7OID Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7OID_001 | 1/A/52:59 | No text annotation | geometric HL_5J7L_139 NA | |
| HL_7OID_002 | 1/A/76:82 | No text annotation | geometric HL_5J7L_141 NA | |
| HL_7OID_003 | 1/A/116:121 | GNRA | homologous HL_4WF9_015 HL_34789.4 | |
| HL_7OID_004 | 1/A/161:169 | No text annotation | homologous HL_7RQB_017 NA | |
| HL_7OID_005 | 1/A/177:186 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_7OID_006 | 1/A/214:219 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_7OID_008 | 1/A/284:293 | No text annotation | homologous HL_7RQB_023 NA | |
| HL_7OID_009 | 1/A/318:326 | No text annotation | geometric HL_5TBW_021 NA | |
| HL_7OID_010 | 1/A/365:370 | No text annotation | homologous HL_7RQB_025 NA | |
| HL_7OID_012 | 1/A/437:444 | GNRA | homologous HL_4WF9_027 HL_34789.4 | |
| HL_7OID_013 | 1/A/459:466 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_7OID_016 | 1/A/609:616 | No text annotation | geometric HL_2Y9H_005 HL_44506.2 | |
| HL_7OID_017 | 1/A/649:654 | No text annotation | geometric HL_5U3G_001 HL_75660.8 | |
| HL_7OID_019 | 1/A/730:733 | Mini UNCG | geometric HL_5F9R_002 NA | |
| HL_7OID_020 | 1/A/758:765 | No text annotation | homologous HL_7RQB_040 NA | |
| HL_7OID_021 | 1/A/827:837 | No text annotation | homologous HL_7RQB_045 NA | |
| HL_7OID_022 | 1/A/848:862 | No text annotation | ||
| HL_7OID_025 | 1/A/942:950 | No text annotation | geometric HL_5TBW_050 NA | |
| HL_7OID_026 | 1/A/1020:1029 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_7OID_028 | 1/A/1142:1150 | No text annotation | homologous HL_7A0S_052 HL_11974.2 | |
| HL_7OID_029 | 1/A/1158:1170 | No text annotation | ||
| HL_7OID_030 | 1/A/1192:1200 | No text annotation | geometric HL_2ZZM_002 HL_33487.1 | |
| HL_7OID_032 | 1/A/1288:1296 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_7OID_033 | 1/A/1345:1352 | No text annotation | homologous HL_7RQB_061 NA | |
| HL_7OID_034 | 1/A/1368:1374 | No text annotation | homologous HL_4WF9_058 HL_48677.1 | |
| HL_7OID_035 | 1/A/1411:1416 | GNRA | homologous HL_7RQB_063 NA | |
| HL_7OID_037 | 1/A/1484:1489 | No text annotation | geometric HL_4WSB_001 HL_19413.2 | |
| HL_7OID_038 | 1/A/1506:1523 | No text annotation | geometric HL_7A0S_074 NA | |
| HL_7OID_039 | 1/A/1546:1554 | No text annotation | geometric HL_7RQB_068 NA | |
| HL_7OID_041 | 1/B/1630:1638 | tRNA anticodon loop | geometric HL_4TUE_034 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7OID_007 | Mini UNCG | ||
| HL_7OID_011 | No text annotation | ||
| HL_7OID_014 | No text annotation | ||
| HL_7OID_015 | GNRA wlth tandem sheared | ||
| HL_7OID_018 | No text annotation | ||
| HL_7OID_023 | No text annotation | ||
| HL_7OID_044 | No text annotation | ||
| HL_7OID_024 | No text annotation | ||
| HL_7OID_027 | No text annotation | ||
| HL_7OID_031 | No text annotation | ||
| HL_7OID_036 | GNRA | ||
| HL_7OID_040 | tRNA D-loop | ||
| HL_7OID_042 | No text annotation | ||
| HL_7OID_043 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7OID_001 | 1/A/2:8, 1/A/127:146 | No text annotation | ||
| IL_7OID_002 | 1/A/12:13, 1/A/98:100 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_7OID_003 | 1/A/69:75, 1/A/83:88 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_4V9F_106 IL_02666.1 | |
| IL_7OID_004 | 1/A/175:177, 1/A/186:188 | Isolated non-canonical cWW pair | homologous IL_5J7L_257 NA | |
| IL_7OID_005 | 1/A/207:209, 1/A/225:227 | Isolated non-canonical cWW pair | geometric IL_3GM7_002 IL_01003.4 | |
| IL_7OID_006 | 1/A/210:213, 1/A/220:224 | No text annotation | ||
| IL_7OID_007 | 1/A/234:236, 1/A/346:348 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_01003.4 | |
| IL_7OID_008 | 1/A/236:240, 1/A/339:346 | tHW-tHW cross-strand stack | homologous IL_7RQB_018 NA | |
| IL_7OID_009 | 1/A/243:245, 1/A/334:336 | Isolated non-canonical cWW pair | geometric IL_5TBW_079 NA | |
| IL_7OID_010 | 1/A/255:257, 1/A/307:309 | Isolated non-canonical cWW pair | geometric IL_5TBW_008 NA | |
| IL_7OID_011 | 1/A/259:260, 1/A/303:305 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_7OID_012 | 1/A/278:281, 1/A/296:298 | Major groove platform with extra cWW | homologous IL_7A0S_019 IL_36931.2 | |
| IL_7OID_013 | 1/A/315:317, 1/A/327:331 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_7OID_014 | 1/A/376:378, 1/A/421:424 | No text annotation | geometric IL_9M86_006 IL_32983.2 | |
| IL_7OID_015 | 1/A/387:393, 1/A/406:412 | No text annotation | ||
| IL_7OID_016 | 1/A/475:477, 1/A/584:585 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_7OID_017 | 1/A/479:483, 1/A/578:582 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_7OID_021 | 1/A/636:643, 1/A/1004:1010 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_7OID_022 | 1/A/659:663, 1/A/771:778 | No text annotation | ||
| IL_7OID_023 | 1/A/707:711, 1/A/741:749 | No text annotation | ||
| IL_7OID_056 | 1/A/714:730, 1/A/733:738 | No text annotation | ||
| IL_7OID_024 | 1/A/786:791, 1/A/996:998 | No text annotation | ||
| IL_7OID_025 | 1/A/797:799, 1/A/988:990 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_7OID_026 | 1/A/800:803, 1/A/986:987 | Major groove platform; stack outside cWW | homologous IL_7RQB_066 NA | |
| IL_7OID_057 | 1/A/800:808, 1/A/983:987 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_7OID_027 | 1/A/803:808, 1/A/983:986 | Intercalated tWH | geometric IL_4WF9_065 IL_28217.1 | |
| IL_7OID_028 | 1/A/808:817, 1/A/978:983 | No text annotation | ||
| IL_7OID_029 | 1/A/820:821, 1/A/973:975 | Single bulged A | homologous IL_5J7L_312 NA | |
| IL_7OID_030 | 1/A/878:881, 1/A/896:897 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_7OID_031 | 1/A/882:883, 1/A/892:895 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_7OID_034 | 1/A/1042:1045, 1/A/1434:1436 | No text annotation | geometric IL_6DME_003 IL_75527.2 | |
| IL_7OID_035 | 1/A/1047:1049, 1/A/1429:1432 | Major groove platform with intercalation | geometric IL_5TBW_092 NA | |
| IL_7OID_036 | 1/A/1060:1062, 1/A/1259:1260 | Single bulged U | homologous IL_7RQB_080 NA | |
| IL_7OID_037 | 1/A/1063:1064, 1/A/1255:1258 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_7OID_058 | 1/A/1074:1076, 1/A/1132:1133 | Minor groove platform | geometric IL_7A0S_003 IL_34520.3 | |
| IL_7OID_040 | 1/A/1186:1190, 1/A/1202:1206 | Double sheared with non-canonical cWW | geometric IL_5J7L_274 NA | |
| IL_7OID_041 | 1/A/1270:1271, 1/A/1315:1317 | Single stack bend | geometric IL_4WF9_089 IL_15011.3 | |
| IL_7OID_042 | 1/A/1271:1272, 1/A/1313:1315 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_7OID_043 | 1/A/1273:1276, 1/A/1310:1312 | Major groove platform with extra pair | homologous IL_7RQB_093 NA | |
| IL_7OID_044 | 1/A/1276:1278, 1/A/1306:1310 | Major groove minor groove platform with extra cWW | geometric IL_5J7L_337 NA | |
| IL_7OID_045 | 1/A/1283:1287, 1/A/1297:1301 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_7OID_046 | 1/A/1324:1325, 1/A/1397:1399 | Major groove platform | homologous IL_7RQB_096 NA | |
| IL_7OID_047 | 1/A/1327:1329, 1/A/1391:1395 | Isolated non-canonical cWW with bulges | geometric IL_7RQB_097 NA | |
| IL_7OID_048 | 1/A/1329:1330, 1/A/1388:1391 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_7OID_049 | 1/A/1338:1340, 1/A/1357:1361 | No text annotation | ||
| IL_7OID_050 | 1/A/1408:1409, 1/A/1418:1420 | Single bulged A | homologous IL_5J7L_344 NA | |
| IL_7OID_051 | 1/A/1445:1447, 1/A/1469:1471 | Isolated non-canonical cWW pair | geometric IL_4JGN_003 IL_01003.4 | |
| IL_7OID_053 | 1/A/1478:1482, 1/A/1491:1493 | C-loop | geometric IL_7RQB_104 NA | |
| IL_7OID_054 | 1/B/1627:1629, 1/B/1639:1641 | No text annotation | geometric IL_4KR9_001 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7OID_018 | Isolated near basepair | ||
| IL_7OID_019 | No text annotation | ||
| IL_7OID_020 | No text annotation | ||
| IL_7OID_032 | Multiple bulged bases | ||
| IL_7OID_033 | No text annotation | ||
| IL_7OID_038 | No text annotation | ||
| IL_7OID_039 | No text annotation | ||
| IL_7OID_052 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_7OID_055 | No text annotation | ||
| IL_7OID_059 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7OID_001 | 1/A/8:11, 1/A/101:115, 1/A/122:127 | No text annotation | ||
| J3_7OID_002 | 1/A/245:251, 1/A/313:315, 1/A/331:334 | No text annotation | homologous J3_7A0S_004 J3_46658.1 | |
| J3_7OID_003 | 1/A/260:262, 1/A/272:276, 1/A/300:303 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_7OID_004 | 1/A/666:673, 1/A/753:757, 1/A/766:768 | No text annotation | ||
| J3_7OID_005 | 1/A/673:675, 1/A/698:705, 1/A/751:753 | No text annotation | ||
| J3_7OID_007 | 1/A/1176:1178, 1/A/1220:1230, 1/A/1239:1245 | No text annotation | ||
| J3_7OID_006 | 1/A/1334:1337, 1/A/1362:1364, 1/A/1378:1384 | No text annotation | homologous J3_7RQB_012 NA | |
| J4_7OID_001 | 1/A/644:647, 1/A/656:657, 1/A/780:783, 1/A/1001:1003 | No text annotation | ||
| J4_7OID_002 | 1/A/666:675, 1/A/698:705, 1/A/751:757, 1/A/766:768 | No text annotation | ||
| J4_7OID_003 | 1/A/822:826, 1/A/838:843, 1/A/867:872, 1/A/967:972 | No text annotation | ||
| J4_7OID_004 | 1/A/874:876, 1/A/899:900, 1/A/917:926, 1/A/960:965 | No text annotation | homologous J4_5J7L_026 NA | |
| J5_7OID_001 | 1/A/157:159, 1/A/171:175, 1/A/188:190, 1/A/635:636, 1/A/1010:1011 | No text annotation | homologous J5_7A0S_003 J5_43153.6 | |
| J5_7OID_002 | 1/A/195:205, 1/A/229:233, 1/A/349:352, 1/A/601:605, 1/A/620:630 | No text annotation | ||
| J5_7OID_003 | 1/A/1050:1057, 1/A/1263:1270, 1/A/1317:1324, 1/A/1399:1405, 1/A/1423:1428 | No text annotation | ||
| J5_7OID_004 | 1/A/1067:1070, 1/A/1137:1140, 1/A/1152:1153, 1/A/1175:1176, 1/A/1245:1252 | No text annotation | homologous J5_7A0S_007 J5_39529.2 | |
| J6_7OID_001 | 1/A/357:362, 1/A/373:375, 1/A/425:428, 1/A/453:457, 1/A/468:473, 1/A/587:596 | No text annotation | ||
| J6_7OID_002 | 1/A/1067:1070, 1/A/1137:1140, 1/A/1152:1153, 1/A/1175:1178, 1/A/1220:1230, 1/A/1239:1252 | No text annotation |
Problematic loops
No problematic loops
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