6SPE Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6SPE_001 | 1/a/12:22 | No text annotation | homologous HL_4LFB_001 HL_73535.1 | |
| HL_6SPE_003 | 1/a/152:157 | GNRA | homologous HL_4LFB_003 HL_34789.4 | |
| HL_6SPE_004 | 1/a/180:185 | No text annotation | geometric HL_2Y9H_003 HL_75660.7 | |
| HL_6SPE_006 | 1/a/253:261 | GNRA related | homologous HL_4LFB_006 HL_87268.2 | |
| HL_6SPE_007 | 1/a/290:295 | GNRA | homologous HL_5J7L_007 NA | |
| HL_6SPE_008 | 1/a/314:327 | No text annotation | homologous HL_6CZR_079 NA | |
| HL_6SPE_009 | 1/a/336:341 | UNCG | homologous HL_6CZR_080 NA | |
| HL_6SPE_010 | 1/a/373:378 | No text annotation | geometric HL_5U3G_001 HL_75660.7 | |
| HL_6SPE_011 | 1/a/413:418 | UNCG | homologous HL_4LFB_011 HL_61337.3 | |
| HL_6SPE_012 | 1/a/456:464 | GNRA wlth extra near cWW | homologous HL_5J7L_012 NA | |
| HL_6SPE_013 | 1/a/516:521 | No text annotation | geometric HL_5J7L_143 NA | |
| HL_6SPE_014 | 1/a/611:617 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_6SPE_015 | 1/a/683:692 | No text annotation | homologous HL_4LFB_015 HL_38491.2 | |
| HL_6SPE_016 | 1/a/720:725 | GNRA | homologous HL_5J7L_016 NA | |
| HL_6SPE_017 | 1/a/780:790 | No text annotation | homologous HL_4LFB_017 HL_38491.2 | |
| HL_6SPE_019 | 1/a/856:861 | GNRA | homologous HL_5J7L_019 NA | |
| HL_6SPE_020 | 1/a/891:896 | GNRA | homologous HL_4LFB_020 HL_34789.4 | |
| HL_6SPE_021 | 1/a/957:966 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_6SPE_022 | 1/a/1006:1011 | GNRA | homologous HL_4LFB_022 HL_34789.4 | |
| HL_6SPE_024 | 1/a/1069:1076 | GNRA with extra cWW | geometric HL_7A0S_056 HL_87268.2 | |
| HL_6SPE_025 | 1/a/1083:1090 | T-loop related | homologous HL_4LFB_025 HL_63894.2 | |
| HL_6SPE_034 | 1/a/1128:1134 | No text annotation | homologous HL_4LFB_026 HL_92935.1 | |
| HL_6SPE_027 | 1/a/1159:1165 | GNRA | homologous HL_4LFB_027 HL_34789.4 | |
| HL_6SPE_028 | 1/a/1259:1264 | GNRA | homologous HL_5J7L_027 NA | |
| HL_6SPE_029 | 1/a/1308:1317 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_6SPE_030 | 1/a/1350:1360 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_6SPE_031 | 1/a/1443:1448 | UNCG | homologous HL_5J7L_030 NA | |
| HL_6SPE_032 | 1/a/1509:1514 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6SPE_002 | No text annotation | ||
| HL_6SPE_033 | No text annotation | ||
| HL_6SPE_005 | Mini UNCG | ||
| HL_6SPE_018 | No text annotation | ||
| HL_6SPE_023 | UNCG | ||
| HL_6SPE_026 | No text annotation | ||
| HL_6SPE_035 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6SPE_001 | 1/a/30:32, 1/a/546:547 | Single bulged G | homologous IL_6CZR_113 NA | |
| IL_6SPE_002 | 1/a/44:45, 1/a/390:392 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_6SPE_003 | 1/a/47:52, 1/a/353:355 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_6SPE_004 | 1/a/54:56, 1/a/350:351 | Minor groove platform | homologous IL_4LFB_004 IL_34520.3 | |
| IL_6SPE_005 | 1/a/63:66, 1/a/97:98 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.2 | |
| IL_6SPE_006 | 1/a/67:69, 1/a/94:96 | Isolated non-canonical cWW pair | geometric IL_3RW6_004 IL_01003.3 | |
| IL_6SPE_007 | 1/a/70:75, 1/a/88:93 | No text annotation | geometric IL_5J7L_057 NA | |
| IL_6SPE_008 | 1/a/122:125, 1/a/225:227 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_6SPE_009 | 1/a/126:130, 1/a/221:224 | No text annotation | homologous IL_4LFB_008 IL_60988.2 | |
| IL_6SPE_010 | 1/a/138:140, 1/a/170:172 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_6SPE_011 | 1/a/141:147, 1/a/162:169 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_6SPE_012 | 1/a/197:200, 1/a/207:208 | Minor groove platform | geometric IL_3MXH_005 IL_87975.1 | |
| IL_6SPE_013 | 1/a/236:241, 1/a/271:278 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_6SPE_068 | 1/a/243:246, 1/a/268:269 | No text annotation | homologous IL_6CZR_405 NA | |
| IL_6SPE_015 | 1/a/286:289, 1/a/296:302 | No text annotation | ||
| IL_6SPE_069 | 1/a/361:363, 1/a/386:387 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_6SPE_016 | 1/a/364:371, 1/a/380:385 | No text annotation | ||
| IL_6SPE_017 | 1/a/403:410, 1/a/421:427 | No text annotation | homologous IL_5J7L_020 NA | |
| IL_6SPE_018 | 1/a/434:436, 1/a/486:491 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_6SPE_019 | 1/a/440:444, 1/a/477:482 | tSH-tHW-tWW | geometric IL_5J7L_022 NA | |
| IL_6SPE_020 | 1/a/444:447, 1/a/473:477 | No text annotation | ||
| IL_6SPE_021 | 1/a/498:505, 1/a/534:535 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_11411.1 | |
| IL_6SPE_022 | 1/a/509:515, 1/a/522:530 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_6SPE_023 | 1/a/563:569, 1/a/874:875 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_6SPE_024 | 1/a/574:578, 1/a/751:755 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_6SPE_025 | 1/a/587:590, 1/a/638:640 | No text annotation | geometric IL_6DME_003 IL_75527.2 | |
| IL_6SPE_026 | 1/a/591:592, 1/a/634:637 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_73108.2 | |
| IL_6SPE_027 | 1/a/599:606, 1/a/622:627 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_6SPE_028 | 1/a/648:649, 1/a/745:748 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_74641.2 | |
| IL_6SPE_029 | 1/a/652:653, 1/a/740:742 | Single stack bend | homologous IL_5J7L_032 NA | |
| IL_6SPE_070 | 1/a/656:660, 1/a/734:737 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_6SPE_031 | 1/a/678:682, 1/a/693:700 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_6SPE_032 | 1/a/768:772, 1/a/798:799 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_6SPE_033 | 1/a/773:777, 1/a/793:797 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_6SPE_034 | 1/a/881:888, 1/a/899:904 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_6SPE_071 | 1/a/916:917, 1/a/1387:1389 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_6SPE_036 | 1/a/919:921, 1/a/1384:1385 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_6SPE_037 | 1/a/927:929, 1/a/1374:1378 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_6SPE_072 | 1/a/947:948, 1/a/1220:1222 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_6SPE_039 | 1/a/987:991, 1/a/1038:1039 | Minor groove platform | homologous IL_5J7L_043 NA | |
| IL_6SPE_042 | 1/a/1042:1044, 1/a/1202:1203 | No text annotation | homologous IL_6CZR_152 NA | |
| IL_6SPE_043 | 1/a/1046:1050, 1/a/1198:1200 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_6SPE_044 | 1/a/1051:1052, 1/a/1193:1197 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_6SPE_045 | 1/a/1054:1055, 1/a/1189:1191 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_6SPE_046 | 1/a/1055:1057, 1/a/1187:1189 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.3 | |
| IL_6SPE_047 | 1/a/1118:1122, 1/a/1138:1143 | No text annotation | homologous IL_5J7L_051 NA | |
| IL_6SPE_048 | 1/a/1123:1126, 1/a/1136:1137 | Minor groove platform | homologous IL_5J7L_052 NA | |
| IL_6SPE_049 | 1/a/1240:1247, 1/a/1278:1285 | No text annotation | ||
| IL_6SPE_050 | 1/a/1249:1252, 1/a/1271:1276 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_6SPE_051 | 1/a/1253:1257, 1/a/1266:1270 | Double sheared with non-canonical cWW | homologous IL_5J7L_056 NA | |
| IL_6SPE_052 | 1/a/1297:1302, 1/a/1323:1328 | No text annotation | homologous IL_4LFB_055 IL_57885.2 | |
| IL_6SPE_053 | 1/a/1393:1395, 1/a/1495:1498 | No text annotation | geometric IL_5J7L_058 NA | |
| IL_6SPE_054 | 1/a/1395:1398, 1/a/1491:1495 | No text annotation | geometric IL_4V88_464 NA | |
| IL_6SPE_055 | 1/a/1399:1401, 1/a/1488:1490 | Isolated non-canonical cWW pair | geometric IL_5MWI_002 IL_01003.3 | |
| IL_6SPE_056 | 1/a/1401:1403, 1/a/1485:1488 | Decoding loop related | geometric IL_2ET8_003 IL_55553.2 | |
| IL_6SPE_057 | 1/a/1406:1408, 1/a/1480:1482 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_6SPE_058 | 1/a/1410:1413, 1/a/1475:1478 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_6SPE_059 | 1/a/1424:1429, 1/a/1460:1464 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_6SPE_060 | 1/a/1434:1436, 1/a/1454:1455 | Single bulged A | homologous IL_5J7L_064 NA | |
| IL_6SPE_061 | 1/a/1439:1442, 1/a/1449:1451 | No text annotation | homologous IL_5J7L_065 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6SPE_062 | Tandem non-canonical cWW pairs | ||
| IL_6SPE_014 | No text annotation | ||
| IL_6SPE_030 | No text annotation | ||
| IL_6SPE_063 | No text annotation | ||
| IL_6SPE_035 | Isolated non-canonical cWW with bulges | ||
| IL_6SPE_064 | No text annotation | ||
| IL_6SPE_038 | Isolated non-canonical cWW pair | ||
| IL_6SPE_040 | Single stack bend | ||
| IL_6SPE_041 | No text annotation | ||
| IL_6SPE_065 | No text annotation | ||
| IL_6SPE_066 | No text annotation | ||
| IL_6SPE_067 | Triple sheared with non-canonical cWW |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6SPE_020 | 1/a/46:47, 1/a/355:361, 1/a/387:389 | No text annotation | geometric J3_4LFB_010 J3_58657.1 | |
| J3_6SPE_021 | 1/a/46:52, 1/a/353:361, 1/a/387:389 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_6SPE_002 | 1/a/580:582, 1/a/645:648, 1/a/748:749 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_6SPE_013 | 1/a/580:582, 1/a/645:649, 1/a/745:749 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_6SPE_022 | 1/a/666:671, 1/a/707:719, 1/a/726:728 | No text annotation | ||
| J3_6SPE_003 | 1/a/820:823, 1/a/851:855, 1/a/862:868 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_6SPE_015 | 1/a/930:933, 1/a/1338:1344, 1/a/1366:1373 | No text annotation | homologous J3_5J7L_052 NA | |
| J3_6SPE_016 | 1/a/937:940, 1/a/1229:1231, 1/a/1331:1334 | No text annotation | homologous J3_4LFB_003 J3_44359.1 | |
| J3_6SPE_023 | 1/a/949:956, 1/a/967:978, 1/a/1215:1219 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_6SPE_006 | 1/a/984:987, 1/a/1039:1041, 1/a/1204:1209 | No text annotation | homologous J3_5J7L_007 NA | |
| J3_6SPE_018 | 1/a/984:991, 1/a/1038:1041, 1/a/1204:1209 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_6SPE_008 | 1/a/1057:1062, 1/a/1101:1107, 1/a/1181:1187 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_6SPE_024 | 1/a/1067:1068, 1/a/1077:1080, 1/a/1093:1096 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_6SPE_010 | 1/a/1110:1112, 1/a/1149:1155, 1/a/1169:1178 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_6SPE_011 | 1/a/1231:1235, 1/a/1290:1297, 1/a/1328:1331 | No text annotation | homologous J3_5J7L_011 NA | |
| J4_6SPE_001 | 1/a/109:116, 1/a/233:234, 1/a/280:283, 1/a/305:306 | No text annotation | homologous J4_6CZR_027 NA | |
| J4_6SPE_004 | 1/a/137:138, 1/a/172:178, 1/a/187:192, 1/a/213:214 | No text annotation | ||
| J4_6SPE_003 | 1/a/569:571, 1/a/758:763, 1/a/804:815, 1/a/873:874 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_6SPE_003 | 1/a/36:39, 1/a/397:400, 1/a/430:434, 1/a/491:494, 1/a/539:542 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_6SPE_004 | 1/a/58:61, 1/a/100:107, 1/a/308:310, 1/a/331:333, 1/a/344:348 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6SPE_001 | No text annotation | ||
| J3_6SPE_012 | No text annotation | ||
| J3_6SPE_014 | No text annotation | ||
| J3_6SPE_004 | No text annotation | ||
| J3_6SPE_005 | No text annotation | ||
| J3_6SPE_017 | No text annotation | ||
| J3_6SPE_007 | No text annotation | ||
| J3_6SPE_019 | No text annotation | ||
| J3_6SPE_009 | No text annotation | ||
| J4_6SPE_002 | No text annotation | ||
| J5_6SPE_001 | No text annotation | ||
| J5_6SPE_002 | No text annotation |
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