4B3T Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_4B3T_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_89881.3 | |
| HL_4B3T_002 | 1/A/80:89 | No text annotation | homologous HL_4LFB_002 HL_31585.1 | |
| HL_4B3T_003 | 1/A/158:163 | GNRA | homologous HL_4LFB_003 HL_37824.3 | |
| HL_4B3T_004 | 1/A/189C:189H | No text annotation | homologous HL_4LFB_004 HL_48417.2 | |
| HL_4B3T_005 | 1/A/201:216 | No text annotation | homologous HL_4LFB_005 HL_46878.1 | |
| HL_4B3T_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_84299.1 | |
| HL_4B3T_007 | 1/A/296:301 | GNRA | homologous HL_5J7L_007 HL_37824.3 | |
| HL_4B3T_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_81205.2 | |
| HL_4B3T_009 | 1/A/342:347 | UNCG | homologous HL_4LFB_009 HL_34617.2 | |
| HL_4B3T_010 | 1/A/379:384 | GNRA | homologous HL_4LFB_010 HL_37824.3 | |
| HL_4B3T_011 | 1/A/419:424 | UNCG | homologous HL_5J7L_011 HL_34617.2 | |
| HL_4B3T_012 | 1/A/458:473 | GNRA | homologous HL_4LFB_012 HL_37824.3 | |
| HL_4B3T_013 | 1/A/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.2 | |
| HL_4B3T_014 | 1/A/617:623 | No text annotation | homologous HL_4LFB_014 HL_20554.2 | |
| HL_4B3T_015 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_75293.3 | |
| HL_4B3T_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_37824.3 | |
| HL_4B3T_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_75293.3 | |
| HL_4B3T_018 | 1/A/838:848 | No text annotation | homologous HL_4LFB_018 HL_46878.1 | |
| HL_4B3T_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_37824.3 | |
| HL_4B3T_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.3 | |
| HL_4B3T_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_50779.2 | |
| HL_4B3T_034 | 1/A/1012:1017 | GNRA | homologous HL_4LFB_022 HL_37824.3 | |
| HL_4B3T_023 | 1/A/1030:1031 | No text annotation | homologous HL_4LFB_023 NA | |
| HL_4B3T_024 | 1/A/1076:1081 | GNRA | homologous HL_4LFB_024 HL_37824.3 | |
| HL_4B3T_025 | 1/A/1089:1096 | No text annotation | homologous HL_4LFB_025 HL_77436.3 | |
| HL_4B3T_026 | 1/A/1134:1140 | No text annotation | homologous HL_4LFB_026 HL_87954.2 | |
| HL_4B3T_027 | 1/A/1165:1171 | GNRA | homologous HL_4LFB_027 HL_37824.3 | |
| HL_4B3T_028 | 1/A/1265:1270 | GNRA | homologous HL_4LFB_028 HL_37824.3 | |
| HL_4B3T_029 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_02887.2 | |
| HL_4B3T_030 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_06226.2 | |
| HL_4B3T_031 | 1/A/1445:1457 | UNCG | homologous HL_4LFB_031 HL_34617.2 | |
| HL_4B3T_032 | 1/A/1515:1520 | GNRA | homologous HL_4LFB_032 HL_37824.3 | |
| HL_4B3T_035 | 1/Z/31:39 | tRNA anticodon loop | geometric HL_4B3R_034 HL_06059.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_4B3T_022 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_4B3T_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_4LFB_001 IL_00225.9 | |
| IL_4B3T_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_4LFB_002 IL_31462.3 | |
| IL_4B3T_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_4LFB_003 IL_14177.1 | |
| IL_4B3T_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_58310.1 | |
| IL_4B3T_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_82107.2 | |
| IL_4B3T_006 | 1/A/67:69, 1/A/100:102 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_10289.1 | |
| IL_4B3T_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_4LFB_007 IL_92540.1 | |
| IL_4B3T_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_64231.3 | |
| IL_4B3T_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_51702.1 | |
| IL_4B3T_010 | 1/A/186:188, 1/A/189L:191 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_10289.1 | |
| IL_4B3T_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.1 | |
| IL_4B3T_012 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_47074.1 | |
| IL_4B3T_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_31461.3 | |
| IL_4B3T_014 | 1/A/367:369, 1/A/392:393 | Single bulged U | homologous IL_4LFB_014 IL_89505.1 | |
| IL_4B3T_015 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_5J7L_018 IL_31461.3 | |
| IL_4B3T_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_4LFB_016 IL_00225.9 | |
| IL_4B3T_017 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_4LFB_017 IL_28026.2 | |
| IL_4B3T_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_88269.3 | |
| IL_4B3T_019 | 1/A/450:455, 1/A/476:483 | No text annotation | homologous IL_4LFB_019 IL_26564.1 | |
| IL_4B3T_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_41203.2 | |
| IL_4B3T_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_4B3T_022 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_4LFB_022 IL_38186.4 | |
| IL_4B3T_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_17136.5 | |
| IL_4B3T_024 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.2 | |
| IL_4B3T_025 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_68140.2 | |
| IL_4B3T_026 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_78349.2 | |
| IL_4B3T_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_50694.5 | |
| IL_4B3T_028 | 1/A/657:658, 1/A/747:749 | Major groove platform | homologous IL_4LFB_028 IL_48076.2 | |
| IL_4B3T_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_68538.1 | |
| IL_4B3T_063 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_49751.2 | |
| IL_4B3T_031 | 1/A/683:688, 1/A/699:707 | Kink-turn | homologous IL_4LFB_031 IL_37722.1 | |
| IL_4B3T_032 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.1 | |
| IL_4B3T_033 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_17136.5 | |
| IL_4B3T_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_41756.2 | |
| IL_4B3T_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_5J7L_039 IL_31462.3 | |
| IL_4B3T_036 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_00225.9 | |
| IL_4B3T_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_4LFB_037 IL_47078.2 | |
| IL_4B3T_038 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_92540.1 | |
| IL_4B3T_064 | 1/A/993:997, 1/A/1044:1045 | Minor groove platform | geometric IL_4LFB_039 IL_47078.2 | |
| IL_4B3T_040 | 1/A/999:1003, 1/A/1038:1042 | No text annotation | ||
| IL_4B3T_041 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_89505.1 | |
| IL_4B3T_042 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_76319.3 | |
| IL_4B3T_043 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_58310.1 | |
| IL_4B3T_044 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_89505.1 | |
| IL_4B3T_045 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_10289.1 | |
| IL_4B3T_046 | 1/A/1124:1128, 1/A/1143:1149 | No text annotation | homologous IL_4LFB_048 IL_85222.1 | |
| IL_4B3T_065 | 1/A/1124:1132, 1/A/1142:1149 | No text annotation | ||
| IL_4B3T_047 | 1/A/1128:1132, 1/A/1142:1143 | Minor groove platform | geometric IL_3MXH_005 IL_15052.3 | |
| IL_4B3T_048 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation | geometric IL_5J7L_053 IL_42032.1 | |
| IL_4B3T_049 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_09129.1 | |
| IL_4B3T_050 | 1/A/1255:1258, 1/A/1277:1282 | No text annotation | ||
| IL_4B3T_051 | 1/A/1259:1260, 1/A/1274:1276 | Not an internal loop | geometric IL_4LFB_053 IL_58310.1 | |
| IL_4B3T_066 | 1/A/1259:1262, 1/A/1273:1276 | Double sheared | homologous IL_4LFB_067 IL_09705.13 | |
| IL_4B3T_052 | 1/A/1260:1262, 1/A/1273:1274 | Minor groove platform | homologous IL_4LFB_054 IL_58310.1 | |
| IL_4B3T_053 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation | geometric IL_4LFB_055 IL_85536.1 | |
| IL_4B3T_054 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | geometric IL_4V88_463 NA | |
| IL_4B3T_055 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_4B3T_056 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | geometric IL_3GM7_005 IL_10289.1 | |
| IL_4B3T_057 | 1/A/1407:1409, 1/A/1491:1494 | Decoding loop related | geometric IL_3C3Z_002 IL_31737.2 | |
| IL_4B3T_058 | 1/A/1412:1414, 1/A/1486:1488 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_10289.1 | |
| IL_4B3T_059 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | homologous IL_4LFB_060 IL_09705.13 | |
| IL_4B3T_060 | 1/A/1431:1435, 1/A/1466:1469 | UAA/GAN variation | homologous IL_4LFB_062 IL_77691.4 | |
| IL_4B3T_061 | 1/A/1435:1437, 1/A/1464:1466 | Isolated non-canonical cWW pair | geometric IL_4LFB_063 IL_10289.1 | |
| IL_4B3T_062 | 1/A/1440:1443, 1/A/1459:1461 | No text annotation | homologous IL_4LFB_064 IL_97255.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_4B3T_030 | No text annotation | ||
| IL_4B3T_039 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_4B3T_010 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | geometric J3_4LFB_010 NA | |
| J3_4B3T_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 NA | |
| J3_4B3T_011 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_4LFB_011 NA | |
| J3_4B3T_015 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 NA | |
| J3_4B3T_012 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_4LFB_012 NA | |
| J3_4B3T_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_4LFB_001 NA | |
| J3_4B3T_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 NA | |
| J3_4B3T_003 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_4LFB_003 NA | |
| J3_4B3T_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 NA | |
| J3_4B3T_005 | 1/A/990:993, 1/A/1045:1047, 1/A/1210:1215 | No text annotation | geometric J3_4LFB_005 NA | |
| J3_4B3T_016 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation | homologous J3_4LFB_016 NA | |
| J3_4B3T_020 | 1/A/999:1006, 1/A/1023:1027, 1/A/1034:1042 | No text annotation | ||
| J3_4B3T_006 | 1/A/1003:1006, 1/A/1023:1027, 1/A/1034:1038 | No text annotation | ||
| J3_4B3T_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 NA | |
| J3_4B3T_018 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 NA | |
| J3_4B3T_008 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_4B3T_019 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 NA | |
| J3_4B3T_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 NA | |
| J4_4B3T_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 NA | |
| J4_4B3T_002 | 1/A/142:144, 1/A/178:183, 1/A/194:198, 1/A/219:221 | No text annotation | homologous J4_4LFB_002 NA | |
| J4_4B3T_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_4LFB_003 NA | |
| J5_4B3T_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 NA | |
| J5_4B3T_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 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_4B3T_017 | No text annotation |
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