9HA3 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9HA3_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_9HA3_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9HA3_010 | 1/A/319:323 | No text annotation | homologous HL_7A0S_011 HL_75660.6 | |
| HL_9HA3_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9HA3_014 | 1/A/462:467 | GNRA | homologous HL_7A0S_015 HL_34789.1 | |
| HL_9HA3_017 | 1/A/564:577 | No text annotation | ||
| HL_9HA3_018 | 1/A/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_9HA3_028 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_9HA3_029 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_4WF9_032 HL_33597.1 | |
| HL_9HA3_030 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_9DFE_032 HL_49081.1 | |
| HL_9HA3_032 | 1/A/1389:1398 | No text annotation | homologous HL_9DFE_034 HL_77449.1 | |
| HL_9HA3_033 | 1/A/1451:1459 | Mini UNCG with extended bulge | homologous HL_5J7L_169 NA | |
| HL_9HA3_038 | 1/A/1630:1636 | GNRA | homologous HL_5J7L_174 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9HA3_001 | No text annotation | ||
| HL_9HA3_004 | No text annotation | ||
| HL_9HA3_005 | No text annotation | ||
| HL_9HA3_006 | No text annotation | ||
| HL_9HA3_007 | No text annotation | ||
| HL_9HA3_008 | No text annotation | ||
| HL_9HA3_009 | T-loop with 2 stacked bulged bases | ||
| HL_9HA3_012 | No text annotation | ||
| HL_9HA3_013 | No text annotation | ||
| HL_9HA3_015 | GNRA | ||
| HL_9HA3_016 | No text annotation | ||
| HL_9HA3_019 | No text annotation | ||
| HL_9HA3_020 | No text annotation | ||
| HL_9HA3_021 | GNRA wlth tandem sheared | ||
| HL_9HA3_022 | No text annotation | ||
| HL_9HA3_023 | No text annotation | ||
| HL_9HA3_024 | Mini UNCG | ||
| HL_9HA3_025 | Mini UNCG | ||
| HL_9HA3_026 | No text annotation | ||
| HL_9HA3_027 | Externally structured | ||
| HL_9HA3_031 | GNRA | ||
| HL_9HA3_034 | Externally structured | ||
| HL_9HA3_035 | UNCG | ||
| HL_9HA3_036 | Mini UNCG | ||
| HL_9HA3_037 | No text annotation | ||
| HL_9HA3_039 | No text annotation | ||
| HL_9HA3_040 | No text annotation | ||
| HL_9HA3_041 | Externally structured | ||
| HL_9HA3_042 | GNRA | ||
| HL_9HA3_043 | GNRA | ||
| HL_9HA3_044 | Ribsomal LSU H95 | ||
| HL_9HA3_045 | No text annotation | ||
| HL_9HA3_046 | Mini UNCG | ||
| HL_9HA3_047 | No text annotation | ||
| HL_9HA3_048 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9HA3_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_7A0S_001 IL_22311.1 | |
| IL_9HA3_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7A0S_002 IL_14190.1 | |
| IL_9HA3_008 | 1/A/239:245, 1/A/253:259 | No text annotation | ||
| IL_9HA3_011 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9HA3_012 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_9HA3_014 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_9HA3_015 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.1 | |
| IL_9HA3_025 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.1 | |
| IL_9HA3_026 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_9HA3_027 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_9HA3_028 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_9HA3_030 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.4 | |
| IL_9HA3_031 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_9HA3_032 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_9HA3_035 | 1/A/1319:1323, 1/A/1331:1333 | No text annotation | geometric IL_8CRE_126 NA | |
| IL_9HA3_036 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_4WF9_051 IL_89021.3 | |
| IL_9HA3_041 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_9HA3_044 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_9HA3_048 | 1/A/1526:1529, 1/A/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_9HA3_055 | 1/A/2636:2640, 1/A/2774:2782 | No text annotation | homologous IL_9DFE_101 IL_04638.4 | |
| IL_9HA3_056 | 1/A/2642:2644, 1/A/2771:2772 | Single stack bend | geometric IL_4V9F_081 IL_15011.1 | |
| IL_9HA3_060 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_9HA3_061 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_4WF9_103 IL_44609.1 | |
| IL_9HA3_065 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation | homologous IL_9DFE_107 IL_05642.1 | |
| IL_9HA3_066 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_9HA3_067 | 1/A/2847:2852, 1/A/2865:2869 | tHS double platform | homologous IL_4WF9_108 IL_48489.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9HA3_003 | Minor groove platform | ||
| IL_9HA3_004 | No text annotation | ||
| IL_9HA3_005 | No text annotation | ||
| IL_9HA3_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9HA3_007 | Single stack bend | ||
| IL_9HA3_009 | No text annotation | ||
| IL_9HA3_010 | No text annotation | ||
| IL_9HA3_013 | Double sheared | ||
| IL_9HA3_016 | No text annotation | ||
| IL_9HA3_017 | Single bulged A | ||
| IL_9HA3_018 | No text annotation | ||
| IL_9HA3_019 | No text annotation | ||
| IL_9HA3_020 | Multiple bulged bases | ||
| IL_9HA3_021 | 90 degree turn | ||
| IL_9HA3_022 | No text annotation | ||
| IL_9HA3_023 | Stack outside cWW | ||
| IL_9HA3_024 | Single stack bend | ||
| IL_9HA3_029 | No text annotation | ||
| IL_9HA3_033 | No text annotation | ||
| IL_9HA3_034 | Major groove platform; stack outside cWW | ||
| IL_9HA3_037 | tSH-tHW-tHS | ||
| IL_9HA3_038 | No text annotation | ||
| IL_9HA3_039 | No text annotation | ||
| IL_9HA3_040 | Single stack bend | ||
| IL_9HA3_042 | tSH-tHW | ||
| IL_9HA3_043 | Single bulged U | ||
| IL_9HA3_045 | tSH-tHW-tHS | ||
| IL_9HA3_046 | 180 degree turn | ||
| IL_9HA3_047 | Single bulged A | ||
| IL_9HA3_049 | No text annotation | ||
| IL_9HA3_050 | Isolated tWW turn | ||
| IL_9HA3_051 | No text annotation | ||
| IL_9HA3_052 | No text annotation | ||
| IL_9HA3_053 | No text annotation | ||
| IL_9HA3_054 | No text annotation | ||
| IL_9HA3_057 | Single stack bend | ||
| IL_9HA3_058 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9HA3_059 | C-loop | ||
| IL_9HA3_062 | UAA/GAN with extra cWW | ||
| IL_9HA3_063 | Single bulged A | ||
| IL_9HA3_064 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9HA3_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_4WF9_010 J3_68715.1 | |
| J3_9HA3_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9HA3_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_9HA3_004 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_7A0S_004 J3_46658.1 | |
| J3_9HA3_005 | 1/A/698:700, 1/A/732:736, 1/A/760:763 | No text annotation | homologous J3_4WF9_003 J3_69816.1 | |
| J3_9HA3_006 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_9HA3_007 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_9HA3_008 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_9HA3_012 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_9HA3_002 | 1/A/297:301, 1/A/316:319, 1/A/323:325, 1/A/337:341 | No text annotation | homologous J4_5J7L_019 NA | |
| J4_9HA3_004 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1649, 1/A/2008:2010 | No text annotation | ||
| J4_9HA3_005 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_9HA3_006 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_9HA3_008 | 1/A/2644:2646, 1/A/2674:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | ||
| J5_9HA3_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:152, 1/A/174:178 | No text annotation | ||
| J5_9HA3_002 | 1/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_9HA3_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_4WF9_004 J5_74302.6 | |
| J6_9HA3_001 | 1/A/45:46, 1/A/179:183, 1/A/215:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9HA3_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_9HA3_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
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9HA3_009 | No text annotation | ||
| J3_9HA3_010 | No text annotation | ||
| J3_9HA3_011 | No text annotation | ||
| J4_9HA3_001 | No text annotation | ||
| J4_9HA3_003 | No text annotation | ||
| J4_9HA3_007 | No text annotation |
Coloring options: