation
HL_8C8X_052No text annotation
HL_8C8X_054No text annotation
HL_8C8X_055Pseudoknot geometry
HL_8C8X_056GNRA
HL_8C8X_057GNRA
HL_8C8X_058No text annotation
HL_8C8X_059No text annotation
HL_8C8X_060GNRA
HL_8C8X_062No text annotation
HL_8C8X_063No text annotation
HL_8C8X_066No text annotation
HL_8C8X_067Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8C8X_0011/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_5J7L_246
NA
IL_8C8X_0021/A/42:44,
1/A/434:437		Minor groove platform with extra cWW
homologous
IL_4WF9_003
IL_82096.1
IL_8C8X_0031/A/81:85,
1/A/97:105		No text annotation
homologous
IL_5J7L_248
NA
IL_8C8X_0041/A/183:184,
1/A/212:214		Single stack bend
homologous
IL_4WF9_007
IL_15011.1
IL_8C8X_0051/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_250
NA
IL_8C8X_0061/A/239:245,
1/A/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
NA
IL_8C8X_0091/A/293:295,
1/A/343:347		No text annotation
homologous
IL_5J7L_254
NA
IL_8C8X_0101/A/481:484,
1/A/496:509		No text annotation
homologous
IL_5J7L_255
NA
IL_8C8X_0111/A/536:539,
1/A/554:557		Double sheared
homologous
IL_4WF9_016
IL_58355.1
IL_8C8X_0121/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
geometric
IL_4ZC7_001
IL_01003.1
IL_8C8X_0131/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_7A0S_013
IL_66798.3
IL_8C8X_0141/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_01003.1
IL_8C8X_0151/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
homologous
IL_5J7L_260
NA
IL_8C8X_0161/A/697:698,
1/A/763:765		Single bulged A
homologous
IL_5J7L_261
NA
IL_8C8X_0171/A/701:707,
1/A/724:731		No text annotation
IL_8C8X_0191/A/775:777,
1/A/787:791		Multiple bulged bases
homologous
IL_7RQB_023
NA
IL_8C8X_1101/A/844:848,
1/A/930:934		No text annotation
homologous
IL_5J7L_399
NA
IL_8C8X_0211/A/847:848,
1/A/930:933		Stack outside cWW
geometric
IL_5J7L_268
NA
IL_8C8X_0221/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
NA
IL_8C8X_0241/A/857:862,
1/A/915:921		No text annotation
IL_8C8X_0251/A/862:863,
1/A/913:915		Single bulged G
geometric
IL_5J7L_271
NA
IL_8C8X_0301/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_4WF9_035
IL_05642.1
IL_8C8X_0311/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_8C8X_0321/A/1004:1011,
1/A/1150:1151		SSU/LSU pseudoknot
geometric
IL_4WF9_037
IL_11411.1
IL_8C8X_0331/A/1011:1013,
1/A/1149:1150		Single bulged U
homologous
IL_5J7L_279
NA
IL_8C8X_0341/A/1018:1024,
1/A/1140:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_8C8X_0351/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
NA
IL_8C8X_0391/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_7A0S_041
IL_42997.4
IL_8C8X_0401/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_8C8X_0411/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_7RQB_047
NA
IL_8C8X_0421/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8C8X_0431/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
homologous
IL_4WF9_049
IL_74641.1
IL_8C8X_1181/A/1319:1323,
1/A/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_8C8X_0451/A/1349:1351,
1/A/1381:1382		Single stack bend
geometric
IL_4WF9_089
IL_15011.1
IL_8C8X_1191/A/1353:1355,
1/A/1376:1379		No text annotation
IL_8C8X_0471/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_8C8X_0501/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_8C8X_0531/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_8C8X_0541/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_8C8X_0551/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_8C8X_0561/A/1489:1491,
1/A/1499:1500		Single bulged A
homologous
IL_5J7L_302
NA
IL_8C8X_0581/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_7A0S_059
IL_12566.5
IL_8C8X_0591/A/1663:1665,
1/A/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_8C8X_0621/A/1686:1691,
1/A/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
NA
IL_8C8X_0661/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_8C8X_0681/A/1841:1842,
1/A/1898:1901		Major groove intercalation
homologous
IL_4WF9_071
IL_78536.1
IL_8C8X_1141/A/1851:1860,
1/A/1882:1891		No text annotation
homologous
IL_5J7L_387
NA
IL_8C8X_0701/A/1864:1867,
1/A/1874:1878		UAA/GAN related
homologous
IL_5J7L_317
NA
IL_8C8X_0721/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_4WF9_078
IL_48076.7
IL_8C8X_0731/A/2054:2056,
1/A/2611:2615		Major groove platform with extra pair
geometric
IL_5TBW_087
NA
IL_8C8X_0741/A/2067:2069,
1/A/2442:2443		Single bulged U
homologous
IL_7RQB_080
NA
IL_8C8X_0761/A/2081:2083,
1/A/2236:2239		Isolated tHS basepair with bulges
homologous
IL_7A0S_077
IL_87316.1
IL_8C8X_0771/A/2085:2087,
1/A/2232:2234		Isolated non-canonical cWW pair
homologous
IL_7A0S_078
IL_71625.1
IL_8C8X_0861/A/2202:2204,
1/A/2220:2221		Single bulged U
homologous
IL_5J7L_331
NA
IL_8C8X_0911/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_7RQB_102
NA
IL_8C8X_0941/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_8C8X_0951/A/2686:2691,
1/A/2718:2723		No text annotation
IL_8C8X_0961/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_4WF9_103
IL_44609.1
IL_8C8X_0991/A/2806:2811,
1/A/2889:2892		No text annotation
geometric
IL_5J7L_351
NA
IL_8C8X_1001/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_8C8X_1011/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_8C8X_1171/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_5J7L_354
NA
IL_8C8X_1071/B/71:79,
1/B/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
NA

Problematic loops

#loop idProblemSequence
IL_8C8X_108No text annotation
IL_8C8X_007No text annotation
IL_8C8X_008No text annotation
IL_8C8X_109No text annotation
IL_8C8X_018No text annotation
IL_8C8X_02090 degree turn
IL_8C8X_111Single stack bend
IL_8C8X_023Single stack bend
IL_8C8X_026C-loop with bulged stacked A's
IL_8C8X_027Isolated non-canonical cWW pair
IL_8C8X_028Double sheared with non-canonical cWW
IL_8C8X_029No text annotation
IL_8C8X_036Isolated non-canonical cWW pair
IL_8C8X_037Tandem non-canonical cWW pairs
IL_8C8X_038No text annotation
IL_8C8X_044No text annotation
IL_8C8X_046No text annotation
IL_8C8X_048No text annotation
IL_8C8X_049UAA/GAN
IL_8C8X_051tSH-tHW
IL_8C8X_052Single bulged U
IL_8C8X_057UAA/GAN variation
IL_8C8X_060Major groove platform; stack outside cWW
IL_8C8X_112No text annotation
IL_8C8X_061Intercalated tWH
IL_8C8X_0636x5 Sarcin-Ricin; G-bulge
IL_8C8X_120No text annotation
IL_8C8X_064No text annotation
IL_8C8X_113No text annotation
IL_8C8X_065Single bulged A
IL_8C8X_067No text annotation
IL_8C8X_069No text annotation
IL_8C8X_071Bulged stacked bases
IL_8C8X_075Minor groove platform
IL_8C8X_078No text annotation
IL_8C8X_079No text annotation
IL_8C8X_080No text annotation
IL_8C8X_081No text annotation
IL_8C8X_121No text annotation
IL_8C8X_115No text annotation
IL_8C8X_082Single stack bend
IL_8C8X_083Kink-turn
IL_8C8X_084No text annotation
IL_8C8X_122No text annotation
IL_8C8X_085No text annotation
IL_8C8X_087Double sheared
IL_8C8X_088No text annotation
IL_8C8X_089Major groove platform
IL_8C8X_090No text annotation
IL_8C8X_092No text annotation
IL_8C8X_093No text annotation
IL_8C8X_116No text annotation
IL_8C8X_097No text annotation
IL_8C8X_123No text annotation
IL_8C8X_098Single bulged A
IL_8C8X_102No text annotation
IL_8C8X_103Major groove intercalation
IL_8C8X_104No text annotation
IL_8C8X_105No text annotation
IL_8C8X_106Symmetric double minor groove platform

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8C8X_0131/A/24:31,
1/A/474:481,
1/A/509:516		No text annotation
J3_8C8X_0141/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_8C8X_0011/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_8C8X_0021/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_8C8X_0031/A/698:700,
1/A/732:736,
1/A/760:763		No text annotation
homologous
J3_7RQB_005
NA
J3_8C8X_0041/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J3_8C8X_0051/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_8C8X_0161/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_8C8X_0151/A/1424:1429,
1/A/1564:1565,
1/A/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_8C8X_0081/A/2091:2093,
1/A/2196:2200,
1/A/2223:2228		Kink-turn 3-way junction
homologous
J3_5J7L_044
NA
J3_8C8X_0091/A/2295:2299,
1/A/2317:2323,
1/A/2332:2337		No text annotation
homologous
J3_5J7L_071
NA
J3_8C8X_0101/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
NA
J3_8C8X_0111/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J4_8C8X_0011/A/268:269,
1/A/370:375,
1/A/399:406,
1/A/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_8C8X_0021/A/297:301,
1/A/316:319,
1/A/323:325,
1/A/337:341		No text annotation
homologous
J4_5J7L_019
NA
J4_8C8X_0031/A/601:604,
1/A/624:628,
1/A/635:638,
1/A/650:656		No text annotation
homologous
J4_5J7L_020
NA
J4_8C8X_0041/A/1270:1276,
1/A/1294:1295,
1/A/1645:1648,
1/A/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_8C8X_0051/A/1310:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_8C8X_0061/A/1313:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_8C8X_0071/A/1444:1445,
1/A/1466:1467,
1/A/1525:1526,
1/A/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_8C8X_0081/A/1772:1776,
1/A/1788:1792,
1/A/1827:1830,
1/A/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_8C8X_0091/A/1833:1835,
1/A/1905:1906,
1/A/1924:1933,
1/A/1967:1972		No text annotation
homologous
J4_5J7L_026
NA
J4_8C8X_0101/A/2285:2289,
1/A/2343:2347,
1/A/2370:2372,
1/A/2381:2383		No text annotation
homologous
J4_9DFE_009
J4_98139.1
J4_8C8X_0111/A/2643:2649,
1/A/2671:2676,
1/A/2731:2735,
1/A/2769:2771		No text annotation
J5_8C8X_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:152,
1/A/174:178		No text annotation
J5_8C8X_0021/A/531:533,
1/A/560:564,
1/A/577:579,
1/A/1261:1262,
1/A/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J5_8C8X_0031/A/584:589,
1/A/668:671,
1/A/809:812,
1/A/1195:1196,
1/A/1250:1256		No text annotation
homologous
J5_7A0S_004
J5_74302.6
J5_8C8X_0041/A/1674:1682,
1/A/1706:1707,
1/A/1751:1752,
1/A/1756:1764,
1/A/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J6_8C8X_0011/A/45:46,
1/A/179:183,
1/A/214:224,
1/A/231:235,
1/A/262:266,
1/A/426:433		No text annotation
J6_8C8X_0031/A/2074:2077,
1/A/2243:2246,
1/A/2258:2259,
1/A/2281:2284,
1/A/2384:2395,
1/A/2421:2435		No text annotation
J7_8C8X_0011/A/8:15,
1/A/525:531,
1/A/2018:2023,
1/A/2040:2043,
1/A/2625:2630,
1/A/2788:2789,
1/A/2894:2895		No text annotation
J7_8C8X_0021/A/817:822,
1/A/835:838,
1/A/940:946,
1/A/971:976,
1/A/987:991,
1/A/1163:1164,
1/A/1185:1190		No text annotation

Problematic loops

#loop idProblemSequence
J3_8C8X_006No text annotation
J3_8C8X_007No text annotation
J3_8C8X_012No text annotation
J6_8C8X_002No text annotation

Coloring options:
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