RNA 3D Hub //

6GC4 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6GC4_0011/A/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_6GC4_0031/A/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.7
HL_6GC4_0051/A/158:168No text annotation
homologous
HL_5J7L_138
NA
HL_6GC4_0071/A/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_6GC4_0101/A/319:323No text annotation
homologous
HL_4WF9_011
HL_75660.7
HL_6GC4_0141/A/462:467GNRA
homologous
HL_4WF9_015
HL_34789.2
HL_6GC4_0221/A/744:753No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_6GC4_0271/A/978:985No text annotation
homologous
HL_7RQB_028
NA
HL_6GC4_0291/A/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_6GC4_0311/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6GC4_0321/A/1363:1368GNRA
homologous
HL_5J7L_167
NA
HL_6GC4_0331/A/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_6GC4_0341/A/1451:1459No text annotation
geometric
HL_5TBW_004
NA
HL_6GC4_0351/A/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_6GC4_0371/A/1565:1568Mini UNCG
homologous
HL_5J7L_172
NA
HL_6GC4_0381/A/1612:1619No text annotation
homologous
HL_4WF9_038
HL_28592.1
HL_6GC4_0671/A/1727:1733No text annotation
homologous
HL_5J7L_214
NA
HL_6GC4_0441/A/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_6GC4_0611/A/2819:2827No text annotation
homologous
HL_5J7L_201
NA

Problematic loops

#loop idProblemSequence
HL_6GC4_002No text annotation
HL_6GC4_004No text annotation
HL_6GC4_006No text annotation
HL_6GC4_008No text annotation
HL_6GC4_009T-loop with 2 stacked bulged bases
HL_6GC4_011T-loop with unstacked turn
HL_6GC4_012No text annotation
HL_6GC4_065No text annotation
HL_6GC4_013No text annotation
HL_6GC4_015GNRA
HL_6GC4_016No text annotation
HL_6GC4_017No text annotation
HL_6GC4_018No text annotation
HL_6GC4_019GNRA
HL_6GC4_020No text annotation
HL_6GC4_021GNRA wlth tandem sheared
HL_6GC4_023No text annotation
HL_6GC4_024No text annotation
HL_6GC4_025No text annotation
HL_6GC4_026GNRA
HL_6GC4_028No text annotation
HL_6GC4_066No text annotation
HL_6GC4_030T-loop with 2 stacked bulged bases
HL_6GC4_036UNCG
HL_6GC4_039GNRA
HL_6GC4_040No text annotation
HL_6GC4_041No text annotation
HL_6GC4_042No text annotation
HL_6GC4_043No text annotation
HL_6GC4_045Externally structured
HL_6GC4_046No text annotation
HL_6GC4_047No text annotation
HL_6GC4_048No text annotation
HL_6GC4_049No text annotation
HL_6GC4_050No text annotation
HL_6GC4_051No text annotation
HL_6GC4_068No text annotation
HL_6GC4_052No text annotation
HL_6GC4_053Pseudoknot geometry
HL_6GC4_054GNRA
HL_6GC4_055GNRA
HL_6GC4_056No text annotation
HL_6GC4_057GNRA
HL_6GC4_058No text annotation
HL_6GC4_059No text annotation
HL_6GC4_060Mini UNCG
HL_6GC4_062GNRA
HL_6GC4_063No text annotation
HL_6GC4_064Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6GC4_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_22311.1
IL_6GC4_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_4WF9_002
IL_14190.2
IL_6GC4_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_62167.2
IL_6GC4_0111/A/481:484,
1/A/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_6GC4_0121/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_6GC4_0131/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.2
IL_6GC4_0141/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
NA
IL_6GC4_0151/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.2
IL_6GC4_0161/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_6GC4_0171/A/697:698,
1/A/763:765		Single bulged A
geometric
IL_5J7L_261
NA
IL_6GC4_0211/A/775:777,
1/A/787:791		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_6GC4_0241/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
NA
IL_6GC4_0251/A/856:862,
1/A/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
homologous
IL_5J7L_270
NA
IL_6GC4_1001/A/856:863,
1/A/913:921		No text annotation
IL_6GC4_0311/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_4WF9_036
IL_08938.1
IL_6GC4_0341/A/1018:1024,
1/A/1140:1144		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_6GC4_0371/A/1038:1041,
1/A/1114:1117		Tandem non-canonical cWW pairs
homologous
IL_5J7L_283
NA
IL_6GC4_0391/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_6GC4_0401/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_6GC4_0411/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6GC4_0431/A/1319:1323,
1/A/1331:1333		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_06671.1
IL_6GC4_0441/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.3
IL_6GC4_0481/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_6GC4_0491/A/1437:1440,
1/A/1551:1555		tSH-tHW
homologous
IL_7A0S_053
IL_74317.1
IL_6GC4_0511/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_6GC4_1031/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_6GC4_0561/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6GC4_0571/A/1663:1665,
1/A/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_6GC4_0601/A/1686:1691,
1/A/1696:1702		tSH-tSH-tHH-tHS
geometric
IL_7RQB_068
NA
IL_6GC4_0631/A/1727:1728,
1/A/1731:1733		Single bulged C
geometric
IL_5J7L_311
NA
IL_6GC4_0641/A/1770:1771,
1/A/1980:1982		Single bulged A
homologous
IL_4WF9_068
IL_14190.2
IL_6GC4_0651/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_6GC4_0681/A/2053:2056,
1/A/2612:2616		No text annotation
IL_6GC4_0811/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
NA
IL_6GC4_0831/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_6GC4_0841/A/2687:2691,
1/A/2718:2722		UAA/GAN related, with intercalation
homologous
IL_4WF9_102
IL_82016.1
IL_6GC4_0851/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_6GC4_0881/A/2806:2811,
1/A/2889:2892		No text annotation
homologous
IL_5J7L_351
NA
IL_6GC4_0901/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA

Problematic loops

#loop idProblemSequence
IL_6GC4_003Minor groove platform
IL_6GC4_097No text annotation
IL_6GC4_004No text annotation
IL_6GC4_005Single stack bend
IL_6GC4_0077x6 Sarcin-Ricin; G-bulge
IL_6GC4_008No text annotation
IL_6GC4_009No text annotation
IL_6GC4_010No text annotation
IL_6GC4_098Isolated non-canonical cWW pair
IL_6GC4_018Single bulged G
IL_6GC4_019Triple sheared
IL_6GC4_020Major groove platform
IL_6GC4_02290 degree turn
IL_6GC4_110No text annotation
IL_6GC4_099No text annotation
IL_6GC4_023Stack outside cWW
IL_6GC4_026Minor groove platform related
IL_6GC4_111No text annotation
IL_6GC4_101No text annotation
IL_6GC4_027C-loop with bulged stacked A's
IL_6GC4_028Isolated non-canonical cWW pair
IL_6GC4_029No text annotation
IL_6GC4_030Single bulged C
IL_6GC4_032SSU/LSU pseudoknot
IL_6GC4_033Single bulged U
IL_6GC4_035No text annotation
IL_6GC4_036Isolated non-canonical cWW pair
IL_6GC4_038Isolated cWS basepair
IL_6GC4_042Major groove platform; stack outside cWW
IL_6GC4_045tSH-tHW-tHS
IL_6GC4_046No text annotation
IL_6GC4_102No text annotation
IL_6GC4_047UAA/GAN
IL_6GC4_050Single bulged U
IL_6GC4_052No text annotation
IL_6GC4_053180 degree turn
IL_6GC4_054Single bulged A
IL_6GC4_112UAA/GAN variation
IL_6GC4_055Triple sheared related
IL_6GC4_058Major groove platform; stack outside cWW
IL_6GC4_104No text annotation
IL_6GC4_059Intercalated tWH
IL_6GC4_105No text annotation
IL_6GC4_0616x5 Sarcin-Ricin; G-bulge
IL_6GC4_062Triple sheared
IL_6GC4_066Minor groove platform, major groove intercalation
IL_6GC4_067Major groove platform
IL_6GC4_106No text annotation
IL_6GC4_069Single bulged U
IL_6GC4_070Minor groove platform
IL_6GC4_071Isolated tHS basepair with bulges
IL_6GC4_107No text annotation
IL_6GC4_072No text annotation
IL_6GC4_073Isolated non-canonical cWW pair
IL_6GC4_074No text annotation
IL_6GC4_113No text annotation
IL_6GC4_075Multiple bulged bases
IL_6GC4_076Kink-turn related
IL_6GC4_108No text annotation
IL_6GC4_077No text annotation
IL_6GC4_078Single bulged U
IL_6GC4_079Double sheared
IL_6GC4_109Double sheared with near cWW
IL_6GC4_080No text annotation
IL_6GC4_0827x6 Sarcin-Ricin; G-bulge
IL_6GC4_086UAA/GAN with extra cWW
IL_6GC4_087Single bulged A
IL_6GC4_089Major groove intercalation
IL_6GC4_091tHS double platform
IL_6GC4_092Major groove intercalation
IL_6GC4_093No text annotation
IL_6GC4_094Major groove minor groove platform; mini C-loop
IL_6GC4_095Symmetric double minor groove platform
IL_6GC4_096Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6GC4_0131/A/30:31,
1/A/474:484,
1/A/496:510		No text annotation
homologous
J3_5J7L_066
NA
J3_6GC4_0141/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6GC4_0021/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_6GC4_0031/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_6GC4_0041/A/698:700,
1/A/732:736,
1/A/760:763		No text annotation
homologous
J3_7RQB_005
NA
J3_6GC4_0061/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_5J7L_042
NA
J3_6GC4_0071/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_6GC4_0151/A/1424:1429,
1/A/1564:1565,
1/A/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_6GC4_0081/A/2091:2093,
1/A/2196:2200,
1/A/2223:2228		No text annotation
homologous
J3_7A0S_009
J3_17460.1
J3_6GC4_0111/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J4_6GC4_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_6GC4_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_6GC4_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_6GC4_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_6GC4_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_6GC4_0131/A/1444:1445,
1/A/1466:1467,
1/A/1525:1526,
1/A/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_6GC4_0071/A/1444:1445,
1/A/1466:1468,
1/A/1524:1526,
1/A/1546:1547		No text annotation
J4_6GC4_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_6GC4_0111/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
J5_6GC4_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:150,
1/A/176:178		No text annotation
homologous
J5_5J7L_013
NA
J5_6GC4_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_6GC4_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_6GC4_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_6GC4_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
J7_6GC4_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_6GC4_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_6GC4_001No text annotation
J3_6GC4_005No text annotation
J3_6GC4_016No text annotation
J3_6GC4_009No text annotation
J3_6GC4_010No text annotation
J3_6GC4_012No text annotation
J4_6GC4_003No text annotation
J4_6GC4_014No text annotation
J4_6GC4_009No text annotation
J4_6GC4_010No text annotation
J4_6GC4_015No text annotation
J4_6GC4_012No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0623 s