RNA 3D Hub //

7S9U Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7S9U_0011/A/67:74No text annotation
homologous
HL_4WF9_001
HL_08550.1
HL_7S9U_0021/A/87:95Pseudoknot geometry
homologous
HL_4WF9_002
HL_00911.1
HL_7S9U_0031/A/122:127No text annotation
homologous
HL_4WF9_003
HL_75660.6
HL_7S9U_0041/A/136:143GNRA wlth tandem sheared
homologous
HL_4WF9_004
HL_98423.1
HL_7S9U_0681/A/159:169No text annotation
homologous
HL_5J7L_138
NA
HL_7S9U_0061/A/197:204No text annotation
homologous
HL_7RQB_006
NA
HL_7S9U_0071/A/228:233No text annotation
homologous
HL_4WF9_007
HL_51020.1
HL_7S9U_0081/A/241:262No text annotation
HL_7S9U_0641/A/280:291No text annotation
HL_7S9U_0101/A/349:356T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_13999.1
HL_7S9U_0111/A/363:367No text annotation
homologous
HL_5J7L_143
NA
HL_7S9U_0121/A/371:379T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_7S9U_0691/A/429:439No text annotation
homologous
HL_5J7L_145
NA
HL_7S9U_0141/A/457:464Pseudoknot geometry
geometric
HL_4GXY_003
NA
HL_7S9U_0151/A/509:514GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_7S9U_0161/A/534:539GNRA
homologous
HL_7RQB_016
NA
HL_7S9U_0171/A/588:595No text annotation
homologous
HL_4WF9_017
HL_50318.1
HL_7S9U_0181/A/610:619T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_7S9U_0191/A/656:662GNRA
geometric
HL_5J7L_026
NA
HL_7S9U_0201/A/675:680GNRA
homologous
HL_7RQB_020
NA
HL_7S9U_0211/A/687:693No text annotation
homologous
HL_7RQB_021
NA
HL_7S9U_0231/A/791:800No text annotation
homologous
HL_7A0S_022
HL_50204.1
HL_7S9U_0241/A/826:832No text annotation
geometric
HL_5U3G_001
NA
HL_7S9U_0251/A/873:878No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_7S9U_0271/A/1001:1008GNRA
homologous
HL_7A0S_026
HL_34789.1
HL_7S9U_0281/A/1024:1031No text annotation
homologous
HL_5J7L_160
NA
HL_7S9U_0301/A/1216:1220Mini UNCG
geometric
HL_5AH5_007
HL_90436.1
HL_7S9U_0311/A/1262:1267GNRA
homologous
HL_4WF9_031
HL_34789.1
HL_7S9U_0321/A/1320:1328T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_33597.1
HL_7S9U_0331/A/1363:1369Pseudoknot geometry with 3' bulge
homologous
HL_4WF9_033
HL_49081.1
HL_7S9U_0341/A/1402:1407GNRA
homologous
HL_5J7L_167
NA
HL_7S9U_0351/A/1428:1437No text annotation
homologous
HL_5J7L_168
NA
HL_7S9U_0651/A/1494:1509No text annotation
HL_7S9U_0361/A/1496:1507No text annotation
geometric
HL_5J7L_018
NA
HL_7S9U_0371/A/1538:1544Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_7S9U_0381/A/1577:1589No text annotation
HL_7S9U_0391/A/1613:1616Mini UNCG
homologous
HL_7A0S_039
HL_90436.1
HL_7S9U_0401/A/1657:1664No text annotation
homologous
HL_7RQB_040
NA
HL_7S9U_0411/A/1675:1681GNRA
homologous
HL_5J7L_174
NA
HL_7S9U_0421/A/1736:1741No text annotation
homologous
HL_7RQB_042
NA
HL_7S9U_0431/A/1764:1769No text annotation
homologous
HL_7RQB_043
NA
HL_7S9U_0441/A/1781:1785No text annotation
homologous
HL_7RQB_044
NA
HL_7S9U_0451/A/1806:1816No text annotation
HL_7S9U_0461/A/1835:1840GNRA related
homologous
HL_5J7L_179
NA
HL_7S9U_0481/A/2056:2065No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_7S9U_0661/A/2236:2246No text annotation
HL_7S9U_0501/A/2238:2244No text annotation
homologous
HL_5J7L_185
NA
HL_7S9U_0701/A/2276:2286Anticodon loop related
geometric
HL_7KGA_001
NA
HL_7S9U_0711/A/2293:2305No text annotation
homologous
HL_4WF9_050
HL_02042.1
HL_7S9U_0541/A/2352:2361Pseudoknot geometry
geometric
HL_3IVK_004
HL_30680.4
HL_7S9U_0551/A/2384:2391No text annotation
homologous
HL_7RQB_057
NA
HL_7S9U_0561/A/2403:2408GNRA
homologous
HL_5J7L_191
NA
HL_7S9U_0571/A/2433:2442No text annotation
homologous
HL_4WF9_055
HL_51853.1
HL_7S9U_0591/A/2730:2735Ribsomal LSU H95
homologous
HL_4WF9_061
HL_12125.1
HL_7S9U_0601/A/2774:2788No text annotation
homologous
HL_7RQB_066
NA
HL_7S9U_0611/A/2823:2828GNRA
geometric
HL_4QLM_001
HL_34789.1
HL_7S9U_0621/A/2844:2852No text annotation
homologous
HL_5J7L_201
NA
HL_7S9U_0631/A/2881:2886GNRA
homologous
HL_7RQB_069
NA

Problematic loops

#loop idProblemSequence
HL_7S9U_005No text annotation
HL_7S9U_009No text annotation
HL_7S9U_013No text annotation
HL_7S9U_022GNRA wlth tandem sheared
HL_7S9U_026No text annotation
HL_7S9U_029No text annotation
HL_7S9U_047No text annotation
HL_7S9U_049No text annotation
HL_7S9U_051No text annotation
HL_7S9U_052No text annotation
HL_7S9U_067No text annotation
HL_7S9U_053No text annotation
HL_7S9U_058No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7S9U_0011/A/36:37,
1/A/489:491		Single bulged A
homologous
IL_7RQB_002
NA
IL_7S9U_0021/A/43:44,
1/A/481:483		Minor groove platform
homologous
IL_5J7L_247
NA
IL_7S9U_0801/A/56:76,
1/A/109:113		No text annotation
geometric
IL_5TBW_144
NA
IL_7S9U_0031/A/81:85,
1/A/97:104		Kink-turn
homologous
IL_7RQB_004
NA
IL_7S9U_0041/A/152:153,
1/A/175:177		Single bulged A
homologous
IL_4WF9_006
IL_14190.1
IL_7S9U_0051/A/186:187,
1/A/215:217		Single stack bend
homologous
IL_4WF9_007
IL_15011.1
IL_7S9U_0061/A/191:197,
1/A/204:211		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_62167.1
IL_7S9U_0071/A/304:306,
1/A/410:414		Major groove minor groove platform with extra cWW
homologous
IL_4WF9_012
IL_46387.2
IL_7S9U_0081/A/310:316,
1/A/404:406		No text annotation
IL_7S9U_0091/A/319:327,
1/A/400:401		No text annotation
IL_7S9U_0101/A/336:338,
1/A/387:391		No text annotation
homologous
IL_5J7L_254
NA
IL_7S9U_0111/A/344:346,
1/A/359:360		Single bulged A
geometric
IL_7A0S_012
IL_14190.1
IL_7S9U_0121/A/528:531,
1/A/542:555		No text annotation
homologous
IL_4WF9_015
IL_44923.1
IL_7S9U_0131/A/582:585,
1/A/598:601		Double sheared
homologous
IL_4WF9_016
IL_58355.1
IL_7S9U_0141/A/608:610,
1/A/619:621		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.1
IL_7S9U_0151/A/639:641,
1/A/707:709		Isolated non-canonical cWW pair
homologous
IL_4WF9_018
IL_71625.1
IL_7S9U_0161/A/650:654,
1/A/664:668		AAA cross-strand stack
homologous
IL_7RQB_016
NA
IL_7S9U_0171/A/719:721,
1/A/853:855		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_01003.1
IL_7S9U_0811/A/719:725,
1/A/846:855		No text annotation
IL_7S9U_0181/A/721:725,
1/A/846:853		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_7S9U_0191/A/744:745,
1/A/810:812		Single bulged A
homologous
IL_5J7L_261
NA
IL_7S9U_0201/A/749:750,
1/A/775:777		Single bulged G
geometric
IL_4V9F_026
IL_28408.1
IL_7S9U_0211/A/750:754,
1/A/771:775		Triple sheared
homologous
IL_4WF9_024
IL_15190.1
IL_7S9U_0221/A/785:787,
1/A/804:805		Major groove platform
homologous
IL_4WF9_026
IL_48076.7
IL_7S9U_0231/A/822:824,
1/A/834:838		Multiple bulged bases
geometric
IL_7RQB_023
NA
IL_7S9U_0911/A/884:885,
1/A/986:988		Single stack bend
homologous
IL_7A0S_022
IL_15011.1
IL_7S9U_0251/A/891:895,
1/A/977:980		No text annotation
homologous
IL_4WF9_029
IL_01742.1
IL_7S9U_0261/A/899:900,
1/A/971:973		Single stack bend
geometric
IL_5VSU_003
IL_15011.1
IL_7S9U_0271/A/903:910,
1/A/960:968		No text annotation
IL_7S9U_0921/A/911:915,
1/A/956:959		C-loop
homologous
IL_7A0S_029
IL_16301.1
IL_7S9U_0291/A/998:1000,
1/A/1009:1011		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_01003.1
IL_7S9U_0301/A/1040:1042,
1/A/1205:1206		Single bulged C
homologous
IL_4WF9_035
IL_05642.1
IL_7S9U_0311/A/1044:1048,
1/A/1199:1203		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_7S9U_0321/A/1050:1057,
1/A/1196:1197		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_7S9U_0331/A/1057:1059,
1/A/1195:1196		Single bulged U
geometric
IL_5J7L_279
NA
IL_7S9U_0341/A/1064:1070,
1/A/1186:1190		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_7S9U_0351/A/1070:1076,
1/A/1170:1186		No text annotation
geometric
IL_5J7L_281
NA
IL_7S9U_0361/A/1076:1080,
1/A/1167:1170		No text annotation
IL_7S9U_0371/A/1237:1239,
1/A/1287:1290		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.4
IL_7S9U_0931/A/1243:1247,
1/A/1279:1283		Partly complementary
geometric
IL_7VYX_004
IL_71154.1
IL_7S9U_0391/A/1248:1255,
1/A/1274:1278		Kink-turn
geometric
IL_7A0S_043
IL_90775.1
IL_7S9U_0401/A/1259:1261,
1/A/1268:1270		Intercalated cWW
homologous
IL_4WF9_047
IL_61702.1
IL_7S9U_0411/A/1302:1309,
1/A/2040:2046		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_048
IL_62167.1
IL_7S9U_0421/A/1349:1352,
1/A/1648:1649		Major groove platform; stack outside cWW
homologous
IL_7A0S_046
IL_74641.1
IL_7S9U_0431/A/1358:1362,
1/A/1370:1372		C-loop
homologous
IL_7A0S_047
IL_06671.1
IL_7S9U_0441/A/1390:1394,
1/A/1415:1419		UAA/GAN
homologous
IL_7A0S_048
IL_89021.3
IL_7S9U_0451/A/1396:1400,
1/A/1409:1413		tSH-tHW-tHS
homologous
IL_4WF9_052
IL_05821.1
IL_7S9U_0461/A/1448:1450,
1/A/1637:1638		Minor groove platform
geometric
IL_4R4V_001
IL_34520.1
IL_7S9U_0471/A/1455:1462,
1/A/1629:1632		No text annotation
IL_7S9U_0481/A/1463:1467,
1/A/1625:1628		Other IL
homologous
IL_4WF9_054
IL_74317.1
IL_7S9U_0491/A/1478:1481,
1/A/1605:1609		No text annotation
IL_7S9U_0501/A/1483:1486,
1/A/1599:1603		tSH-tHW
homologous
IL_5J7L_297
NA
IL_7S9U_0511/A/1494:1496,
1/A/1507:1509		Isolated non-canonical cWW pair
geometric
IL_2ZKO_001
IL_01003.1
IL_7S9U_0841/A/1514:1526,
1/A/1558:1571		No text annotation
IL_7S9U_0521/A/1527:1530,
1/A/1552:1557		No text annotation
IL_7S9U_0531/A/1530:1531,
1/A/1550:1552		Single stack bend
geometric
IL_7KGA_003
NA
IL_7S9U_0541/A/1535:1537,
1/A/1545:1546		Single bulged A
homologous
IL_5J7L_302
NA
IL_7S9U_0551/A/1573:1576,
1/A/1590:1594		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_7S9U_0561/A/1696:1701,
1/A/2033:2035		No text annotation
homologous
IL_4WF9_062
IL_12566.5
IL_7S9U_0571/A/1708:1710,
1/A/2024:2026		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_7S9U_0581/A/1711:1714,
1/A/2022:2023		Major groove platform; stack outside cWW
homologous
IL_4WF9_064
IL_74641.1
IL_7S9U_0871/A/1711:1719,
1/A/2019:2023		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_7S9U_0591/A/1714:1719,
1/A/2019:2022		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.1
IL_7S9U_0601/A/1731:1736,
1/A/1741:1747		tSH-tSH-tHH-tHS
geometric
IL_4V9F_063
IL_20700.1
IL_7S9U_0611/A/1756:1761,
1/A/1772:1776		tSH-tHW-tWW
geometric
IL_5J7L_022
NA
IL_7S9U_0621/A/1799:1800,
1/A/2009:2011		Single bulged A
homologous
IL_7A0S_064
IL_14190.1
IL_7S9U_0631/A/1827:1833,
1/A/1842:1850		Kink-turn related
homologous
IL_7RQB_070
NA
IL_7S9U_0641/A/2079:2081,
1/A/2646:2647		Major groove platform
homologous
IL_7RQB_078
NA
IL_7S9U_0651/A/2101:2103,
1/A/2464:2467		No text annotation
geometric
IL_4N0T_004
IL_32983.1
IL_7S9U_0661/A/2109:2115,
1/A/2262:2269		No text annotation
IL_7S9U_0671/A/2231:2233,
1/A/2249:2250		No text annotation
IL_7S9U_0891/A/2312:2326,
1/A/2350:2354		No text annotation
IL_7S9U_0691/A/2379:2382,
1/A/2393:2396		Double sheared
homologous
IL_5J7L_333
NA
IL_7S9U_0701/A/2430:2432,
1/A/2443:2444		Single bulged U
homologous
IL_5J7L_334
NA
IL_7S9U_0711/A/2665:2669,
1/A/2803:2811		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.4
IL_7S9U_0721/A/2680:2687,
1/A/2692:2698		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_7S9U_0731/A/2709:2713,
1/A/2754:2756		C-loop
homologous
IL_5J7L_347
NA
IL_7S9U_0741/A/2716:2720,
1/A/2747:2751		UAA/GAN related, with intercalation
homologous
IL_4WF9_102
IL_82016.1
IL_7S9U_0751/A/2724:2725,
1/A/2740:2743		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_7S9U_0941/A/2766:2772,
1/A/2790:2796		No text annotation
IL_7S9U_0771/A/2863:2864,
1/A/2903:2905		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_7S9U_0781/A/2868:2870,
1/A/2896:2899		No text annotation
homologous
IL_4WF9_107
IL_05502.1
IL_7S9U_0791/A/2872:2877,
1/A/2890:2894		tHS double platform
homologous
IL_4WF9_108
IL_48489.1

Problematic loops

#loop idProblemSequence
IL_7S9U_024No text annotation
IL_7S9U_082No text annotation
IL_7S9U_083No text annotation
IL_7S9U_028No text annotation
IL_7S9U_038No text annotation
IL_7S9U_085No text annotation
IL_7S9U_086No text annotation
IL_7S9U_088No text annotation
IL_7S9U_068No text annotation
IL_7S9U_076No text annotation
IL_7S9U_090No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7S9U_0111/A/24:31,
1/A/521:528,
1/A/555:562		No text annotation
J3_7S9U_0121/A/32:35,
1/A/492:508,
1/A/515:520		No text annotation
homologous
J3_9DFE_003
J3_07616.1
J3_7S9U_0011/A/56:67,
1/A/74:76,
1/A/109:113		No text annotation
homologous
J3_4WF9_001
J3_47707.1
J3_7S9U_0021/A/272:277,
1/A/294:303,
1/A/415:417		No text annotation
J3_7S9U_0131/A/272:277,
1/A/294:306,
1/A/410:417		No text annotation
J3_7S9U_0141/A/340:344,
1/A/360:369,
1/A/381:385		No text annotation
homologous
J3_4WF9_015
J3_77124.1
J3_7S9U_0031/A/730:736,
1/A/820:822,
1/A/838:841		No text annotation
homologous
J3_5J7L_038
NA
J3_7S9U_0041/A/745:747,
1/A/779:783,
1/A/807:810		No text annotation
homologous
J3_4WF9_003
J3_69816.1
J3_7S9U_0051/A/1337:1342,
1/A/1670:1672,
1/A/1684:1687		No text annotation
homologous
J3_7A0S_006
J3_32852.7
J3_7S9U_0061/A/1344:1348,
1/A/1650:1656,
1/A/1665:1668		No text annotation
homologous
J3_4WF9_005
J3_68164.1
J3_7S9U_0151/A/1383:1389,
1/A/1420:1424,
1/A/1441:1442		No text annotation
homologous
J3_7A0S_018
J3_94309.1
J3_7S9U_0161/A/1470:1475,
1/A/1612:1613,
1/A/1616:1622		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_7S9U_0181/A/2120:2122,
1/A/2225:2230,
1/A/2251:2257		No text annotation
homologous
J3_4WF9_007
J3_07703.1
J3_7S9U_0081/A/2322:2326,
1/A/2350:2352,
1/A/2361:2368		No text annotation
J3_7S9U_0171/A/2359:2376,
1/A/2399:2401,
1/A/2410:2414		No text annotation
J3_7S9U_0091/A/2818:2820,
1/A/2831:2836,
1/A/2914:2918		No text annotation
homologous
J3_7A0S_012
J3_20574.1
J3_7S9U_0101/A/2839:2840,
1/A/2856:2861,
1/A/2907:2911		No text annotation
homologous
J3_7A0S_013
J3_76911.2
J4_7S9U_0011/A/271:272,
1/A/417:422,
1/A/446:453,
1/A/468:471		No text annotation
homologous
J4_4WF9_001
J4_94698.1
J4_7S9U_0021/A/340:344,
1/A/360:363,
1/A/367:369,
1/A/381:385		No text annotation
homologous
J4_7A0S_002
J4_16174.1
J4_7S9U_0031/A/645:648,
1/A/670:674,
1/A/681:684,
1/A/696:703		No text annotation
homologous
J4_5J7L_020
NA
J4_7S9U_0041/A/1310:1315,
1/A/1333:1334,
1/A/1690:1693,
1/A/2038:2039		No text annotation
homologous
J4_4WF9_004
J4_64571.6
J4_7S9U_0051/A/1349:1353,
1/A/1377:1382,
1/A/1443:1444,
1/A/1642:1649		No text annotation
homologous
J4_4WF9_005
J4_77353.1
J4_7S9U_0061/A/1488:1492,
1/A/1511:1513,
1/A/1572:1573,
1/A/1594:1597		No text annotation
J4_7S9U_0071/A/1801:1805,
1/A/1817:1821,
1/A/1856:1859,
1/A/2004:2008		No text annotation
homologous
J4_5J7L_025
NA
J4_7S9U_0081/A/2672:2675,
1/A/2703:2705,
1/A/2760:2764,
1/A/2798:2800		No text annotation
homologous
J4_5J7L_028
NA
J5_7S9U_0011/A/47:54,
1/A/115:120,
1/A/129:130,
1/A/149:151,
1/A/178:180		No text annotation
homologous
J5_4WF9_001
J5_27223.1
J5_7S9U_0021/A/271:277,
1/A/294:306,
1/A/410:422,
1/A/446:453,
1/A/468:471		No text annotation
J5_7S9U_0031/A/628:634,
1/A/714:718,
1/A/856:859,
1/A/1236:1237,
1/A/1290:1296		No text annotation
J5_7S9U_0041/A/1719:1727,
1/A/1751:1752,
1/A/1780:1781,
1/A/1785:1793,
1/A/2017:2019		No text annotation
homologous
J5_4WF9_005
J5_99177.1
J6_7S9U_0011/A/45:46,
1/A/181:186,
1/A/217:227,
1/A/234:238,
1/A/265:269,
1/A/473:480		No text annotation
J7_7S9U_0031/A/864:869,
1/A/882:883,
1/A/989:992,
1/A/1017:1022,
1/A/1033:1037,
1/A/1209:1210,
1/A/1226:1231		No text annotation
J7_7S9U_0041/A/2103:2106,
1/A/2272:2275,
1/A/2287:2288,
1/A/2310:2312,
1/A/2354:2358,
1/A/2415:2424,
1/A/2450:2464		No text annotation
J10_7S9U_0011/A/8:15,
1/A/571:579,
1/A/604:608,
1/A/621:623,
1/A/1301:1302,
1/A/2046:2052,
1/A/2069:2072,
1/A/2654:2659,
1/A/2817:2818,
1/A/2918:2919		No text annotation

Problematic loops

#loop idProblemSequence
J3_7S9U_007No text annotation
J7_7S9U_001No text annotation
J7_7S9U_002No text annotation

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