9JSR Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9JSR_001 | 1/A/59:68 | No text annotation | geometric HL_8B0X_033 HL_35677.5 | |
| HL_9JSR_002 | 1/A/87:95 | No text annotation | geometric HL_8B0X_034 HL_65821.1 | |
| HL_9JSR_003 | 1/A/123:128 | No text annotation | homologous HL_7A0S_003 HL_82710.3 | |
| HL_9JSR_009 | 1/A/305:312 | T-loop with 1 bulged base | homologous HL_7A0S_010 HL_13999.3 | |
| HL_9JSR_010 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_7A0S_012 HL_27670.4 | |
| HL_9JSR_012 | 1/A/462:467 | GNRA | homologous HL_7A0S_015 HL_34789.3 | |
| HL_9JSR_013 | 1/A/487:493 | GNRA | homologous HL_7A0S_016 HL_34789.3 | |
| HL_9JSR_015 | 1/A/566:575 | T-loop with 2 stacked bulged bases | homologous HL_7A0S_018 HL_33597.3 | |
| HL_9JSR_016 | 1/A/611:617 | No text annotation | geometric HL_9E6Q_019 HL_42293.1 | |
| HL_9JSR_022 | 1/A/978:985 | No text annotation | homologous HL_7A0S_027 HL_47171.1 | |
| HL_9JSR_023 | 1/A/1135:1139 | No text annotation | ||
| HL_9JSR_025 | 1/A/1222:1227 | GNRA | homologous HL_7A0S_031 HL_34789.3 | |
| HL_9JSR_026 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_7A0S_032 HL_33597.3 | |
| HL_9JSR_027 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_7A0S_033 HL_49081.1 | |
| HL_9JSR_028 | 1/A/1389:1398 | No text annotation | homologous HL_7A0S_035 HL_77449.1 | |
| HL_9JSR_029 | 1/A/1612:1619 | No text annotation | homologous HL_7A0S_040 HL_28592.2 | |
| HL_9JSR_030 | 1/A/1630:1636 | GNRA | geometric HL_5LM7_001 HL_34789.3 | |
| HL_9JSR_031 | 1/A/2027:2036 | No text annotation | homologous HL_7A0S_049 HL_78372.1 | |
| HL_9JSR_033 | 1/A/2701:2706 | Ribsomal LSU H95 | homologous HL_7A0S_064 HL_12125.2 | |
| HL_9JSR_035 | 1/A/2819:2827 | No text annotation | homologous HL_7A0S_067 HL_37889.1 | |
| HL_9JSR_036 | 1/A/2856:2861 | GNRA | homologous HL_7A0S_068 HL_34789.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9JSR_004 | No text annotation | ||
| HL_9JSR_005 | No text annotation | ||
| HL_9JSR_006 | No text annotation | ||
| HL_9JSR_007 | No text annotation | ||
| HL_9JSR_008 | No text annotation | ||
| HL_9JSR_011 | Pseudoknot geometry | ||
| HL_9JSR_014 | No text annotation | ||
| HL_9JSR_017 | No text annotation | ||
| HL_9JSR_018 | No text annotation | ||
| HL_9JSR_019 | No text annotation | ||
| HL_9JSR_020 | No text annotation | ||
| HL_9JSR_021 | GNRA | ||
| HL_9JSR_024 | No text annotation | ||
| HL_9JSR_032 | GNRA | ||
| HL_9JSR_034 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9JSR_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_7A0S_001 IL_22311.1 | |
| IL_9JSR_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7A0S_002 IL_14190.2 | |
| IL_9JSR_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_7A0S_003 IL_34520.3 | |
| IL_9JSR_004 | 1/A/81:85, 1/A/97:105 | Kink-turn | homologous IL_7A0S_004 IL_94910.1 | |
| IL_9JSR_005 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_7A0S_005 IL_15011.2 | |
| IL_9JSR_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.3 | |
| IL_9JSR_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_1NBS_007 IL_02666.1 | |
| IL_9JSR_009 | 1/A/291:295, 1/A/343:349 | No text annotation | ||
| IL_9JSR_010 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_7A0S_009 IL_44923.1 | |
| IL_9JSR_011 | 1/A/536:539, 1/A/554:557 | No text annotation | geometric IL_8B0X_076 IL_58355.2 | |
| IL_9JSR_012 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_7A0S_013 IL_66798.3 | |
| IL_9JSR_014 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.3 | |
| IL_9JSR_015 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | homologous IL_7A0S_015 IL_73855.1 | |
| IL_9JSR_016 | 1/A/844:847, 1/A/933:934 | No text annotation | geometric IL_8B0X_087 IL_79144.1 | |
| IL_9JSR_017 | 1/A/844:848, 1/A/930:934 | No text annotation | geometric IL_8B0X_179 IL_01742.1 | |
| IL_9JSR_018 | 1/A/847:848, 1/A/930:933 | No text annotation | geometric IL_8B0X_088 IL_36175.2 | |
| IL_9JSR_019 | 1/A/850:851, 1/A/926:928 | No text annotation | geometric IL_8OI5_088 IL_15011.2 | |
| IL_9JSR_023 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_7A0S_032 IL_05642.2 | |
| IL_9JSR_024 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_9JSR_025 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_7A0S_034 IL_11411.1 | |
| IL_9JSR_026 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_7A0S_035 IL_97561.3 | |
| IL_9JSR_027 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_9JSR_028 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | geometric IL_9DFE_045 IL_68574.5 | |
| IL_9JSR_029 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_7A0S_043 IL_90775.2 | |
| IL_9JSR_030 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_045 IL_62167.3 | |
| IL_9JSR_031 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | geometric IL_8P9A_417 IL_74641.2 | |
| IL_9JSR_032 | 1/A/1319:1323, 1/A/1331:1333 | C-loop | homologous IL_7A0S_047 IL_06671.1 | |
| IL_9JSR_035 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation | homologous IL_7A0S_059 IL_12566.5 | |
| IL_9JSR_036 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_7A0S_060 IL_10432.1 | |
| IL_9JSR_037 | 1/A/1666:1669, 1/A/1993:1994 | No text annotation | geometric IL_9E6Q_063 IL_74641.2 | |
| IL_9JSR_038 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | geometric IL_8OI5_079 IL_80252.1 | |
| IL_9JSR_039 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | homologous IL_7A0S_062 IL_28217.1 | |
| IL_9JSR_040 | 1/A/2049:2052, 1/A/2617:2619 | No text annotation | geometric IL_9AXU_085 IL_75527.2 | |
| IL_9JSR_041 | 1/A/2052:2054, 1/A/2613:2617 | No text annotation | geometric IL_2OEU_001 IL_46387.3 | |
| IL_9JSR_042 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 | |
| IL_9JSR_044 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_7A0S_095 IL_63596.12 | |
| IL_9JSR_045 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_7A0S_096 IL_82016.1 | |
| IL_9JSR_046 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_7A0S_097 IL_44609.2 | |
| IL_9JSR_047 | 1/A/2737:2742, 1/A/2762:2767 | UAA/GAN with extra cWW | homologous IL_7A0S_098 IL_91079.1 | |
| IL_9JSR_048 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation | ||
| IL_9JSR_049 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation | homologous IL_7A0S_099 IL_28408.2 | |
| IL_9JSR_050 | 1/A/2843:2846, 1/A/2870:2874 | No text annotation | geometric IL_8B0X_169 IL_60988.2 | |
| IL_9JSR_051 | 1/A/2847:2852, 1/A/2865:2869 | No text annotation | homologous IL_7A0S_101 IL_48489.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9JSR_008 | No text annotation | ||
| IL_9JSR_013 | Single stack bend | ||
| IL_9JSR_020 | Single stack bend | ||
| IL_9JSR_021 | No text annotation | ||
| IL_9JSR_022 | Minor groove platform | ||
| IL_9JSR_033 | UAA/GAN | ||
| IL_9JSR_034 | No text annotation | ||
| IL_9JSR_043 | Sarcin-Ricin target in LSU H95; G-bulge |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9JSR_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_7A0S_001 J3_68715.1 | |
| J3_9JSR_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_7A0S_016 J3_07616.1 | |
| J3_9JSR_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_7A0S_002 J3_01004.1 | |
| J3_9JSR_004 | 1/A/297:301, 1/A/316:325, 1/A/337:341 | No text annotation | geometric J3_8B0X_034 J3_77124.1 | |
| J3_9JSR_005 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_7A0S_006 J3_32852.7 | |
| J3_9JSR_006 | 1/A/1306:1309, 1/A/1605:1612, 1/A/1619:1622 | No text annotation | ||
| J3_9JSR_007 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | ||
| J3_9JSR_008 | 1/A/2789:2791, 1/A/2805:2806, 1/A/2892:2894 | No text annotation | ||
| J3_9JSR_009 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | ||
| J4_9JSR_001 | 1/A/268:271, 1/A/366:375, 1/A/399:406, 1/A/421:424 | No text annotation | ||
| J4_9JSR_002 | 1/A/601:604, 1/A/624:628, 1/A/635:638, 1/A/650:656 | No text annotation | ||
| J4_9JSR_003 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_7A0S_004 J4_64571.6 | |
| J4_9JSR_004 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1406, 1/A/1596:1604 | No text annotation | ||
| J4_9JSR_005 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1406, 1/A/1596:1603 | No text annotation | ||
| J4_9JSR_006 | 1/A/2643:2648, 1/A/2672:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | ||
| J5_9JSR_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | ||
| J5_9JSR_002 | 1/A/531:533, 1/A/560:566, 1/A/575:579, 1/A/1261:1262, 1/A/2017:2018 | No text annotation | ||
| J5_9JSR_003 | 1/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 | |
| J6_9JSR_001 | 1/A/45:46, 1/A/179:183, 1/A/214:225, 1/A/230:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9JSR_001 | 1/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_9JSR_002 | 1/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
No problematic loops
Coloring options: