4GKJ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_4GKJ_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_89881.5 | |
| HL_4GKJ_002 | 1/A/78:84 | No text annotation | homologous HL_4LFB_002 HL_31585.3 | |
| HL_4GKJ_003 | 1/A/152:157 | GNRA | homologous HL_4LFB_003 HL_37824.7 | |
| HL_4GKJ_004 | 1/A/186:191 | No text annotation | homologous HL_4LFB_004 HL_48417.5 | |
| HL_4GKJ_005 | 1/A/207:211 | Mini UNCG | homologous HL_4LFB_005 HL_48778.2 | |
| HL_4GKJ_006 | 1/A/254:262 | GNRA related | homologous HL_4LFB_006 HL_84299.4 | |
| HL_4GKJ_007 | 1/A/291:296 | GNRA | homologous HL_4LFB_007 HL_37824.7 | |
| HL_4GKJ_008 | 1/A/315:328 | No text annotation | homologous HL_4LFB_008 HL_81205.3 | |
| HL_4GKJ_009 | 1/A/337:342 | UNCG | homologous HL_4LFB_009 HL_34617.5 | |
| HL_4GKJ_010 | 1/A/374:379 | GNRA | homologous HL_4LFB_010 HL_37824.7 | |
| HL_4GKJ_011 | 1/A/414:419 | UNCG | homologous HL_4LFB_011 HL_34617.5 | |
| HL_4GKJ_012 | 1/A/452:458 | GNRA | homologous HL_4LFB_012 HL_37824.7 | |
| HL_4GKJ_013 | 1/A/505:510 | No text annotation | geometric HL_5J7L_143 HL_75660.5 | |
| HL_4GKJ_014 | 1/A/600:606 | No text annotation | homologous HL_4LFB_014 HL_10453.3 | |
| HL_4GKJ_015 | 1/A/672:681 | No text annotation | homologous HL_4LFB_015 HL_75293.5 | |
| HL_4GKJ_016 | 1/A/709:714 | GNRA | homologous HL_4LFB_016 HL_37824.7 | |
| HL_4GKJ_017 | 1/A/769:779 | No text annotation | homologous HL_4LFB_017 HL_75293.5 | |
| HL_4GKJ_018 | 1/A/821:825 | Mini UNCG | homologous HL_4LFB_018 HL_48778.2 | |
| HL_4GKJ_019 | 1/A/839:844 | GNRA | homologous HL_4LFB_019 HL_37824.7 | |
| HL_4GKJ_020 | 1/A/874:879 | GNRA | homologous HL_4LFB_020 HL_37824.7 | |
| HL_4GKJ_021 | 1/A/940:949 | No text annotation | homologous HL_4LFB_021 HL_50779.4 | |
| HL_4GKJ_022 | 1/A/990:995 | GNRA | homologous HL_4LFB_022 HL_37824.7 | |
| HL_4GKJ_023 | 1/A/1008:1013 | No text annotation | homologous HL_4LFB_023 NA | |
| HL_4GKJ_024 | 1/A/1058:1063 | GNRA | homologous HL_4LFB_024 HL_37824.7 | |
| HL_4GKJ_025 | 1/A/1071:1078 | T-loop related | homologous HL_4LFB_025 HL_77436.5 | |
| HL_4GKJ_026 | 1/A/1116:1122 | No text annotation | homologous HL_5J7L_025 HL_87954.2 | |
| HL_4GKJ_027 | 1/A/1147:1152 | GNRA | homologous HL_4LFB_027 HL_37824.7 | |
| HL_4GKJ_028 | 1/A/1246:1251 | GNRA | homologous HL_4LFB_028 HL_37824.7 | |
| HL_4GKJ_029 | 1/A/1295:1304 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_02887.3 | |
| HL_4GKJ_030 | 1/A/1337:1348 | No text annotation | homologous HL_4LFB_030 HL_06226.4 | |
| HL_4GKJ_031 | 1/A/1429:1434 | UNCG | homologous HL_4LFB_031 HL_34617.5 | |
| HL_4GKJ_032 | 1/A/1492:1497 | GNRA | homologous HL_4LFB_032 HL_37824.7 |
Problematic loops
No problematic loops
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_4GKJ_001 | 1/A/30:32, 1/A/535:536 | Single bulged G | homologous IL_4LFB_001 IL_00225.13 | |
| IL_4GKJ_002 | 1/A/44:45, 1/A/391:393 | Single bulged A | homologous IL_4LFB_002 IL_31462.5 | |
| IL_4GKJ_003 | 1/A/47:52, 1/A/354:356 | No text annotation | homologous IL_4LFB_003 IL_14177.2 | |
| IL_4GKJ_004 | 1/A/54:56, 1/A/351:352 | Minor groove platform | homologous IL_4LFB_004 IL_51454.2 | |
| IL_4GKJ_005 | 1/A/63:66, 1/A/96:97 | Multiple bulged bases | homologous IL_5J7L_005 IL_82107.4 | |
| IL_4GKJ_006 | 1/A/67:69, 1/A/93:95 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_87907.2 | |
| IL_4GKJ_007 | 1/A/122:125, 1/A/226:227 | Multiple bulged bases | homologous IL_4LFB_007 IL_33761.2 | |
| IL_4GKJ_008 | 1/A/126:130, 1/A/222:225 | No text annotation | homologous IL_4LFB_008 IL_64231.5 | |
| IL_4GKJ_009 | 1/A/142:147, 1/A/162:168 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_12745.1 | |
| IL_4GKJ_010 | 1/A/180:182, 1/A/195:197 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_87907.2 | |
| IL_4GKJ_011 | 1/A/237:242, 1/A/272:279 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 IL_46174.3 | |
| IL_4GKJ_012 | 1/A/244:247, 1/A/269:270 | No text annotation | homologous IL_4LFB_012 IL_47074.2 | |
| IL_4GKJ_013 | 1/A/287:288, 1/A/299:303 | C-loop | homologous IL_4LFB_013 IL_03109.3 | |
| IL_4GKJ_014 | 1/A/362:364, 1/A/387:388 | Single bulged U | homologous IL_4LFB_014 IL_89505.4 | |
| IL_4GKJ_015 | 1/A/366:370, 1/A/384:385 | C-loop | homologous IL_5J7L_018 IL_03109.3 | |
| IL_4GKJ_016 | 1/A/370:371, 1/A/382:384 | Single bulged G | geometric IL_4LFB_016 IL_00225.13 | |
| IL_4GKJ_069 | 1/A/404:411, 1/A/422:428 | No text annotation | homologous IL_4LFB_017 IL_28026.3 | |
| IL_4GKJ_018 | 1/A/440:444, 1/A/467:472 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_4LFB_018 IL_88269.4 | |
| IL_4GKJ_019 | 1/A/444:449, 1/A/461:467 | No text annotation | geometric IL_4LFB_019 IL_31561.1 | |
| IL_4GKJ_020 | 1/A/487:494, 1/A/523:524 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_41203.4 | |
| IL_4GKJ_021 | 1/A/498:504, 1/A/511:519 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_4GKJ_022 | 1/A/552:558, 1/A/857:858 | No text annotation | homologous IL_4LFB_022 IL_38186.6 | |
| IL_4GKJ_023 | 1/A/563:567, 1/A/740:744 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_17136.7 | |
| IL_4GKJ_024 | 1/A/577:579, 1/A/627:628 | Major groove platform | homologous IL_4LFB_024 IL_48076.6 | |
| IL_4GKJ_025 | 1/A/580:581, 1/A/623:626 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_68140.4 | |
| IL_4GKJ_026 | 1/A/588:595, 1/A/611:616 | No text annotation | homologous IL_4LFB_026 IL_78349.3 | |
| IL_4GKJ_027 | 1/A/637:638, 1/A/734:737 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_50694.7 | |
| IL_4GKJ_028 | 1/A/640:641, 1/A/730:732 | Major groove platform | homologous IL_4LFB_028 IL_48076.6 | |
| IL_4GKJ_029 | 1/A/645:649, 1/A/723:726 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_85033.2 | |
| IL_4GKJ_065 | 1/A/656:660, 1/A/696:700 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_49751.4 | |
| IL_4GKJ_031 | 1/A/666:671, 1/A/682:690 | Kink-turn | homologous IL_4LFB_031 IL_95727.1 | |
| IL_4GKJ_032 | 1/A/757:761, 1/A/787:788 | Left turn | homologous IL_4LFB_032 IL_29346.2 | |
| IL_4GKJ_033 | 1/A/762:766, 1/A/782:786 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_17136.7 | |
| IL_4GKJ_034 | 1/A/864:871, 1/A/882:887 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_41756.4 | |
| IL_4GKJ_035 | 1/A/899:900, 1/A/1375:1377 | Single bulged A | homologous IL_4LFB_035 IL_31462.5 | |
| IL_4GKJ_036 | 1/A/902:904, 1/A/1372:1373 | Single bulged G | homologous IL_5J7L_040 IL_00225.13 | |
| IL_4GKJ_037 | 1/A/910:912, 1/A/1362:1366 | Minor groove platform | homologous IL_5J7L_041 IL_47078.3 | |
| IL_4GKJ_038 | 1/A/930:931, 1/A/1207:1209 | Minor groove platform | homologous IL_4LFB_038 IL_51454.2 | |
| IL_4GKJ_039 | 1/A/970:974, 1/A/1026:1027 | Minor groove platform | geometric IL_4LFB_039 IL_47078.3 | |
| IL_4GKJ_041 | 1/A/1030:1032, 1/A/1189:1190 | Single bulged U | homologous IL_4LFB_042 IL_89505.4 | |
| IL_4GKJ_066 | 1/A/1034:1038, 1/A/1185:1187 | Isolated cWS basepair | homologous IL_4LFB_044 IL_76319.5 | |
| IL_4GKJ_043 | 1/A/1039:1040, 1/A/1180:1184 | Minor groove platform | homologous IL_4LFB_045 IL_95583.2 | |
| IL_4GKJ_044 | 1/A/1042:1043, 1/A/1176:1178 | Single bulged U | geometric IL_6CZR_156 NA | |
| IL_4GKJ_045 | 1/A/1043:1045, 1/A/1174:1176 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_28037.2 | |
| IL_4GKJ_047 | 1/A/1106:1114, 1/A/1124:1131 | No text annotation | ||
| IL_4GKJ_048 | 1/A/1140:1143, 1/A/1156:1162 | No text annotation | geometric IL_5J7L_053 IL_42032.1 | |
| IL_4GKJ_049 | 1/A/1228:1234, 1/A/1265:1271 | No text annotation | homologous IL_4LFB_051 IL_09129.2 | |
| IL_4GKJ_050 | 1/A/1236:1239, 1/A/1258:1263 | 180 degree turn | homologous IL_6CZR_161 NA | |
| IL_4GKJ_051 | 1/A/1240:1241, 1/A/1255:1257 | Not an internal loop | homologous IL_4LFB_053 NA | |
| IL_4GKJ_068 | 1/A/1240:1243, 1/A/1254:1257 | Double sheared | homologous IL_4LFB_067 IL_09705.15 | |
| IL_4GKJ_052 | 1/A/1241:1243, 1/A/1254:1255 | Minor groove platform | geometric IL_4LFB_054 IL_51454.2 | |
| IL_4GKJ_053 | 1/A/1284:1289, 1/A/1310:1315 | No text annotation | geometric IL_4LFB_055 IL_85536.2 | |
| IL_4GKJ_054 | 1/A/1381:1383, 1/A/1478:1481 | No text annotation | homologous IL_4LFB_056 IL_61438.4 | |
| IL_4GKJ_055 | 1/A/1383:1386, 1/A/1474:1478 | No text annotation | geometric IL_4V88_464 NA | |
| IL_4GKJ_056 | 1/A/1387:1389, 1/A/1471:1473 | Isolated non-canonical cWW pair | geometric IL_4ZC7_004 IL_87907.2 | |
| IL_4GKJ_057 | 1/A/1389:1391, 1/A/1468:1471 | Decoding loop related | geometric IL_3C3Z_002 IL_31737.3 | |
| IL_4GKJ_058 | 1/A/1394:1396, 1/A/1463:1465 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_87907.2 | |
| IL_4GKJ_059 | 1/A/1398:1401, 1/A/1458:1461 | Double sheared | homologous IL_4LFB_060 IL_09705.15 | |
| IL_4GKJ_061 | 1/A/1417:1419, 1/A/1441:1443 | Isolated non-canonical cWW pair | homologous IL_4LFB_063 IL_87907.2 | |
| IL_4GKJ_062 | 1/A/1422:1427, 1/A/1436:1438 | Isolated basepair with bulged bases | homologous IL_6CZR_172 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_4GKJ_063 | Single bulged G, near cWW | ||
| IL_4GKJ_017 | No text annotation | ||
| IL_4GKJ_064 | No text annotation | ||
| IL_4GKJ_030 | No text annotation | ||
| IL_4GKJ_040 | Partly complementary | ||
| IL_4GKJ_042 | Tandem non-canonical cWW pairs | ||
| IL_4GKJ_046 | No text annotation | ||
| IL_4GKJ_067 | No text annotation | ||
| IL_4GKJ_060 | UAA/GAN variation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_4GKJ_009 | 1/A/46:47, 1/A/356:362, 1/A/388:390 | No text annotation | geometric J3_4LFB_010 J3_67856.4 | |
| J3_4GKJ_013 | 1/A/46:52, 1/A/354:362, 1/A/388:390 | No text annotation | homologous J3_4LFB_014 J3_46317.4 | |
| J3_4GKJ_010 | 1/A/569:571, 1/A/634:637, 1/A/737:738 | No text annotation | geometric J3_4LFB_011 J3_56052.5 | |
| J3_4GKJ_014 | 1/A/569:571, 1/A/634:638, 1/A/734:738 | No text annotation | homologous J3_4LFB_015 J3_17385.4 | |
| J3_4GKJ_011 | 1/A/655:656, 1/A/700:708, 1/A/715:717 | No text annotation | homologous J3_4LFB_012 J3_11934.4 | |
| J3_4GKJ_001 | 1/A/809:812, 1/A/834:838, 1/A/845:851 | No text annotation | homologous J3_4LFB_001 J3_85054.4 | |
| J3_4GKJ_002 | 1/A/913:916, 1/A/1325:1331, 1/A/1354:1361 | No text annotation | homologous J3_4LFB_002 J3_25303.4 | |
| J3_4GKJ_003 | 1/A/920:923, 1/A/1216:1218, 1/A/1318:1321 | No text annotation | homologous J3_4LFB_003 J3_52655.4 | |
| J3_4GKJ_004 | 1/A/932:939, 1/A/950:961, 1/A/1202:1206 | No text annotation | homologous J3_4LFB_004 J3_83516.4 | |
| J3_4GKJ_005 | 1/A/967:970, 1/A/1027:1029, 1/A/1191:1196 | No text annotation | homologous J3_4LFB_005 J3_82572.1 | |
| J3_4GKJ_015 | 1/A/967:974, 1/A/1026:1029, 1/A/1191:1196 | No text annotation | homologous J3_4LFB_016 J3_76475.2 | |
| J3_4GKJ_019 | 1/A/977:987, 1/A/998:1007, 1/A/1014:1023 | No text annotation | ||
| J3_4GKJ_006 | 1/A/1045:1050, 1/A/1089:1095, 1/A/1168:1174 | No text annotation | homologous J3_4LFB_007 J3_08394.3 | |
| J3_4GKJ_017 | 1/A/1055:1056, 1/A/1065:1068, 1/A/1081:1084 | No text annotation | homologous J3_4LFB_017 J3_79369.1 | |
| J3_4GKJ_007 | 1/A/1098:1100, 1/A/1137:1140, 1/A/1162:1165 | No text annotation | homologous J3_4LFB_008 J3_82365.4 | |
| J3_4GKJ_018 | 1/A/1098:1100, 1/A/1137:1143, 1/A/1156:1165 | No text annotation | homologous J3_4LFB_018 J3_17791.2 | |
| J3_4GKJ_008 | 1/A/1218:1222, 1/A/1277:1284, 1/A/1315:1318 | No text annotation | homologous J3_4LFB_009 J3_37047.6 | |
| J4_4GKJ_001 | 1/A/108:115, 1/A/234:235, 1/A/281:284, 1/A/306:307 | No text annotation | homologous J4_4LFB_001 J4_35578.3 | |
| J4_4GKJ_002 | 1/A/136:138, 1/A/172:177, 1/A/200:204, 1/A/214:216 | No text annotation | homologous J4_4LFB_002 J4_88771.1 | |
| J4_4GKJ_003 | 1/A/558:560, 1/A/747:752, 1/A/793:804, 1/A/856:857 | No text annotation | homologous J4_4LFB_003 J4_61885.6 | |
| J5_4GKJ_001 | 1/A/36:39, 1/A/398:401, 1/A/431:436, 1/A/476:483, 1/A/528:531 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_4GKJ_002 | 1/A/58:61, 1/A/99:106, 1/A/309:311, 1/A/332:334, 1/A/345:349 | No text annotation | homologous J5_4LFB_002 J5_59910.6 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_4GKJ_016 | No text annotation |
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