4LF5 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_4LF5_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_89881.5 | |
| HL_4LF5_034 | 1/A/80:89 | No text annotation | homologous HL_4LFB_002 HL_31585.3 | |
| HL_4LF5_003 | 1/A/158:163 | GNRA | homologous HL_4LFB_003 HL_37824.7 | |
| HL_4LF5_004 | 1/A/190B:190G | No text annotation | homologous HL_4LFB_004 HL_48417.5 | |
| HL_4LF5_005 | 1/A/201:216 | Mini UNCG | homologous HL_6CZR_234 NA | |
| HL_4LF5_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_84299.4 | |
| HL_4LF5_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_37824.7 | |
| HL_4LF5_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_81205.3 | |
| HL_4LF5_009 | 1/A/342:347 | UNCG | homologous HL_4LFB_009 HL_34617.5 | |
| HL_4LF5_010 | 1/A/379:384 | GNRA | homologous HL_4LFB_010 HL_37824.7 | |
| HL_4LF5_011 | 1/A/419:424 | UNCG | homologous HL_4LFB_011 HL_34617.5 | |
| HL_4LF5_012 | 1/A/458:474 | GNRA | homologous HL_4LFB_012 HL_37824.7 | |
| HL_4LF5_033 | 1/A/522:527 | GNRA variation | homologous HL_4LFB_033 HL_37824.7 | |
| HL_4LF5_014 | 1/A/617:623 | No text annotation | homologous HL_4LFB_014 HL_10453.3 | |
| HL_4LF5_015 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_75293.5 | |
| HL_4LF5_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_37824.7 | |
| HL_4LF5_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_75293.5 | |
| HL_4LF5_018 | 1/A/838:848 | Mini UNCG | homologous HL_4LFB_018 HL_48778.2 | |
| HL_4LF5_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_37824.7 | |
| HL_4LF5_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.7 | |
| HL_4LF5_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_50779.4 | |
| HL_4LF5_022 | 1/A/1012:1017 | GNRA | homologous HL_4LFB_022 HL_37824.7 | |
| HL_4LF5_023 | 1/A/1030:1031 | No text annotation | homologous HL_4LFB_023 NA | |
| HL_4LF5_024 | 1/A/1076:1081 | GNRA | homologous HL_4LFB_024 HL_37824.7 | |
| HL_4LF5_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_77436.5 | |
| HL_4LF5_026 | 1/A/1134:1140 | No text annotation | homologous HL_4LFB_026 HL_87954.2 | |
| HL_4LF5_027 | 1/A/1165:1171 | GNRA | homologous HL_4LFB_027 HL_37824.7 | |
| HL_4LF5_028 | 1/A/1265:1270 | GNRA | homologous HL_4LFB_028 HL_37824.7 | |
| HL_4LF5_029 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_02887.3 | |
| HL_4LF5_030 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_06226.4 | |
| HL_4LF5_031 | 1/A/1449:1454 | UNCG | homologous HL_4LFB_031 HL_34617.5 | |
| HL_4LF5_032 | 1/A/1515:1520 | GNRA | geometric HL_6CU1_002 HL_37824.7 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_4LF5_002 | No text annotation | ||
| HL_4LF5_013 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_4LF5_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_4LFB_001 IL_00225.13 | |
| IL_4LF5_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_4LFB_002 IL_31462.5 | |
| IL_4LF5_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_4LFB_003 IL_14177.2 | |
| IL_4LF5_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_51454.2 | |
| IL_4LF5_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_82107.4 | |
| IL_4LF5_006 | 1/A/67:69, 1/A/99:102 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_87907.2 | |
| IL_4LF5_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_4LFB_007 IL_33761.2 | |
| IL_4LF5_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_64231.5 | |
| IL_4LF5_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_12745.1 | |
| IL_4LF5_010 | 1/A/186:188, 1/A/190K:191 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_87907.2 | |
| IL_4LF5_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.3 | |
| IL_4LF5_012 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_47074.2 | |
| IL_4LF5_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_03109.3 | |
| IL_4LF5_014 | 1/A/367:369, 1/A/392:393 | Single bulged U | homologous IL_4LFB_014 IL_89505.4 | |
| IL_4LF5_015 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_4LFB_015 IL_03109.3 | |
| IL_4LF5_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_4LFB_016 IL_00225.13 | |
| IL_4LF5_017 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_4LFB_017 IL_28026.3 | |
| IL_4LF5_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_88269.4 | |
| IL_4LF5_019 | 1/A/450:455, 1/A/477:483 | No text annotation | homologous IL_4LFB_019 IL_31561.1 | |
| IL_4LF5_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_41203.4 | |
| IL_4LF5_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_4LF5_022 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_5J7L_026 IL_38186.6 | |
| IL_4LF5_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_17136.7 | |
| IL_4LF5_024 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.6 | |
| IL_4LF5_025 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 IL_68140.4 | |
| IL_4LF5_026 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_78349.3 | |
| IL_4LF5_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_50694.7 | |
| IL_4LF5_028 | 1/A/657:658, 1/A/747:749 | Major groove platform | homologous IL_4LFB_028 IL_48076.6 | |
| IL_4LF5_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_85033.2 | |
| IL_4LF5_062 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_49751.4 | |
| IL_4LF5_031 | 1/A/683:688, 1/A/699:707 | Kink-turn | homologous IL_4LFB_031 IL_95727.1 | |
| IL_4LF5_032 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.2 | |
| IL_4LF5_033 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_17136.7 | |
| IL_4LF5_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_41756.4 | |
| IL_4LF5_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_4LFB_035 IL_31462.5 | |
| IL_4LF5_036 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_00225.13 | |
| IL_4LF5_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 IL_47078.3 | |
| IL_4LF5_039 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_51454.2 | |
| IL_4LF5_068 | 1/A/993:998, 1/A/1043:1045 | No text annotation | ||
| IL_4LF5_041 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_5J7L_046 IL_89505.4 | |
| IL_4LF5_043 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | geometric IL_4LFB_044 IL_76319.5 | |
| IL_4LF5_044 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_95583.2 | |
| IL_4LF5_045 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_89505.4 | |
| IL_4LF5_046 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_28037.2 | |
| IL_4LF5_069 | 1/A/1124:1132, 1/A/1142:1149 | No text annotation | ||
| IL_4LF5_048 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation | homologous IL_4LFB_050 IL_42032.1 | |
| IL_4LF5_049 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_09129.2 | |
| IL_4LF5_050 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_6CZR_161 NA | |
| IL_4LF5_051 | 1/A/1259:1260, 1/A/1274:1276 | Not an internal loop | geometric IL_4LFB_053 NA | |
| IL_4LF5_063 | 1/A/1259:1262, 1/A/1273:1276 | Double sheared | homologous IL_4LFB_067 IL_09705.15 | |
| IL_4LF5_052 | 1/A/1260:1262, 1/A/1273:1274 | Minor groove platform | homologous IL_4LFB_054 IL_51454.2 | |
| IL_4LF5_064 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation | homologous IL_4LFB_055 IL_85536.2 | |
| IL_4LF5_054 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | geometric IL_4V88_463 NA | |
| IL_4LF5_065 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | homologous IL_4LFB_068 IL_65718.4 | |
| IL_4LF5_066 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | homologous IL_5J7L_363 IL_87907.2 | |
| IL_4LF5_067 | 1/A/1407:1415, 1/A/1485:1494 | No text annotation | ||
| IL_4LF5_057 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | homologous IL_4LFB_060 IL_09705.15 | |
| IL_4LF5_058 | 1/A/1431:1435, 1/A/1466:1469 | UAA/GAN variation | geometric IL_4LFB_062 IL_77691.5 | |
| IL_4LF5_059 | 1/A/1435:1437, 1/A/1464:1466 | Isolated non-canonical cWW pair | homologous IL_4LFB_063 IL_87907.2 | |
| IL_4LF5_060 | 1/A/1440:1447, 1/A/1459:1461 | No text annotation | homologous IL_4LFB_064 IL_49061.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_4LF5_061 | Isolated non-canonical cWW pair | ||
| IL_4LF5_030 | No text annotation | ||
| IL_4LF5_038 | Isolated non-canonical cWW pair | ||
| IL_4LF5_040 | No text annotation | ||
| IL_4LF5_042 | Isolated non-canonical cWW pair | ||
| IL_4LF5_047 | No text annotation | ||
| IL_4LF5_053 | No text annotation | ||
| IL_4LF5_055 | No text annotation | ||
| IL_4LF5_056 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_4LF5_010 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | geometric J3_4LFB_010 J3_67856.4 | |
| J3_4LF5_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_46317.4 | |
| J3_4LF5_011 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_6CZR_016 NA | |
| J3_4LF5_015 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.4 | |
| J3_4LF5_012 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_4LFB_012 J3_11934.4 | |
| J3_4LF5_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_4LFB_001 J3_85054.4 | |
| J3_4LF5_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_25303.4 | |
| J3_4LF5_003 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_4LFB_003 J3_52655.4 | |
| J3_4LF5_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_83516.4 | |
| J3_4LF5_005 | 1/A/990:993, 1/A/1045:1047, 1/A/1210:1215 | No text annotation | geometric J3_4LFB_005 J3_82572.1 | |
| J3_4LF5_021 | 1/A/990:998, 1/A/1043:1047, 1/A/1210:1215 | No text annotation | ||
| J3_4LF5_022 | 1/A/1002:1006, 1/A/1023:1028, 1/A/1033:1039 | No text annotation | ||
| J3_4LF5_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_08394.3 | |
| J3_4LF5_019 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_79369.1 | |
| J3_4LF5_008 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | homologous J3_4LFB_008 J3_82365.4 | |
| J3_4LF5_020 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 J3_17791.2 | |
| J3_4LF5_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_37047.6 | |
| J4_4LF5_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 J4_35578.3 | |
| J4_4LF5_002 | 1/A/142:144, 1/A/178:183, 1/A/194:198, 1/A/219:221 | No text annotation | homologous J4_4LFB_002 J4_88771.1 | |
| J4_4LF5_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_4LFB_003 J4_61885.6 | |
| J5_4LF5_001 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_4LF5_002 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation | homologous J5_4LFB_002 J5_59910.6 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_4LF5_016 | No text annotation | ||
| J3_4LF5_017 | No text annotation | ||
| J3_4LF5_018 | No text annotation | ||
| J3_4LF5_006 | No text annotation |
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