RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9BSS_0011/A/59:68Pseudoknot with intercalation
homologous
HL_4WF9_067
HL_17803.3
HL_9BSS_0021/A/87:95Purine riboswitch
geometric
HL_4LX6_002
HL_56046.1
HL_9BSS_0031/A/122:127No text annotation
homologous
HL_5J7L_136
NA
HL_9BSS_0041/A/136:143GNRA with tandem sheared
homologous
HL_4WF9_004
HL_98423.5
HL_9BSS_0051/A/159:169No text annotation
homologous
HL_5J7L_138
NA
HL_9BSS_0061/A/197:204No text annotation
homologous
HL_4WF9_006
HL_02262.1
HL_9BSS_0071/A/228:233No text annotation
homologous
HL_7A0S_007
HL_23875.1
HL_9BSS_0081/A/249:255No text annotation
homologous
HL_4WF9_008
HL_76371.4
HL_9BSS_0101/A/349:356T-loop with 2 stacked bulged bases
homologous
HL_5J7L_142
NA
HL_9BSS_0111/A/363:367No text annotation
geometric
HL_5J7L_143
NA
HL_9BSS_0121/A/371:379T-loop with unstacked turn
homologous
HL_4WF9_012
HL_27670.6
HL_9BSS_0131/A/429:439No text annotation
HL_9BSS_0141/A/457:464Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.5
HL_9BSS_0151/A/509:514GNRA
homologous
HL_4WF9_015
HL_34789.6
HL_9BSS_0161/A/534:539GNRA
homologous
HL_9DFE_015
HL_34789.6
HL_9BSS_0171/A/588:595No text annotation
homologous
HL_4WF9_017
HL_50318.1
HL_9BSS_0181/A/610:619T-loop with 2 stacked bulged bases
homologous
HL_4WF9_018
HL_33597.6
HL_9BSS_0191/A/656:662GNRA related
geometric
HL_5J7L_179
NA
HL_9BSS_0201/A/675:680GNRA
homologous
HL_9DFE_018
HL_34789.6
HL_9BSS_0231/A/791:800No text annotation
homologous
HL_4WF9_023
HL_50204.3
HL_9BSS_0241/A/826:832UNCG variation
homologous
HL_7A0S_023
HL_23875.1
HL_9BSS_0251/A/1024:1031No text annotation
homologous
HL_4WF9_028
HL_47171.3
HL_9BSS_0271/A/1262:1267GNRA
homologous
HL_7A0S_031
HL_34789.6
HL_9BSS_0281/A/1320:1328T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_33597.6
HL_9BSS_0291/A/1363:1369Pseudoknot geometry with 3' bulge
homologous
HL_4WF9_033
HL_49081.2
HL_9BSS_0301/A/1402:1407GNRA
homologous
HL_5J7L_167
NA
HL_9BSS_0311/A/1428:1437No text annotation
homologous
HL_5J7L_168
NA
HL_9BSS_0321/A/1494:1509No text annotation
HL_9BSS_0331/A/1538:1544Pseudoknot geometry with 3' bulge
homologous
HL_9DFE_036
HL_49081.2
HL_9BSS_0341/A/1657:1664No text annotation
homologous
HL_4WF9_038
HL_28592.4
HL_9BSS_0351/A/1675:1681GNRA
homologous
HL_5J7L_174
NA
HL_9BSS_0361/A/1736:1741UNCG
homologous
HL_5J7L_175
NA
HL_9BSS_0371/A/1781:1785No text annotation
homologous
HL_9DFE_042
HL_80709.5
HL_9BSS_0381/A/1806:1816No text annotation
homologous
HL_4WF9_043
HL_87681.3
HL_9BSS_0391/A/1835:1840GNRA
homologous
HL_9DFE_044
HL_34789.6
HL_9BSS_0401/A/2056:2065No text annotation
homologous
HL_5J7L_183
NA
HL_9BSS_0411/A/2238:2244No text annotation
homologous
HL_5J7L_185
NA
HL_9BSS_0441/A/2426:2448No text annotation
HL_9BSS_0451/A/2580:2586No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_9BSS_0461/A/2623:2628GNRA
homologous
HL_5J7L_196
NA
HL_9BSS_0481/A/2730:2735Ribsomal LSU H95
homologous
HL_4WF9_061
HL_12125.4
HL_9BSS_0491/A/2774:2788No text annotation
homologous
HL_9DFE_064
HL_53269.4
HL_9BSS_0511/A/2844:2852No text annotation
homologous
HL_4WF9_064
HL_37889.3
HL_9BSS_0521/A/2881:2886GNRA
homologous
HL_7A0S_068
HL_34789.6

Problematic loops

#loop idProblemSequence
HL_9BSS_009No text annotation
HL_9BSS_021Mini UNCG
HL_9BSS_022GNRA with tandem sheared
HL_9BSS_026No text annotation
HL_9BSS_042Pseudoknot geometry
HL_9BSS_043GNRA
HL_9BSS_047GNRA
HL_9BSS_050No text annotation
HL_9BSS_053No text annotation
HL_9BSS_054Externally structured

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9BSS_0011/A/24:30,
1/A/556:562		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_22311.3
IL_9BSS_0021/A/36:37,
1/A/489:491		Single bulged A
homologous
IL_7A0S_002
IL_14190.4
IL_9BSS_0031/A/43:44,
1/A/481:483		Minor groove platform
homologous
IL_5J7L_247
NA
IL_9BSS_0041/A/81:85,
1/A/97:104		Kink-turn
homologous
IL_4WF9_004
IL_71972.2
IL_9BSS_0051/A/152:153,
1/A/175:177		Single bulged A
homologous
IL_4WF9_006
IL_14190.4
IL_9BSS_0061/A/186:187,
1/A/215:217		Single stack bend
homologous
IL_5J7L_249
NA
IL_9BSS_0071/A/191:197,
1/A/204:211		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.5
IL_9BSS_0081/A/241:248,
1/A/256:262		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_009
IL_62167.5
IL_9BSS_0101/A/308:316,
1/A/404:408		No text annotation
IL_9BSS_0111/A/319:327,
1/A/400:401		No text annotation
IL_9BSS_0121/A/336:338,
1/A/387:391		No text annotation
homologous
IL_9DFE_011
IL_76658.1
IL_9BSS_0131/A/344:346,
1/A/359:360		Single bulged A
geometric
IL_1U63_004
IL_14190.4
IL_9BSS_0141/A/528:531,
1/A/542:555		No text annotation
homologous
IL_4WF9_015
IL_44923.3
IL_9BSS_0151/A/582:585,
1/A/598:601		Double sheared
homologous
IL_4WF9_016
IL_58355.4
IL_9BSS_0161/A/608:610,
1/A/619:621		Isolated non-canonical cWW pair
homologous
IL_4WF9_017
IL_01334.1
IL_9BSS_0171/A/639:641,
1/A/707:709		Isolated non-canonical cWW pair
homologous
IL_4WF9_018
IL_01334.1
IL_9BSS_0181/A/650:654,
1/A/664:668		No text annotation
homologous
IL_9DFE_014
IL_66798.3
IL_9BSS_0191/A/719:721,
1/A/853:855		Isolated non-canonical cWW pair
homologous
IL_7A0S_014
IL_01003.6
IL_9BSS_0201/A/721:725,
1/A/846:853		tHW-tHW cross-strand stack
homologous
IL_5J7L_260
NA
IL_9BSS_0211/A/744:745,
1/A/810:812		Single bulged A
homologous
IL_5J7L_261
NA
IL_9BSS_0221/A/749:750,
1/A/775:777		Single bulged G
homologous
IL_5J7L_262
NA
IL_9BSS_0231/A/750:754,
1/A/771:775		Triple sheared
homologous
IL_4WF9_024
IL_15190.4
IL_9BSS_0241/A/785:787,
1/A/804:805		Major groove platform
homologous
IL_4WF9_026
IL_48076.10
IL_9BSS_0251/A/822:824,
1/A/834:838		No text annotation
geometric
IL_8VTW_022
NA
IL_9BSS_0261/A/884:885,
1/A/986:988		Single stack bend
homologous
IL_7A0S_022
IL_15011.5
IL_9BSS_0271/A/891:895,
1/A/977:980		No text annotation
homologous
IL_4WF9_029
IL_01742.1
IL_9BSS_0281/A/899:902,
1/A/969:973		No text annotation
IL_9BSS_0291/A/902:910,
1/A/960:969		No text annotation
IL_9BSS_0301/A/998:1000,
1/A/1009:1011		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_01003.6
IL_9BSS_0311/A/1040:1042,
1/A/1205:1206		Single bulged C
homologous
IL_4WF9_035
IL_05642.5
IL_9BSS_0321/A/1044:1048,
1/A/1199:1203		UAA/GAN
homologous
IL_4WF9_036
IL_08938.3
IL_9BSS_0331/A/1050:1057,
1/A/1196:1197		SSU/LSU pseudoknot
homologous
IL_4WF9_037
IL_46868.2
IL_9BSS_0341/A/1057:1059,
1/A/1195:1196		Single bulged U
homologous
IL_5J7L_279
NA
IL_9BSS_0351/A/1064:1070,
1/A/1186:1190		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_9BSS_0361/A/1070:1076,
1/A/1170:1186		No text annotation
IL_9BSS_0371/A/1077:1080,
1/A/1167:1169		Isolated non-canonical cWW pair
homologous
IL_9DFE_040
IL_76400.2
IL_9BSS_0381/A/1237:1239,
1/A/1287:1290		Isolated cWS basepair
homologous
IL_4WF9_044
IL_84227.1
IL_9BSS_0391/A/1243:1255,
1/A/1274:1283		No text annotation
IL_9BSS_0401/A/1259:1261,
1/A/1268:1270		Intercalated cWW
homologous
IL_4WF9_047
IL_53541.1
IL_9BSS_0411/A/1302:1309,
1/A/2040:2046		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_048
IL_62167.5
IL_9BSS_0421/A/1349:1352,
1/A/1648:1649		Major groove intercalation
geometric
IL_4V9F_021
IL_71421.5
IL_9BSS_0431/A/1358:1362,
1/A/1370:1372		C-loop
homologous
IL_7A0S_047
IL_06671.3
IL_9BSS_0441/A/1390:1394,
1/A/1415:1419		UAA/GAN
homologous
IL_7A0S_048
IL_89021.4
IL_9BSS_0451/A/1396:1400,
1/A/1409:1413		tSH-tWH-tHS
homologous
IL_5J7L_293
NA
IL_9BSS_0461/A/1448:1450,
1/A/1637:1638		Minor groove platform
geometric
IL_4V9F_034
IL_98469.1
IL_9BSS_0471/A/1455:1462,
1/A/1629:1632		No text annotation
IL_9BSS_0481/A/1463:1467,
1/A/1625:1628		Other IL
homologous
IL_4WF9_054
IL_74317.1
IL_9BSS_0491/A/1470:1475,
1/A/1612:1622		No text annotation
IL_9BSS_0501/A/1478:1481,
1/A/1605:1609		No text annotation
IL_9BSS_0511/A/1483:1486,
1/A/1599:1603		tSH-tHW
homologous
IL_5J7L_297
NA
IL_9BSS_0521/A/1488:1490,
1/A/1595:1597		Isolated non-canonical cWW pair
geometric
IL_5MWI_003
IL_01003.6
IL_9BSS_0531/A/1514:1524,
1/A/1560:1571		No text annotation
IL_9BSS_0551/A/1535:1537,
1/A/1545:1546		Single bulged A
homologous
IL_5J7L_302
NA
IL_9BSS_0561/A/1573:1576,
1/A/1590:1594		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_9BSS_0571/A/1696:1701,
1/A/2033:2035		No text annotation
homologous
IL_5J7L_304
NA
IL_9BSS_0581/A/1708:1710,
1/A/2024:2026		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_9BSS_0591/A/1711:1714,
1/A/2022:2023		Major groove platform; stack outside cWW
geometric
IL_4WF9_064
IL_74641.4
IL_9BSS_0601/A/1711:1719,
1/A/2019:2023		No text annotation
geometric
IL_4WF9_117
IL_80252.3
IL_9BSS_0611/A/1714:1719,
1/A/2019:2022		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.3
IL_9BSS_0621/A/1731:1736,
1/A/1741:1747		tSH-tSH-tHH-tHS
homologous
IL_7A0S_063
IL_20700.3
IL_9BSS_0631/A/1799:1800,
1/A/2009:2011		Single bulged A
homologous
IL_7A0S_064
IL_14190.4
IL_9BSS_0641/A/1826:1833,
1/A/1842:1851		No text annotation
IL_9BSS_0651/A/2079:2081,
1/A/2646:2647		Major groove platform
homologous
IL_5J7L_320
NA
IL_9BSS_0661/A/2083:2085,
1/A/2641:2644		No text annotation
homologous
IL_5J7L_321
NA
IL_9BSS_0671/A/2096:2098,
1/A/2471:2472		Single bulged U
homologous
IL_9DFE_080
IL_97561.7
IL_9BSS_0681/A/2099:2100,
1/A/2467:2470		Minor groove platform
homologous
IL_5J7L_324
NA
IL_9BSS_0691/A/2110:2116,
1/A/2261:2268		No text annotation
IL_9BSS_0701/A/2124:2126,
1/A/2221:2223		Isolated non-canonical cWW pair
geometric
IL_7ECP_001
NA
IL_9BSS_0741/A/2231:2233,
1/A/2249:2250		Single bulged G
homologous
IL_4WF9_125
IL_28408.4
IL_9BSS_0751/A/2379:2382,
1/A/2393:2396		Double sheared
homologous
IL_9DFE_089
IL_58355.4
IL_9BSS_0771/A/2536:2537,
1/A/2609:2611		Multiple bulged bases
geometric
IL_8C3A_400
NA
IL_9BSS_0781/A/2539:2541,
1/A/2603:2607		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
NA
IL_9BSS_0791/A/2541:2542,
1/A/2600:2603		No text annotation
homologous
IL_4WF9_096
IL_44609.4
IL_9BSS_0801/A/2551:2552,
1/A/2569:2572		Major groove platform with intercalation
homologous
IL_4WF9_097
IL_94991.3
IL_9BSS_0811/A/2620:2621,
1/A/2630:2632		Major groove platform
geometric
IL_3OXE_003
IL_48076.10
IL_9BSS_0821/A/2665:2669,
1/A/2803:2811		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.4
IL_9BSS_0831/A/2681:2687,
1/A/2692:2697		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_7A0S_094
IL_16458.6
IL_9BSS_0841/A/2709:2713,
1/A/2754:2756		C-loop
homologous
IL_4WF9_101
IL_63596.14
IL_9BSS_0851/A/2716:2720,
1/A/2747:2751		UAA/GAN related, with intercalation
homologous
IL_4WF9_102
IL_82016.1
IL_9BSS_0861/A/2724:2725,
1/A/2740:2743		Multiple bulged bases
homologous
IL_4WF9_103
IL_44609.4
IL_9BSS_0871/A/2766:2771,
1/A/2791:2796		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_9BSS_0881/A/2863:2864,
1/A/2903:2905		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_9BSS_0891/A/2868:2870,
1/A/2896:2899		No text annotation
homologous
IL_4WF9_107
IL_05502.2
IL_9BSS_0901/A/2872:2877,
1/A/2890:2894		tHS double platform
homologous
IL_4WF9_108
IL_48489.3

Problematic loops

#loop idProblemSequence
IL_9BSS_009No text annotation
IL_9BSS_054No text annotation
IL_9BSS_071Isolated non-canonical cWW pair
IL_9BSS_072Isolated non-canonical cWW pair
IL_9BSS_073No text annotation
IL_9BSS_076Major groove intercalation
IL_9BSS_091Major groove intercalation
IL_9BSS_092No text annotation
IL_9BSS_093No text annotation
IL_9BSS_094No text annotation
IL_9BSS_095Bacterial 5S Loop E
IL_9BSS_096Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9BSS_0011/A/30:31,
1/A/521:528,
1/A/555:556		No text annotation
homologous
J3_7A0S_001
J3_68715.3
J3_9BSS_0021/A/32:35,
1/A/492:508,
1/A/515:520		No text annotation
homologous
J3_4WF9_012
J3_07616.3
J3_9BSS_0031/A/56:57,
1/A/70:76,
1/A/109:113		No text annotation
homologous
J3_9DFE_004
J3_01004.3
J3_9BSS_0041/A/340:344,
1/A/360:369,
1/A/381:385		No text annotation
homologous
J3_4WF9_015
J3_77124.1
J3_9BSS_0051/A/730:736,
1/A/820:822,
1/A/838:841		No text annotation
homologous
J3_4WF9_002
J3_46658.3
J3_9BSS_0061/A/745:747,
1/A/779:783,
1/A/807:810		No text annotation
homologous
J3_4WF9_003
J3_69816.3
J3_9BSS_0071/A/1337:1342,
1/A/1670:1672,
1/A/1684:1687		No text annotation
homologous
J3_5J7L_041
NA
J3_9BSS_0081/A/1344:1348,
1/A/1650:1656,
1/A/1665:1668		No text annotation
homologous
J3_4WF9_005
J3_68164.1
J3_9BSS_0091/A/1383:1389,
1/A/1420:1424,
1/A/1441:1442		No text annotation
homologous
J3_7A0S_018
J3_94309.3
J3_9BSS_0101/A/2120:2124,
1/A/2223:2230,
1/A/2251:2257		No text annotation
homologous
J3_4WF9_018
NA
J3_9BSS_0121/A/2546:2549,
1/A/2574:2576,
1/A/2590:2596		No text annotation
homologous
J3_4WF9_009
J3_32601.6
J3_9BSS_0131/A/2818:2820,
1/A/2831:2836,
1/A/2914:2918		No text annotation
homologous
J3_7A0S_012
J3_20574.1
J3_9BSS_0141/A/2839:2840,
1/A/2856:2861,
1/A/2907:2911		No text annotation
homologous
J3_4WF9_021
J3_76911.2
J3_9BSS_0151/B/9:14,
1/B/66:69,
1/B/103:107		No text annotation
J4_9BSS_0011/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_9BSS_0021/A/645:648,
1/A/670:674,
1/A/681:684,
1/A/696:703		No text annotation
homologous
J4_5J7L_020
NA
J4_9BSS_0031/A/1310:1315,
1/A/1333:1334,
1/A/1690:1693,
1/A/2038:2039		No text annotation
homologous
J4_4WF9_004
J4_19484.1
J4_9BSS_0041/A/1349:1353,
1/A/1377:1382,
1/A/1443:1444,
1/A/1642:1649		No text annotation
homologous
J4_4WF9_005
J4_77353.2
J4_9BSS_0051/A/1352:1353,
1/A/1377:1382,
1/A/1443:1444,
1/A/1642:1648		No text annotation
homologous
J4_4WF9_006
J4_48150.2
J4_9BSS_0061/A/1490:1492,
1/A/1511:1513,
1/A/1572:1573,
1/A/1594:1595		No text annotation
J4_9BSS_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_9BSS_0091/A/2672:2675,
1/A/2703:2705,
1/A/2760:2764,
1/A/2798:2800		No text annotation
homologous
J4_5J7L_028
NA
J5_9BSS_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_27223.3
J5_9BSS_0021/A/271:276,
1/A/295:303,
1/A/415:422,
1/A/446:453,
1/A/468:471		No text annotation
J5_9BSS_0031/A/577:579,
1/A/604:608,
1/A/621:623,
1/A/1301:1302,
1/A/2046:2047		No text annotation
homologous
J5_5J7L_014
NA
J5_9BSS_0041/A/628:633,
1/A/715:718,
1/A/856:859,
1/A/1236:1237,
1/A/1290:1296		No text annotation
homologous
J5_4WF9_004
J5_74302.6
J5_9BSS_0051/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_99177.3
J6_9BSS_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_9BSS_0011/A/7:15,
1/A/571:577,
1/A/2047:2052,
1/A/2069:2072,
1/A/2654:2659,
1/A/2817:2818,
1/A/2918:2920		No text annotation
J7_9BSS_0021/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

Problematic loops

#loop idProblemSequence
J3_9BSS_011No text annotation
J4_9BSS_008No text annotation

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