RNA 3D Hub //

9HA5 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9HA5_0011/A/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_9HA5_0021/A/87:95No text annotation
homologous
HL_5J7L_135
NA
HL_9HA5_0031/A/123:128No text annotation
homologous
HL_5J7L_136
NA
HL_9HA5_0061/A/194:201No text annotation
homologous
HL_4WF9_006
HL_48677.1
HL_9HA5_0071/A/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_9HA5_0091/A/305:312T-loop with 2 stacked bulged bases
homologous
HL_5J7L_142
NA
HL_9HA5_0101/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_9HA5_0121/A/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.4
HL_9HA5_0131/A/462:467GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_9HA5_0141/A/487:493GNRA
homologous
HL_5J7L_148
NA
HL_9HA5_0161/A/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_9HA5_0171/A/611:617No text annotation
geometric
HL_5J7L_151
NA
HL_9HA5_0211/A/744:753No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_9HA5_0221/A/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_9HA5_0271/A/1222:1227GNRA
homologous
HL_7A0S_031
HL_34789.1
HL_9HA5_0281/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_9HA5_0291/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_9HA5_0301/A/1363:1368GNRA
homologous
HL_9DFE_033
HL_34789.1
HL_9HA5_0311/A/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_9HA5_0321/A/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
NA
HL_9HA5_0331/A/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_9HA5_0351/A/1565:1568Mini UNCG
homologous
HL_5J7L_172
NA
HL_9HA5_0361/A/1612:1619No text annotation
homologous
HL_7A0S_040
HL_28592.1
HL_9HA5_0371/A/1630:1636GNRA
homologous
HL_5J7L_174
NA
HL_9HA5_0381/A/1691:1696UNCG
homologous
HL_9DFE_040
HL_61337.1
HL_9HA5_0401/A/1752:1756No text annotation
homologous
HL_9DFE_042
HL_80709.4
HL_9HA5_0411/A/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_9HA5_0421/A/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_9HA5_0431/A/2027:2036No text annotation
homologous
HL_5J7L_183
NA
HL_9HA5_0451/A/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_9HA5_0481/A/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_9HA5_0491/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_34789.1

Problematic loops

#loop idProblemSequence
HL_9HA5_004No text annotation
HL_9HA5_005No text annotation
HL_9HA5_008No text annotation
HL_9HA5_011No text annotation
HL_9HA5_015Mini UNCG with extended bulge
HL_9HA5_018GNRA
HL_9HA5_019No text annotation
HL_9HA5_020GNRA wlth tandem sheared
HL_9HA5_023No text annotation
HL_9HA5_024GNRA
HL_9HA5_025No text annotation
HL_9HA5_026No text annotation
HL_9HA5_034UNCG
HL_9HA5_039No text annotation
HL_9HA5_044GNRA
HL_9HA5_046No text annotation
HL_9HA5_047Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9HA5_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
homologous
IL_5J7L_245
NA
IL_9HA5_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_7A0S_002
IL_14190.1
IL_9HA5_0031/A/43:44,
1/A/434:436		Minor groove platform
homologous
IL_5J7L_247
NA
IL_9HA5_0041/A/81:85,
1/A/97:105		No text annotation
homologous
IL_5J7L_248
NA
IL_9HA5_0051/A/183:184,
1/A/212:214		Single stack bend
homologous
IL_7A0S_005
IL_15011.1
IL_9HA5_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.1
IL_9HA5_0101/A/293:295,
1/A/343:347		No text annotation
homologous
IL_5J7L_254
NA
IL_9HA5_0111/A/481:484,
1/A/496:509		No text annotation
homologous
IL_9DFE_012
IL_44923.1
IL_9HA5_0121/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_9HA5_0131/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
homologous
IL_4WF9_017
IL_71625.1
IL_9HA5_0151/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.1
IL_9HA5_0161/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
homologous
IL_7A0S_015
IL_73855.1
IL_9HA5_0171/A/697:698,
1/A/763:765		Single bulged A
homologous
IL_5J7L_261
NA
IL_9HA5_0181/A/702:707,
1/A/724:730		No text annotation
geometric
IL_4V88_462
NA
IL_9HA5_0191/A/738:740,
1/A/757:758		Major groove platform
homologous
IL_4WF9_026
IL_48076.7
IL_9HA5_0201/A/775:777,
1/A/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_9HA5_0291/A/1018:1024,
1/A/1140:1144		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_9HA5_0301/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
NA
IL_9HA5_0311/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_7A0S_041
IL_42997.4
IL_9HA5_0321/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_9HA5_0331/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_9HA5_0341/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_9HA5_0351/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
geometric
IL_4V9F_008
IL_74641.1
IL_9HA5_0361/A/1319:1323,
1/A/1331:1333		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_06671.1
IL_9HA5_0371/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.3
IL_9HA5_0381/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_9HA5_0391/A/1415:1416,
1/A/1582:1587		No text annotation
homologous
IL_5J7L_294
NA
IL_9HA5_0401/A/1417:1421,
1/A/1577:1581		UAA/GAN
homologous
IL_5J7L_295
NA
IL_9HA5_0411/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_9HA5_0421/A/1437:1440,
1/A/1551:1555		tSH-tHW
homologous
IL_5J7L_297
NA
IL_9HA5_0431/A/1450:1451,
1/A/1459:1461		Single bulged U
homologous
IL_5J7L_298
NA
IL_9HA5_0441/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_9HA5_0451/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_9HA5_0461/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_9HA5_0471/A/1489:1491,
1/A/1499:1500		Single bulged A
homologous
IL_9DFE_061
IL_14190.1
IL_9HA5_0481/A/1526:1529,
1/A/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_9HA5_0491/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_9HA5_0501/A/1663:1665,
1/A/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_9HA5_0511/A/1666:1669,
1/A/1993:1994		Major groove platform; stack outside cWW
geometric
IL_8C3A_082
NA
IL_9HA5_0521/A/1666:1674,
1/A/1990:1994		No text annotation
geometric
IL_8C3A_484
NA
IL_9HA5_0531/A/1669:1674,
1/A/1990:1993		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.1
IL_9HA5_0541/A/1686:1691,
1/A/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
NA
IL_9HA5_0551/A/1712:1718,
1/A/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
NA
IL_9HA5_0581/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_5J7L_313
NA
IL_9HA5_0591/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_9HA5_0601/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
NA
IL_9HA5_0621/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_9HA5_0631/A/2687:2691,
1/A/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_9HA5_0641/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_9HA5_0671/A/2806:2811,
1/A/2889:2892		No text annotation
homologous
IL_5J7L_351
NA
IL_9HA5_0681/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_4WF9_106
IL_78536.1
IL_9HA5_0691/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_9HA5_0701/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_5J7L_354
NA

Problematic loops

#loop idProblemSequence
IL_9HA5_0077x6 Sarcin-Ricin; G-bulge
IL_9HA5_008No text annotation
IL_9HA5_009No text annotation
IL_9HA5_014AAA cross-strand stack
IL_9HA5_02190 degree turn
IL_9HA5_022Stack outside cWW
IL_9HA5_023Single stack bend
IL_9HA5_0247x7 Sarcin-Ricin with intercalated A; G-bulge
IL_9HA5_025Single bulged C
IL_9HA5_026UAA/GAN
IL_9HA5_027SSU/LSU pseudoknot
IL_9HA5_028Single bulged U
IL_9HA5_056Triple sheared
IL_9HA5_057Single bulged A
IL_9HA5_061Sarcin-Ricin target in LSU H95; G-bulge
IL_9HA5_065UAA/GAN with extra cWW
IL_9HA5_066Single bulged A

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9HA5_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_4WF9_010
J3_68715.1
J3_9HA5_0021/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_9HA5_0031/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_9HA5_0041/A/297:301,
1/A/316:325,
1/A/337:341		No text annotation
homologous
J3_4WF9_015
J3_77124.1
J3_9HA5_0051/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_9HA5_0061/A/698:700,
1/A/732:736,
1/A/760:763		No text annotation
homologous
J3_4WF9_003
J3_69816.1
J3_9HA5_0071/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_7A0S_006
J3_32852.7
J3_9HA5_0081/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_9HA5_0091/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_9HA5_0101/A/1424:1429,
1/A/1564:1565,
1/A/1568:1574		No text annotation
homologous
J3_5J7L_069
NA
J3_9HA5_0111/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
NA
J3_9HA5_0121/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J4_9HA5_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_9HA5_0031/A/1270:1276,
1/A/1294:1295,
1/A/1645:1648,
1/A/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_9HA5_0041/A/1310:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_9HA5_0051/A/1313:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_9HA5_0061/A/1444:1445,
1/A/1466:1467,
1/A/1525:1526,
1/A/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_9HA5_0071/A/1772:1776,
1/A/1788:1792,
1/A/1827:1830,
1/A/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_9HA5_0081/A/2643:2646,
1/A/2674:2676,
1/A/2731:2735,
1/A/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J5_9HA5_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:151,
1/A/175:178		No text annotation
J5_9HA5_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_9HA5_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_5J7L_015
NA
J5_9HA5_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_9HA5_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_9HA5_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

Problematic loops

#loop idProblemSequence
J4_9HA5_002No text annotation
J7_9HA5_002No text annotation

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