RNA 3D Hub //

3J9W Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J9W_0061/AA/267:275GNRA related
homologous
HL_4LFB_006
HL_36455.1
HL_3J9W_0081/AA/328:341No text annotation
homologous
HL_5J7L_008
NA
HL_3J9W_0131/AA/531:536No text annotation
geometric
HL_4WF9_003
HL_75660.6
HL_3J9W_0151/AA/698:707No text annotation
homologous
HL_5J7L_015
NA
HL_3J9W_0161/AA/735:740GNRA
homologous
HL_5J7L_016
NA
HL_3J9W_0171/AA/795:805No text annotation
homologous
HL_5J7L_017
NA
HL_3J9W_0201/AA/907:912GNRA
homologous
HL_4LFB_020
HL_34789.1
HL_3J9W_0211/AA/973:982No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_3J9W_0321/AA/1525:1530GNRA
homologous
HL_4LFB_032
HL_34789.1
HL_3J9W_0331/AX/13:22tRNA D-loop
homologous
HL_4TUE_033
NA
HL_3J9W_0341/AX/31:39No text annotation
homologous
HL_4V8N_144
NA
HL_3J9W_0351/AX/53:61T-loop with 2 stacked bulged bases
homologous
HL_4WJ4_003
NA
HL_3J9W_0361/BA/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_3J9W_0371/BA/87:95Pseudoknot geometry
homologous
HL_4WF9_002
HL_00911.1
HL_3J9W_0381/BA/122:127No text annotation
homologous
HL_4WF9_003
HL_75660.6
HL_3J9W_0401/BA/159:169No text annotation
homologous
HL_5J7L_138
NA
HL_3J9W_0411/BA/197:204No text annotation
geometric
HL_5J7L_139
NA
HL_3J9W_0421/BA/228:233No text annotation
homologous
HL_4WF9_007
HL_51020.1
HL_3J9W_0431/BA/249:255No text annotation
homologous
HL_4WF9_008
HL_76371.1
HL_3J9W_0451/BA/349:356T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_13999.1
HL_3J9W_0461/BA/363:367No text annotation
homologous
HL_5J7L_143
NA
HL_3J9W_0471/BA/371:379T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_3J9W_0481/BA/429:439No text annotation
homologous
HL_5J7L_145
NA
HL_3J9W_0491/BA/457:464Pseudoknot geometry
homologous
HL_5J7L_146
NA
HL_3J9W_0501/BA/509:514GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_3J9W_0511/BA/534:539GNRA
homologous
HL_7A0S_016
HL_34789.1
HL_3J9W_0521/BA/588:595No text annotation
homologous
HL_4WF9_017
HL_50318.1
HL_3J9W_0531/BA/610:619T-loop with 2 stacked bulged bases
geometric
HL_4WF9_018
HL_33597.1
HL_3J9W_0541/BA/656:662No text annotation
geometric
HL_3IGI_004
HL_37569.1
HL_3J9W_0551/BA/675:680GNRA
homologous
HL_5J7L_152
NA
HL_3J9W_0561/BA/687:693No text annotation
homologous
HL_7RQB_021
NA
HL_3J9W_0581/BA/791:800No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_3J9W_0591/BA/826:832No text annotation
geometric
HL_5U3G_001
NA
HL_3J9W_0601/BA/873:878No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_3J9W_0621/BA/1001:1008GNRA
homologous
HL_7A0S_026
HL_34789.1
HL_3J9W_0631/BA/1024:1031No text annotation
homologous
HL_5J7L_160
NA
HL_3J9W_0671/BA/1262:1267GNRA
homologous
HL_4WF9_031
HL_34789.1
HL_3J9W_0681/BA/1320:1328T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_33597.1
HL_3J9W_0691/BA/1363:1369Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_3J9W_0701/BA/1402:1407GNRA
homologous
HL_5J7L_167
NA
HL_3J9W_0711/BA/1428:1437No text annotation
homologous
HL_7RQB_036
NA
HL_3J9W_0721/BA/1496:1507UNCG variation
geometric
HL_5J7L_200
NA
HL_3J9W_0751/BA/1613:1616Mini UNCG
homologous
HL_7A0S_039
HL_90436.1
HL_3J9W_0761/BA/1657:1664No text annotation
homologous
HL_7RQB_040
NA
HL_3J9W_0771/BA/1675:1681GNRA
homologous
HL_5J7L_174
NA
HL_3J9W_0781/BA/1736:1741UNCG
geometric
HL_4PMI_004
NA
HL_3J9W_0791/BA/1764:1769No text annotation
homologous
HL_7RQB_043
NA
HL_3J9W_0801/BA/1781:1785No text annotation
homologous
HL_7A0S_044
HL_80709.4
HL_3J9W_0811/BA/1806:1816No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_3J9W_0821/BA/1835:1840GNRA related
homologous
HL_5J7L_179
NA
HL_3J9W_0841/BA/1939:1949No text annotation
geometric
HL_5TBW_049
NA
HL_3J9W_0851/BA/1978:1986No text annotation
homologous
HL_5J7L_182
NA
HL_3J9W_0861/BA/2056:2065No text annotation
homologous
HL_7RQB_050
NA
HL_3J9W_0881/BA/2238:2244No text annotation
homologous
HL_5J7L_185
NA
HL_3J9W_0891/BA/2277:2285No text annotation
homologous
HL_7RQB_053
NA
HL_3J9W_0901/BA/2293:2305No text annotation
homologous
HL_4WF9_050
HL_02042.1
HL_3J9W_1101/BA/2333:2341No text annotation
homologous
HL_5J7L_219
NA
HL_3J9W_0921/BA/2353:2360Pseudoknot geometry
homologous
HL_7A0S_055
HL_52651.1
HL_3J9W_0931/BA/2384:2391GNRA with extra cWW
homologous
HL_4WF9_053
HL_45359.1
HL_3J9W_0941/BA/2403:2408GNRA
homologous
HL_5J7L_191
NA
HL_3J9W_0951/BA/2433:2442No text annotation
homologous
HL_7A0S_058
HL_51853.1
HL_3J9W_0971/BA/2557:2564No text annotation
homologous
HL_7RQB_061
NA
HL_3J9W_0981/BA/2580:2586No text annotation
homologous
HL_7A0S_061
HL_48677.1
HL_3J9W_0991/BA/2623:2628GNRA
homologous
HL_7RQB_063
NA
HL_3J9W_1011/BA/2730:2735Ribsomal LSU H95
homologous
HL_7A0S_064
HL_12125.1
HL_3J9W_1021/BA/2774:2788No text annotation
homologous
HL_5J7L_199
NA
HL_3J9W_1041/BA/2844:2852No text annotation
homologous
HL_5J7L_201
NA
HL_3J9W_1051/BA/2881:2886GNRA
homologous
HL_5J7L_202
NA
HL_3J9W_1071/BB/84:88Mini UNCG
homologous
HL_5J7L_204
NA

Problematic loops

#loop idProblemSequence
HL_3J9W_001No text annotation
HL_3J9W_002No text annotation
HL_3J9W_003GNRA
HL_3J9W_004No text annotation
HL_3J9W_005UNCG
HL_3J9W_007GNRA
HL_3J9W_009UNCG
HL_3J9W_010GNRA
HL_3J9W_011UNCG
HL_3J9W_012GNRA
HL_3J9W_014GNRA-like with tWH
HL_3J9W_018No text annotation
HL_3J9W_019GNRA
HL_3J9W_022GNRA
HL_3J9W_023UNCG variation
HL_3J9W_024GNRA
HL_3J9W_025T-loop related
HL_3J9W_026T-loop related
HL_3J9W_027GNRA
HL_3J9W_028GNRA
HL_3J9W_029T-loop with 3 stacked bulged bases
HL_3J9W_030No text annotation
HL_3J9W_031No text annotation
HL_3J9W_039GNRA wlth tandem sheared
HL_3J9W_044No text annotation
HL_3J9W_057GNRA wlth tandem sheared
HL_3J9W_061No text annotation
HL_3J9W_108No text annotation
HL_3J9W_064No text annotation
HL_3J9W_065GNRA wlth tandem sheared
HL_3J9W_066Mini UNCG
HL_3J9W_109No text annotation
HL_3J9W_073Pseudoknot geometry with 3' bulge
HL_3J9W_074No text annotation
HL_3J9W_083GNRA
HL_3J9W_087No text annotation
HL_3J9W_091No text annotation
HL_3J9W_096No text annotation
HL_3J9W_100GNRA
HL_3J9W_103GNRA related
HL_3J9W_106No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J9W_0011/AA/32:34,
1/AA/561:562		Single bulged G
homologous
IL_4LFB_001
IL_28408.1
IL_3J9W_0031/AA/49:54,
1/AA/367:369		No text annotation
geometric
IL_5J7L_003
NA
IL_3J9W_1941/AA/127:130,
1/AA/239:240		Multiple bulged bases
homologous
IL_6CZR_119
NA
IL_3J9W_0091/AA/131:135,
1/AA/235:238		No text annotation
homologous
IL_4LFB_008
IL_60988.1
IL_3J9W_1851/AA/257:260,
1/AA/282:283		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_3J9W_0131/AA/300:301,
1/AA/312:316		C-loop
homologous
IL_6CZR_125
NA
IL_3J9W_0151/AA/383:384,
1/AA/395:397		Single bulged G
homologous
IL_5J7L_019
NA
IL_3J9W_0201/AA/578:584,
1/AA/890:891		No text annotation
homologous
IL_4LFB_022
IL_20847.1
IL_3J9W_0211/AA/589:593,
1/AA/766:770		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_3J9W_0261/AA/663:664,
1/AA/760:763		Major groove platform; stack outside cWW
geometric
IL_4LFB_027
IL_74641.1
IL_3J9W_1881/AA/682:686,
1/AA/722:726		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
NA
IL_3J9W_0301/AA/693:697,
1/AA/708:715		Kink-turn
homologous
IL_5J7L_035
NA
IL_3J9W_0321/AA/788:792,
1/AA/808:812		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_3J9W_0331/AA/897:904,
1/AA/915:920		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_3J9W_1951/AA/932:933,
1/AA/1402:1404		Single bulged A
homologous
IL_4LFB_035
IL_14190.1
IL_3J9W_0351/AA/935:937,
1/AA/1399:1400		Single bulged G
homologous
IL_4LFB_036
IL_28408.1
IL_3J9W_0511/AA/1312:1317,
1/AA/1338:1343		No text annotation
geometric
IL_5J7L_057
NA
IL_3J9W_0521/AA/1408:1410,
1/AA/1511:1514		No text annotation
geometric
IL_4V88_463
NA
IL_3J9W_0531/AA/1410:1413,
1/AA/1507:1511		No text annotation
geometric
IL_4V88_464
NA
IL_3J9W_0541/AA/1414:1416,
1/AA/1504:1506		Isolated non-canonical cWW pair
geometric
IL_5Y85_006
IL_01003.1
IL_3J9W_0551/AA/1416:1418,
1/AA/1501:1504		Decoding loop related
geometric
IL_2O3X_003
IL_61702.1
IL_3J9W_0561/AA/1421:1423,
1/AA/1496:1498		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_3J9W_0571/AA/1425:1428,
1/AA/1491:1494		Double sheared
homologous
IL_6CZR_169
NA
IL_3J9W_0581/AA/1433:1436,
1/AA/1483:1486		Tandem non-canonical cWW pairs
geometric
IL_5TBW_100
NA
IL_3J9W_0591/AA/1439:1444,
1/AA/1476:1480		Triple sheared related
geometric
IL_5J7L_063
NA
IL_3J9W_0601/AA/1444:1446,
1/AA/1474:1476		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_01003.1
IL_3J9W_0611/AA/1449:1452,
1/AA/1469:1471		Isolated tHS basepair with bulges
geometric
IL_7RQB_012
NA
IL_3J9W_0651/BA/24:30,
1/BA/556:562		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_3J9W_0661/BA/36:37,
1/BA/489:491		Single bulged A
homologous
IL_7A0S_002
IL_14190.1
IL_3J9W_1971/BA/43:44,
1/BA/481:483		Minor groove platform
homologous
IL_5J7L_247
NA
IL_3J9W_0681/BA/81:85,
1/BA/97:104		Kink-turn
homologous
IL_7RQB_004
NA
IL_3J9W_0691/BA/152:153,
1/BA/175:177		Single bulged A
homologous
IL_4WF9_006
IL_14190.1
IL_3J9W_0701/BA/191:197,
1/BA/204:211		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_006
NA
IL_3J9W_0711/BA/241:248,
1/BA/256:262		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_009
IL_62167.1
IL_3J9W_0741/BA/319:327,
1/BA/400:401		No text annotation
IL_3J9W_0751/BA/336:338,
1/BA/387:391		No text annotation
homologous
IL_5J7L_254
NA
IL_3J9W_0761/BA/344:346,
1/BA/359:360		Single bulged A
geometric
IL_3MJA_001
NA
IL_3J9W_0771/BA/528:531,
1/BA/542:555		No text annotation
geometric
IL_5J7L_255
NA
IL_3J9W_0781/BA/582:585,
1/BA/598:601		Double sheared
homologous
IL_5J7L_256
NA
IL_3J9W_0791/BA/608:610,
1/BA/619:621		Isolated non-canonical cWW pair
homologous
IL_4WF9_017
IL_71625.1
IL_3J9W_0801/BA/639:641,
1/BA/707:709		Isolated non-canonical cWW pair
homologous
IL_4WF9_018
IL_71625.1
IL_3J9W_0811/BA/650:654,
1/BA/664:668		AAA cross-strand stack
homologous
IL_7RQB_016
NA
IL_3J9W_0821/BA/719:721,
1/BA/853:855		Isolated non-canonical cWW pair
homologous
IL_7A0S_014
IL_01003.1
IL_3J9W_0831/BA/721:725,
1/BA/846:853		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_3J9W_0841/BA/744:745,
1/BA/810:812		Single bulged A
homologous
IL_5J7L_261
NA
IL_3J9W_0851/BA/749:750,
1/BA/775:777		Single bulged G
homologous
IL_5J7L_262
NA
IL_3J9W_0861/BA/750:754,
1/BA/771:775		Triple sheared
geometric
IL_4WF9_024
IL_15190.1
IL_3J9W_0871/BA/785:787,
1/BA/804:805		Major groove platform
homologous
IL_4WF9_026
IL_48076.7
IL_3J9W_0881/BA/822:824,
1/BA/834:838		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_3J9W_0891/BA/884:885,
1/BA/986:988		Single stack bend
homologous
IL_7A0S_022
IL_15011.1
IL_3J9W_1991/BA/891:895,
1/BA/977:980		No text annotation
homologous
IL_4WF9_029
IL_01742.1
IL_3J9W_1901/BA/899:900,
1/BA/971:973		Single stack bend
geometric
IL_5TBW_101
NA
IL_3J9W_0921/BA/903:909,
1/BA/962:968		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_4WF9_031
IL_94128.1
IL_3J9W_0931/BA/909:910,
1/BA/960:962		Minor groove platform
homologous
IL_4WF9_032
IL_34520.1
IL_3J9W_1911/BA/911:915,
1/BA/956:959		C-loop
homologous
IL_4WF9_033
IL_16301.1
IL_3J9W_0981/BA/998:1000,
1/BA/1009:1011		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_01003.1
IL_3J9W_0991/BA/1040:1042,
1/BA/1205:1206		Single bulged C
homologous
IL_4WF9_035
IL_05642.1
IL_3J9W_1001/BA/1044:1048,
1/BA/1199:1203		UAA/GAN
homologous
IL_7RQB_036
NA
IL_3J9W_1011/BA/1050:1057,
1/BA/1196:1197		SSU/LSU pseudoknot
homologous
IL_4WF9_037
IL_11411.1
IL_3J9W_1021/BA/1057:1059,
1/BA/1195:1196		Single bulged U
geometric
IL_5J7L_279
NA
IL_3J9W_1031/BA/1064:1070,
1/BA/1186:1190		Kink-turn related
geometric
IL_4WF9_039
IL_57188.6
IL_3J9W_1041/BA/1070:1076,
1/BA/1170:1186		No text annotation
geometric
IL_4WF9_040
IL_50715.4
IL_3J9W_1051/BA/1077:1080,
1/BA/1167:1169		Isolated non-canonical cWW pair
homologous
IL_5J7L_282
NA
IL_3J9W_2001/BA/1238:1239,
1/BA/1287:1289		No text annotation
IL_3J9W_1101/BA/1243:1247,
1/BA/1279:1283		No text annotation
geometric
IL_5TBW_121
NA
IL_3J9W_1111/BA/1248:1255,
1/BA/1274:1278		Kink-turn
homologous
IL_7A0S_043
IL_90775.1
IL_3J9W_1121/BA/1259:1261,
1/BA/1268:1270		Intercalated cWW
homologous
IL_4WF9_047
IL_61702.1
IL_3J9W_1131/BA/1302:1309,
1/BA/2040:2046		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_049
NA
IL_3J9W_1141/BA/1349:1352,
1/BA/1648:1649		Major groove platform; stack outside cWW
homologous
IL_7RQB_050
NA
IL_3J9W_1151/BA/1358:1362,
1/BA/1370:1372		C-loop
homologous
IL_7RQB_051
NA
IL_3J9W_1161/BA/1390:1394,
1/BA/1415:1419		UAA/GAN
homologous
IL_5J7L_292
NA
IL_3J9W_1171/BA/1396:1400,
1/BA/1409:1413		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_3J9W_1181/BA/1448:1450,
1/BA/1637:1638		Minor groove platform
geometric
IL_4V9F_034
IL_34520.1
IL_3J9W_1201/BA/1463:1467,
1/BA/1625:1628		Other IL
homologous
IL_4WF9_054
IL_74317.1
IL_3J9W_1211/BA/1478:1481,
1/BA/1605:1609		No text annotation
IL_3J9W_1221/BA/1483:1486,
1/BA/1599:1603		tSH-tHW
homologous
IL_5J7L_297
NA
IL_3J9W_1231/BA/1488:1490,
1/BA/1595:1597		Isolated non-canonical cWW pair
geometric
IL_4K31_001
IL_71625.1
IL_3J9W_1241/BA/1494:1496,
1/BA/1507:1509		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_3J9W_1251/BA/1514:1518,
1/BA/1567:1571		No text annotation
IL_3J9W_1281/BA/1535:1537,
1/BA/1545:1546		Single bulged A
homologous
IL_5J7L_302
NA
IL_3J9W_1291/BA/1573:1576,
1/BA/1590:1594		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_3J9W_1301/BA/1696:1701,
1/BA/2033:2035		No text annotation
homologous
IL_4WF9_062
IL_12566.5
IL_3J9W_1311/BA/1708:1710,
1/BA/2024:2026		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_3J9W_1321/BA/1711:1714,
1/BA/2022:2023		Major groove platform; stack outside cWW
homologous
IL_7A0S_061
IL_74641.1
IL_3J9W_1931/BA/1711:1719,
1/BA/2019:2023		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_3J9W_1331/BA/1714:1719,
1/BA/2019:2022		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.1
IL_3J9W_1341/BA/1731:1736,
1/BA/1741:1747		tSH-tSH-tHH-tHS
homologous
IL_7RQB_068
NA
IL_3J9W_1351/BA/1756:1761,
1/BA/1772:1776		No text annotation
IL_3J9W_1361/BA/1799:1800,
1/BA/2009:2011		Single bulged A
homologous
IL_5J7L_312
NA
IL_3J9W_1371/BA/1827:1833,
1/BA/1842:1850		Kink-turn related
homologous
IL_7RQB_070
NA
IL_3J9W_1381/BA/1866:1869,
1/BA/1931:1932		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_3J9W_1391/BA/1870:1871,
1/BA/1927:1930		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_3J9W_1401/BA/1875:1878,
1/BA/1922:1923		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_316
NA
IL_3J9W_1411/BA/1880:1884,
1/BA/1916:1920		UAA/GAN with extra stack
homologous
IL_4WF9_073
IL_89021.3
IL_3J9W_1421/BA/1885:1889,
1/BA/1911:1915		Triple sheared
homologous
IL_7RQB_075
NA
IL_3J9W_1431/BA/1893:1896,
1/BA/1903:1907		UAA/GAN related
homologous
IL_5J7L_317
NA
IL_3J9W_1441/BA/1962:1963,
1/BA/1993:1996		Bulged stacked bases
homologous
IL_5J7L_318
NA
IL_3J9W_1451/BA/1963:1974,
1/BA/1990:1993		No text annotation
geometric
IL_4WF9_077
IL_84014.1
IL_3J9W_1461/BA/2079:2081,
1/BA/2646:2647		Major groove platform
homologous
IL_4WF9_078
IL_48076.7
IL_3J9W_1471/BA/2083:2085,
1/BA/2641:2644		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_3J9W_1481/BA/2096:2098,
1/BA/2471:2472		Single bulged U
homologous
IL_7A0S_075
IL_97561.1
IL_3J9W_1491/BA/2099:2100,
1/BA/2467:2470		Minor groove platform
homologous
IL_4WF9_081
IL_34520.1
IL_3J9W_1501/BA/2110:2112,
1/BA/2265:2268		Isolated tHS basepair with bulges
homologous
IL_7RQB_082
NA
IL_3J9W_1511/BA/2124:2126,
1/BA/2221:2223		Isolated non-canonical cWW pair
geometric
IL_5J7L_326
NA
IL_3J9W_1561/BA/2231:2233,
1/BA/2249:2250		Single bulged G
geometric
IL_3NDB_004
NA
IL_3J9W_1581/BA/2379:2382,
1/BA/2393:2396		Double sheared
homologous
IL_5J7L_333
NA
IL_3J9W_1591/BA/2430:2432,
1/BA/2443:2444		Single bulged U
homologous
IL_5J7L_334
NA
IL_3J9W_1601/BA/2482:2483,
1/BA/2527:2529		Single stack bend
geometric
IL_4WF9_089
IL_15011.1
IL_3J9W_1611/BA/2483:2484,
1/BA/2525:2527		Major groove platform
homologous
IL_4WF9_090
IL_48076.7
IL_3J9W_1621/BA/2486:2488,
1/BA/2522:2523		Major groove platform
geometric
IL_4WF9_091
IL_48076.7
IL_3J9W_1631/BA/2488:2490,
1/BA/2518:2522		Major groove minor groove platform with extra cWW
homologous
IL_4WF9_092
IL_36931.1
IL_3J9W_1641/BA/2495:2499,
1/BA/2509:2513		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_3J9W_1651/BA/2536:2537,
1/BA/2609:2611		Major groove platform
homologous
IL_4WF9_094
IL_46637.1
IL_3J9W_1661/BA/2539:2541,
1/BA/2603:2607		Isolated non-canonical cWW with bulges
geometric
IL_7RQB_097
NA
IL_3J9W_1671/BA/2541:2542,
1/BA/2600:2603		No text annotation
homologous
IL_5J7L_341
NA
IL_3J9W_1681/BA/2551:2552,
1/BA/2569:2572		Major groove platform with intercalation
homologous
IL_7RQB_099
NA
IL_3J9W_1691/BA/2620:2621,
1/BA/2630:2632		Single bulged A
homologous
IL_7RQB_101
NA
IL_3J9W_1701/BA/2665:2669,
1/BA/2803:2811		tSH-tHS-tHW
homologous
IL_7A0S_093
IL_04638.4
IL_3J9W_1711/BA/2681:2687,
1/BA/2692:2697		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_5J7L_346
NA
IL_3J9W_1721/BA/2709:2713,
1/BA/2754:2756		C-loop
homologous
IL_5J7L_347
NA
IL_3J9W_1731/BA/2716:2720,
1/BA/2747:2751		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_3J9W_1741/BA/2724:2725,
1/BA/2740:2743		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_3J9W_1751/BA/2766:2771,
1/BA/2791:2796		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_3J9W_1761/BA/2863:2864,
1/BA/2903:2905		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_3J9W_1771/BA/2868:2870,
1/BA/2896:2899		No text annotation
homologous
IL_4WF9_107
IL_05502.1
IL_3J9W_1781/BA/2872:2877,
1/BA/2890:2894		tHS double platform
homologous
IL_4WF9_108
IL_48489.1
IL_3J9W_1791/BB/15:16,
1/BB/63:65		Major groove intercalation
homologous
IL_4WF9_112
IL_14190.1
IL_3J9W_1801/BB/21:27,
1/BB/53:58		No text annotation
IL_3J9W_1821/BB/32:36,
1/BB/42:46		Symmetric double minor groove platform
homologous
IL_7RQB_114
NA
IL_3J9W_1831/BB/69:77,
1/BB/95:103		Bacterial 5S Loop E
homologous
IL_7RQB_115
NA
IL_3J9W_1841/BB/78:80,
1/BB/92:94		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA

Problematic loops

#loop idProblemSequence
IL_3J9W_002Single bulged A
IL_3J9W_004Minor groove platform
IL_3J9W_005Multiple bulged bases
IL_3J9W_006Isolated non-canonical cWW pair
IL_3J9W_007Double sheared with non-canonical cWW
IL_3J9W_008Isolated non-canonical cWW pair
IL_3J9W_010tWH-tWH-tHW-tHW
IL_3J9W_011Kink-turn with non-sequential stacking
IL_3J9W_012No text annotation
IL_3J9W_014C-loop
IL_3J9W_016No text annotation
IL_3J9W_017Major groove minor groove platform; mini C-loop
IL_3J9W_186No text annotation
IL_3J9W_187Single stack bend
IL_3J9W_018SSU/LSU pseudoknot
IL_3J9W_019Kink-turn related
IL_3J9W_022Major groove platform
IL_3J9W_023Major groove minor groove platform; mini C-loop
IL_3J9W_024Single bulged U
IL_3J9W_025No text annotation
IL_3J9W_027No text annotation
IL_3J9W_028Tandem non-canonical cWW pairs
IL_3J9W_029No text annotation
IL_3J9W_031Left turn
IL_3J9W_034Isolated non-canonical cWW pair
IL_3J9W_036Minor groove platform
IL_3J9W_037Minor groove platform
IL_3J9W_038Minor groove platform
IL_3J9W_039Single stack bend
IL_3J9W_189No text annotation
IL_3J9W_040Single bulged U
IL_3J9W_041Isolated cWS basepair
IL_3J9W_042Minor groove platform
IL_3J9W_043Single bulged A
IL_3J9W_044Isolated non-canonical cWW pair
IL_3J9W_196Minor groove platform
IL_3J9W_045No text annotation
IL_3J9W_046Minor groove platform
IL_3J9W_047No text annotation
IL_3J9W_048No text annotation
IL_3J9W_049180 degree turn
IL_3J9W_050Double sheared with non-canonical cWW
IL_3J9W_062No text annotation
IL_3J9W_063Isolated non-canonical cWW pair
IL_3J9W_064No text annotation
IL_3J9W_067No text annotation
IL_3J9W_072Major groove minor groove platform with extra cWW
IL_3J9W_198Major groove minor groove platform; mini C-loop
IL_3J9W_073No text annotation
IL_3J9W_090No text annotation
IL_3J9W_091No text annotation
IL_3J9W_094No text annotation
IL_3J9W_095Minor groove platform with extra cWW
IL_3J9W_192Double sheared with non-canonical cWW
IL_3J9W_096Minor groove platform
IL_3J9W_097Single bulged A
IL_3J9W_106Kink-turn
IL_3J9W_107No text annotation
IL_3J9W_108No text annotation
IL_3J9W_109Isolated cWS basepair
IL_3J9W_119No text annotation
IL_3J9W_126No text annotation
IL_3J9W_127No text annotation
IL_3J9W_152No text annotation
IL_3J9W_153No text annotation
IL_3J9W_154No text annotation
IL_3J9W_155Kink-turn
IL_3J9W_157Isolated tHS basepair with bulges
IL_3J9W_181Major groove minor groove platform; mini C-loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J9W_0011/AA/48:49,
1/AA/369:377,
1/AA/400:403		No text annotation
J3_3J9W_0271/AA/48:54,
1/AA/367:377,
1/AA/400:403		No text annotation
J3_3J9W_0021/AA/595:597,
1/AA/660:663,
1/AA/763:764		No text annotation
homologous
J3_5J7L_002
NA
J3_3J9W_0281/AA/595:597,
1/AA/660:664,
1/AA/760:764		No text annotation
homologous
J3_5J7L_051
NA
J3_3J9W_0031/AA/681:682,
1/AA/726:734,
1/AA/741:743		No text annotation
homologous
J3_5J7L_003
NA
J3_3J9W_0301/AA/965:972,
1/AA/983:994,
1/AA/1230:1234		No text annotation
homologous
J3_4LFB_004
J3_88451.1
J3_3J9W_0091/AA/1073:1078,
1/AA/1117:1123,
1/AA/1196:1202		No text annotation
homologous
J3_5J7L_008
NA
J3_3J9W_0121/AA/1246:1250,
1/AA/1305:1312,
1/AA/1343:1346		No text annotation
homologous
J3_5J7L_011
NA
J3_3J9W_0131/BA/30:31,
1/BA/521:528,
1/BA/555:556		No text annotation
homologous
J3_7A0S_001
J3_68715.1
J3_3J9W_0341/BA/30:31,
1/BA/521:531,
1/BA/542:556		No text annotation
homologous
J3_4WF9_011
J3_17917.1
J3_3J9W_0351/BA/32:35,
1/BA/492:508,
1/BA/515:520		No text annotation
homologous
J3_9DFE_003
J3_07616.1
J3_3J9W_0411/BA/56:57,
1/BA/70:76,
1/BA/109:113		No text annotation
homologous
J3_9DFE_004
J3_01004.1
J3_3J9W_0151/BA/272:276,
1/BA/295:302,
1/BA/416:417		No text annotation
homologous
J3_7RQB_003
NA
J3_3J9W_0361/BA/730:736,
1/BA/820:822,
1/BA/838:841		No text annotation
homologous
J3_4WF9_002
J3_46658.1
J3_3J9W_0171/BA/745:747,
1/BA/779:783,
1/BA/807:810		No text annotation
homologous
J3_4WF9_003
J3_69816.1
J3_3J9W_0191/BA/1337:1342,
1/BA/1670:1672,
1/BA/1684:1687		No text annotation
homologous
J3_7RQB_007
NA
J3_3J9W_0201/BA/1344:1348,
1/BA/1650:1656,
1/BA/1665:1668		No text annotation
homologous
J3_4WF9_005
J3_68164.1
J3_3J9W_0371/BA/1383:1389,
1/BA/1420:1424,
1/BA/1441:1442		No text annotation
homologous
J3_4WF9_016
J3_94309.1
J3_3J9W_0381/BA/1470:1475,
1/BA/1612:1613,
1/BA/1616:1622		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_3J9W_0211/BA/2120:2122,
1/BA/2225:2230,
1/BA/2251:2257		No text annotation
homologous
J3_4WF9_007
J3_07703.1
J3_3J9W_0391/BA/2311:2313,
1/BA/2413:2424,
1/BA/2450:2456		No text annotation
homologous
J3_5J7L_070
NA
J3_3J9W_0221/BA/2324:2326,
1/BA/2350:2352,
1/BA/2361:2366		No text annotation
homologous
J3_4WF9_008
J3_05327.1
J3_3J9W_0231/BA/2546:2549,
1/BA/2574:2576,
1/BA/2590:2596		No text annotation
homologous
J3_5J7L_046
NA
J3_3J9W_0401/BA/2818:2820,
1/BA/2831:2836,
1/BA/2914:2918		No text annotation
homologous
J3_4WF9_020
J3_24127.1
J3_3J9W_0251/BA/2839:2840,
1/BA/2856:2861,
1/BA/2907:2911		No text annotation
homologous
J3_7A0S_013
J3_76911.2
J3_3J9W_0261/BB/9:14,
1/BB/66:68,
1/BB/104:107		No text annotation
J4_3J9W_0011/AA/113:121,
1/AA/246:248,
1/AA/294:297,
1/AA/319:320		No text annotation
J4_3J9W_0031/AA/584:586,
1/AA/773:778,
1/AA/819:830,
1/AA/889:890		No text annotation
homologous
J4_4LFB_003
J4_14595.1
J4_3J9W_0041/AX/7:10,
1/AX/25:27,
1/AX/43:49,
1/AX/65:66		tRNA junction
homologous
J4_5E81_027
NA
J4_3J9W_0051/BA/271:272,
1/BA/417:422,
1/BA/446:453,
1/BA/468:471		No text annotation
homologous
J4_4WF9_001
J4_94698.1
J4_3J9W_0061/BA/340:344,
1/BA/360:363,
1/BA/367:369,
1/BA/381:385		No text annotation
homologous
J4_4WF9_002
J4_16174.1
J4_3J9W_0071/BA/645:648,
1/BA/670:674,
1/BA/681:684,
1/BA/696:703		No text annotation
homologous
J4_5J7L_020
NA
J4_3J9W_0081/BA/1310:1315,
1/BA/1333:1334,
1/BA/1690:1693,
1/BA/2038:2039		No text annotation
homologous
J4_4WF9_004
J4_64571.6
J4_3J9W_0091/BA/1349:1353,
1/BA/1377:1382,
1/BA/1443:1444,
1/BA/1642:1649		No text annotation
homologous
J4_4WF9_005
J4_77353.1
J4_3J9W_0101/BA/1352:1353,
1/BA/1377:1382,
1/BA/1443:1444,
1/BA/1642:1648		No text annotation
homologous
J4_4WF9_006
J4_48150.1
J4_3J9W_0111/BA/1490:1492,
1/BA/1511:1513,
1/BA/1572:1573,
1/BA/1594:1595		No text annotation
J4_3J9W_0121/BA/1801:1805,
1/BA/1817:1821,
1/BA/1856:1859,
1/BA/2004:2008		No text annotation
homologous
J4_5J7L_025
NA
J4_3J9W_0131/BA/1862:1864,
1/BA/1934:1935,
1/BA/1953:1962,
1/BA/1996:2001		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_3J9W_0141/BA/2314:2318,
1/BA/2372:2376,
1/BA/2399:2401,
1/BA/2410:2412		No text annotation
homologous
J4_9DFE_009
J4_98139.1
J4_3J9W_0151/BA/2672:2675,
1/BA/2703:2705,
1/BA/2760:2764,
1/BA/2798:2800		No text annotation
homologous
J4_9DFE_010
J4_77044.5
J5_3J9W_0031/BA/47:54,
1/BA/115:120,
1/BA/129:130,
1/BA/149:151,
1/BA/178:180		No text annotation
homologous
J5_4WF9_001
J5_27223.1
J5_3J9W_0041/BA/271:276,
1/BA/295:302,
1/BA/416:422,
1/BA/446:453,
1/BA/468:471		No text annotation
J5_3J9W_0051/BA/577:579,
1/BA/604:608,
1/BA/621:623,
1/BA/1301:1302,
1/BA/2046:2047		No text annotation
homologous
J5_5J7L_014
NA
J5_3J9W_0061/BA/628:633,
1/BA/715:718,
1/BA/856:859,
1/BA/1236:1237,
1/BA/1290:1296		No text annotation
homologous
J5_7A0S_004
J5_74302.6
J5_3J9W_0071/BA/1719:1727,
1/BA/1751:1752,
1/BA/1780:1781,
1/BA/1785:1793,
1/BA/2017:2019		No text annotation
homologous
J5_4WF9_005
J5_99177.1
J5_3J9W_0081/BA/2086:2093,
1/BA/2475:2482,
1/BA/2529:2535,
1/BA/2612:2617,
1/BA/2635:2640		No text annotation
J5_3J9W_0091/BA/2103:2106,
1/BA/2272:2275,
1/BA/2287:2288,
1/BA/2310:2311,
1/BA/2456:2464		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J6_3J9W_0011/BA/45:46,
1/BA/181:187,
1/BA/215:227,
1/BA/234:238,
1/BA/265:269,
1/BA/473:480		No text annotation
J6_3J9W_0021/BA/2103:2106,
1/BA/2272:2275,
1/BA/2287:2288,
1/BA/2310:2313,
1/BA/2413:2424,
1/BA/2450:2464		No text annotation
J7_3J9W_0031/BA/8:15,
1/BA/571:577,
1/BA/2047:2052,
1/BA/2069:2072,
1/BA/2654:2659,
1/BA/2817:2818,
1/BA/2918:2919		No text annotation
J7_3J9W_0021/BA/864:869,
1/BA/882:883,
1/BA/989:992,
1/BA/1017:1022,
1/BA/1033:1037,
1/BA/1209:1210,
1/BA/1226:1231		No text annotation

Problematic loops

#loop idProblemSequence
J3_3J9W_004No text annotation
J3_3J9W_029No text annotation
J3_3J9W_005No text annotation
J3_3J9W_006No text annotation
J3_3J9W_007No text annotation
J3_3J9W_031No text annotation
J3_3J9W_008No text annotation
J3_3J9W_032No text annotation
J3_3J9W_010No text annotation
J3_3J9W_011No text annotation
J3_3J9W_033No text annotation
J3_3J9W_014No text annotation
J3_3J9W_016No text annotation
J3_3J9W_018No text annotation
J3_3J9W_024No text annotation
J4_3J9W_002No text annotation
J5_3J9W_001No text annotation
J5_3J9W_002No text annotation
J7_3J9W_001No text annotation

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