9H9H Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H9H_002 | 1/3/31:39 | tRNA anticodon loop | geometric HL_4V90_033 NA | |
| HL_9H9H_004 | 1/A/12:22 | No text annotation | geometric HL_4LFB_001 HL_31940.1 | |
| HL_9H9H_006 | 1/A/158:163 | GNRA | geometric HL_8CRE_215 HL_34789.1 | |
| HL_9H9H_007 | 1/A/186:191 | GNRA | geometric HL_2R8S_001 HL_34789.1 | |
| HL_9H9H_008 | 1/A/207:212 | No text annotation | ||
| HL_9H9H_009 | 1/A/259:267 | GNRA related | geometric HL_5J7L_006 NA | |
| HL_9H9H_010 | 1/A/296:301 | GNRA | geometric HL_5J7L_007 NA | |
| HL_9H9H_011 | 1/A/320:333 | No text annotation | geometric HL_5J7L_008 NA | |
| HL_9H9H_012 | 1/A/342:347 | UNCG | geometric HL_9DFE_040 HL_61337.1 | |
| HL_9H9H_013 | 1/A/379:384 | GNRA | geometric HL_5F9F_003 HL_34789.1 | |
| HL_9H9H_014 | 1/A/419:424 | UNCG | geometric HL_5J7L_030 NA | |
| HL_9H9H_015 | 1/A/462:470 | GNRA wlth extra near cWW | geometric HL_5J7L_012 NA | |
| HL_9H9H_016 | 1/A/522:527 | GNRA variation | geometric HL_4LFB_033 HL_34789.1 | |
| HL_9H9H_017 | 1/A/617:623 | GNRA-like with tWH | geometric HL_4LFB_014 HL_92337.1 | |
| HL_9H9H_018 | 1/A/689:698 | No text annotation | geometric HL_4LFB_015 HL_38491.1 | |
| HL_9H9H_019 | 1/A/726:731 | GNRA | geometric HL_8CRE_211 HL_34789.1 | |
| HL_9H9H_020 | 1/A/786:796 | No text annotation | geometric HL_5J7L_017 NA | |
| HL_9H9H_022 | 1/A/862:867 | GNRA | geometric HL_4LFB_019 HL_34789.1 | |
| HL_9H9H_023 | 1/A/897:902 | GNRA | geometric HL_8CRE_215 HL_34789.1 | |
| HL_9H9H_024 | 1/A/963:972 | No text annotation | geometric HL_4LFB_021 HL_97521.1 | |
| HL_9H9H_027 | 1/A/1076:1081 | GNRA | geometric HL_8P9A_147 HL_34789.1 | |
| HL_9H9H_028 | 1/A/1089:1096 | T-loop related | geometric HL_4LFB_025 HL_63894.1 | |
| HL_9H9H_031 | 1/A/1265:1270 | GNRA | geometric HL_4V9F_033 HL_34789.1 | |
| HL_9H9H_032 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | geometric HL_4LFB_029 HL_93658.1 | |
| HL_9H9H_033 | 1/A/1356:1366 | No text annotation | geometric HL_5J7L_029 NA | |
| HL_9H9H_034 | 1/A/1449:1454 | UNCG | geometric HL_8P9A_200 HL_61337.1 | |
| HL_9H9H_035 | 1/A/1515:1520 | GNRA | geometric HL_5J7L_031 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H9H_001 | tRNA D-loop | ||
| HL_9H9H_003 | No text annotation | ||
| HL_9H9H_005 | No text annotation | ||
| HL_9H9H_021 | No text annotation | ||
| HL_9H9H_025 | GNRA | ||
| HL_9H9H_026 | UNCG | ||
| HL_9H9H_029 | No text annotation | ||
| HL_9H9H_030 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H9H_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | geometric IL_5J7L_001 NA | |
| IL_9H9H_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | geometric IL_5J7L_002 NA | |
| IL_9H9H_003 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_9H9H_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | geometric IL_8P9A_377 IL_34520.1 | |
| IL_9H9H_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | geometric IL_5J7L_005 NA | |
| IL_9H9H_006 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW | geometric IL_5J7L_006 NA | |
| IL_9H9H_007 | 1/A/70:73, 1/A/97:98 | Minor groove platform | geometric IL_5J7L_007 NA | |
| IL_9H9H_009 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW pair | geometric IL_5J7L_009 NA | |
| IL_9H9H_010 | 1/A/132:136, 1/A/227:230 | No text annotation | geometric IL_4LFB_008 IL_60988.1 | |
| IL_9H9H_011 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair | geometric IL_4WF9_045 IL_10892.1 | |
| IL_9H9H_012 | 1/A/147:153, 1/A/168:175 | tWH-tWH-tHW-tHW | geometric IL_5J7L_012 NA | |
| IL_9H9H_014 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | geometric IL_5J7L_014 NA | |
| IL_9H9H_015 | 1/A/249:252, 1/A/274:275 | No text annotation | geometric IL_4LFB_012 IL_22002.1 | |
| IL_9H9H_016 | 1/A/292:293, 1/A/304:308 | C-loop | geometric IL_4LFB_013 IL_06671.1 | |
| IL_9H9H_017 | 1/A/367:369, 1/A/392:393 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_9H9H_018 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_5J7L_018 NA | |
| IL_9H9H_019 | 1/A/375:376, 1/A/387:389 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_9H9H_020 | 1/A/409:416, 1/A/427:433 | No text annotation | geometric IL_5J7L_020 NA | |
| IL_9H9H_021 | 1/A/440:442, 1/A/492:497 | No text annotation | geometric IL_5J7L_021 NA | |
| IL_9H9H_022 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW | geometric IL_5J7L_022 NA | |
| IL_9H9H_023 | 1/A/450:455, 1/A/477:483 | No text annotation | geometric IL_5J7L_023 NA | |
| IL_9H9H_024 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | geometric IL_4LFB_020 IL_11411.1 | |
| IL_9H9H_025 | 1/A/515:521, 1/A/528:536 | No text annotation | geometric IL_8P9A_404 IL_52042.1 | |
| IL_9H9H_026 | 1/A/569:575, 1/A/880:881 | No text annotation | geometric IL_4LFB_022 IL_20847.1 | |
| IL_9H9H_027 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | geometric IL_5J7L_027 NA | |
| IL_9H9H_028 | 1/A/594:596, 1/A/644:645 | Major groove platform | geometric IL_3NKB_002 NA | |
| IL_9H9H_029 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | geometric IL_5J7L_029 NA | |
| IL_9H9H_030 | 1/A/605:612, 1/A/628:633 | No text annotation | geometric IL_5J7L_030 NA | |
| IL_9H9H_031 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | geometric IL_4LFB_027 IL_74641.1 | |
| IL_9H9H_032 | 1/A/659:660, 1/A/745:747 | Single stack bend | geometric IL_8CRE_091 NA | |
| IL_9H9H_033 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | geometric IL_5J7L_033 NA | |
| IL_9H9H_034 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | geometric IL_4LFB_065 IL_71154.1 | |
| IL_9H9H_035 | 1/A/684:688, 1/A/699:706 | Kink-turn | geometric IL_5J7L_035 NA | |
| IL_9H9H_036 | 1/A/774:778, 1/A/804:805 | Left turn | geometric IL_4LFB_032 IL_29346.3 | |
| IL_9H9H_037 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | geometric IL_8CRE_438 IL_05821.1 | |
| IL_9H9H_038 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_5J7L_038 NA | |
| IL_9H9H_039 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | geometric IL_8CRE_443 IL_14190.1 | |
| IL_9H9H_040 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | geometric IL_5J7L_040 NA | |
| IL_9H9H_041 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | geometric IL_4LFB_037 IL_61370.1 | |
| IL_9H9H_042 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | geometric IL_4LFB_038 IL_34520.1 | |
| IL_9H9H_043 | 1/A/993:997, 1/A/1044:1045 | Minor groove platform | geometric IL_5J7L_043 NA | |
| IL_9H9H_044 | 1/A/998:999, 1/A/1041:1043 | Single stack bend | geometric IL_7KGA_003 NA | |
| IL_9H9H_045 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | geometric IL_5J7L_046 NA | |
| IL_9H9H_046 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | geometric IL_4LFB_044 IL_82453.1 | |
| IL_9H9H_047 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | geometric IL_5J7L_048 NA | |
| IL_9H9H_048 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_9H9H_049 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_9H9H_050 | 1/A/1124:1128, 1/A/1144:1149 | No text annotation | geometric IL_5J7L_051 NA | |
| IL_9H9H_051 | 1/A/1129:1132, 1/A/1142:1143 | Minor groove platform | geometric IL_5J7L_052 NA | |
| IL_9H9H_052 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation | geometric IL_5J7L_053 NA | |
| IL_9H9H_053 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | geometric IL_5J7L_054 NA | |
| IL_9H9H_054 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | geometric IL_5J7L_055 NA | |
| IL_9H9H_055 | 1/A/1259:1263, 1/A/1272:1276 | Double sheared with non-canonical cWW | geometric IL_5J7L_056 NA | |
| IL_9H9H_056 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation | geometric IL_5J7L_057 NA | |
| IL_9H9H_057 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | geometric IL_8CRE_466 IL_18228.1 | |
| IL_9H9H_058 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4LFB_068 IL_25873.1 | |
| IL_9H9H_059 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | geometric IL_1UN6_005 IL_01003.1 | |
| IL_9H9H_060 | 1/A/1407:1409, 1/A/1491:1494 | No text annotation | geometric IL_8UO6_002 NA | |
| IL_9H9H_061 | 1/A/1412:1416, 1/A/1484:1488 | No text annotation | ||
| IL_9H9H_062 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | geometric IL_6YML_002 IL_58355.1 | |
| IL_9H9H_063 | 1/A/1430:1435, 1/A/1466:1470 | Triple sheared related | geometric IL_5J7L_063 NA | |
| IL_9H9H_064 | 1/A/1440:1442, 1/A/1460:1461 | No text annotation | ||
| IL_9H9H_065 | 1/A/1445:1448, 1/A/1455:1457 | No text annotation | geometric IL_5J7L_065 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H9H_008 | Single bulged G | ||
| IL_9H9H_013 | Minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H9H_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | geometric J3_4LFB_010 J3_58657.1 | |
| J3_9H9H_002 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | geometric J3_5J7L_050 NA | |
| J3_9H9H_003 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_4LFB_011 J3_01633.1 | |
| J3_9H9H_004 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | geometric J3_4LFB_015 J3_17385.5 | |
| J3_9H9H_005 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | geometric J3_5J7L_003 NA | |
| J3_9H9H_006 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | geometric J3_5J7L_004 NA | |
| J3_9H9H_007 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | geometric J3_5J7L_052 NA | |
| J3_9H9H_008 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | geometric J3_4LFB_003 J3_44359.1 | |
| J3_9H9H_009 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | geometric J3_5J7L_006 NA | |
| J3_9H9H_010 | 1/A/990:993, 1/A/1045:1047, 1/A/1210:1215 | No text annotation | geometric J3_4LFB_005 J3_84394.1 | |
| J3_9H9H_011 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation | geometric J3_5J7L_053 NA | |
| J3_9H9H_013 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | geometric J3_4LFB_007 J3_01343.1 | |
| J3_9H9H_014 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | geometric J3_4LFB_017 J3_11018.1 | |
| J3_9H9H_015 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | geometric J3_5J7L_010 NA | |
| J3_9H9H_016 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | geometric J3_5J7L_054 NA | |
| J3_9H9H_017 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | geometric J3_4LFB_009 J3_03192.1 | |
| J4_9H9H_001 | 1/3/5:9, 1/3/25:27, 1/3/43:49, 1/3/65:67 | No text annotation | ||
| J4_9H9H_002 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | ||
| J4_9H9H_003 | 1/A/142:144, 1/A/178:184, 1/A/193:198, 1/A/219:221 | No text annotation | ||
| J4_9H9H_004 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | ||
| J5_9H9H_001 | 1/A/36:39, 1/A/403:406, 1/A/436:440, 1/A/497:500, 1/A/545:548 | No text annotation | ||
| J5_9H9H_002 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | ||
| J5_9H9H_003 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9H9H_012 | No text annotation |
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