7M4U Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7M4U_001 | 1/a/14:24 | No text annotation | homologous HL_4LFB_001 HL_73535.1 | |
| HL_7M4U_003 | 1/a/154:159 | GNRA | homologous HL_5J7L_003 NA | |
| HL_7M4U_004 | 1/a/182:187 | UNCG | geometric HL_5Y85_004 HL_61337.4 | |
| HL_7M4U_006 | 1/a/255:263 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_7M4U_007 | 1/a/292:297 | GNRA | homologous HL_5J7L_007 NA | |
| HL_7M4U_008 | 1/a/316:329 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_7M4U_009 | 1/a/338:343 | UNCG | homologous HL_6CZR_080 NA | |
| HL_7M4U_010 | 1/a/375:380 | GNRA | homologous HL_5J7L_010 NA | |
| HL_7M4U_011 | 1/a/415:420 | No text annotation | geometric HL_5TBW_018 NA | |
| HL_7M4U_012 | 1/a/458:466 | GNRA wlth extra near cWW | homologous HL_5J7L_012 NA | |
| HL_7M4U_033 | 1/a/519:524 | GNRA variation | homologous HL_5J7L_205 NA | |
| HL_7M4U_014 | 1/a/614:620 | GNRA-like with tWH | homologous HL_4LFB_014 HL_86621.1 | |
| HL_7M4U_015 | 1/a/686:695 | No text annotation | homologous HL_5J7L_015 NA | |
| HL_7M4U_016 | 1/a/723:728 | GNRA | homologous HL_5J7L_016 NA | |
| HL_7M4U_017 | 1/a/783:793 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_7M4U_019 | 1/a/859:864 | GNRA | homologous HL_4LFB_019 HL_34789.4 | |
| HL_7M4U_020 | 1/a/894:899 | GNRA | homologous HL_4LFB_020 HL_34789.4 | |
| HL_7M4U_021 | 1/a/960:969 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_7M4U_022 | 1/a/1009:1014 | GNRA | homologous HL_4LFB_022 HL_34789.4 | |
| HL_7M4U_024 | 1/a/1073:1078 | GNRA | homologous HL_4LFB_024 HL_34789.4 | |
| HL_7M4U_025 | 1/a/1086:1093 | T-loop related | homologous HL_4LFB_025 HL_63894.2 | |
| HL_7M4U_026 | 1/a/1131:1137 | No text annotation | homologous HL_5J7L_025 NA | |
| HL_7M4U_034 | 1/a/1162:1168 | GNRA | homologous HL_4LFB_027 HL_34789.4 | |
| HL_7M4U_028 | 1/a/1262:1267 | GNRA | homologous HL_5J7L_027 NA | |
| HL_7M4U_029 | 1/a/1311:1320 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_7M4U_030 | 1/a/1353:1363 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_7M4U_031 | 1/a/1446:1451 | No text annotation | geometric HL_5J7L_143 NA | |
| HL_7M4U_032 | 1/a/1512:1517 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7M4U_002 | Mini UNCG | ||
| HL_7M4U_005 | No text annotation | ||
| HL_7M4U_013 | No text annotation | ||
| HL_7M4U_018 | No text annotation | ||
| HL_7M4U_023 | No text annotation | ||
| HL_7M4U_027 | tRNA anticodon loop |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7M4U_001 | 1/a/32:34, 1/a/549:550 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_7M4U_002 | 1/a/46:47, 1/a/392:394 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_7M4U_003 | 1/a/49:54, 1/a/355:357 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_7M4U_004 | 1/a/56:58, 1/a/352:353 | Minor groove platform | homologous IL_4LFB_004 IL_34520.3 | |
| IL_7M4U_005 | 1/a/65:68, 1/a/99:100 | Multiple bulged bases | homologous IL_5J7L_005 NA | |
| IL_7M4U_006 | 1/a/69:71, 1/a/96:98 | Isolated non-canonical cWW pair | homologous IL_6CZR_118 NA | |
| IL_7M4U_007 | 1/a/73:77, 1/a/90:94 | No text annotation | geometric IL_5TBW_121 NA | |
| IL_7M4U_008 | 1/a/124:127, 1/a/227:229 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_7M4U_009 | 1/a/128:132, 1/a/223:226 | Minor groove platform related | homologous IL_5J7L_010 NA | |
| IL_7M4U_010 | 1/a/140:142, 1/a/172:174 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_7M4U_011 | 1/a/143:149, 1/a/164:171 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_7M4U_012 | 1/a/199:202, 1/a/209:210 | Minor groove platform | geometric IL_7RQB_073 NA | |
| IL_7M4U_013 | 1/a/238:243, 1/a/273:280 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.4 | |
| IL_7M4U_014 | 1/a/245:248, 1/a/270:271 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_7M4U_015 | 1/a/288:289, 1/a/300:304 | C-loop | homologous IL_6CZR_125 NA | |
| IL_7M4U_016 | 1/a/363:365, 1/a/388:389 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_7M4U_017 | 1/a/367:371, 1/a/385:386 | C-loop | homologous IL_5J7L_018 NA | |
| IL_7M4U_069 | 1/a/367:372, 1/a/383:386 | C-loop with extra cWW pair | geometric IL_4V88_408 NA | |
| IL_7M4U_018 | 1/a/371:372, 1/a/383:385 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_7M4U_019 | 1/a/405:412, 1/a/423:429 | No text annotation | homologous IL_4LFB_017 IL_62329.1 | |
| IL_7M4U_020 | 1/a/436:438, 1/a/489:494 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_7M4U_021 | 1/a/442:446, 1/a/480:485 | tSH-tHW-tWW | homologous IL_5J7L_022 NA | |
| IL_7M4U_022 | 1/a/446:449, 1/a/476:480 | No text annotation | ||
| IL_7M4U_023 | 1/a/452:453, 1/a/471:473 | Single stack bend | geometric IL_5J7L_032 NA | |
| IL_7M4U_024 | 1/a/501:508, 1/a/537:538 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_11411.1 | |
| IL_7M4U_025 | 1/a/512:518, 1/a/525:533 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_7M4U_026 | 1/a/566:572, 1/a/877:878 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_7M4U_027 | 1/a/577:581, 1/a/754:758 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_7M4U_028 | 1/a/591:593, 1/a/641:642 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_7M4U_029 | 1/a/594:595, 1/a/637:640 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_7M4U_030 | 1/a/602:609, 1/a/625:630 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_7M4U_031 | 1/a/651:652, 1/a/748:751 | Major groove platform; stack outside cWW | geometric IL_4LFB_027 IL_74641.2 | |
| IL_7M4U_032 | 1/a/656:657, 1/a/742:744 | Single stack bend | homologous IL_5J7L_032 NA | |
| IL_7M4U_033 | 1/a/659:663, 1/a/737:740 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_7M4U_070 | 1/a/670:674, 1/a/710:714 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_71154.3 | |
| IL_7M4U_035 | 1/a/681:685, 1/a/696:703 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_7M4U_036 | 1/a/771:775, 1/a/801:802 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_7M4U_037 | 1/a/776:780, 1/a/796:800 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_7M4U_038 | 1/a/884:891, 1/a/902:907 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_7M4U_039 | 1/a/919:920, 1/a/1390:1392 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_7M4U_040 | 1/a/922:924, 1/a/1387:1388 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_7M4U_041 | 1/a/930:932, 1/a/1377:1381 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_7M4U_042 | 1/a/950:951, 1/a/1223:1225 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_7M4U_043 | 1/a/990:994, 1/a/1041:1042 | Minor groove platform | homologous IL_4LFB_039 IL_61370.1 | |
| IL_7M4U_044 | 1/a/995:996, 1/a/1038:1040 | Single stack bend | homologous IL_5J7L_044 NA | |
| IL_7M4U_045 | 1/a/1003:1006, 1/a/1017:1020 | Tandem non-canonical cWW pairs | geometric IL_6MWN_005 IL_71194.2 | |
| IL_7M4U_046 | 1/a/1045:1047, 1/a/1205:1206 | Single bulged U | homologous IL_5J7L_046 NA | |
| IL_7M4U_048 | 1/a/1049:1053, 1/a/1201:1203 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_7M4U_049 | 1/a/1054:1055, 1/a/1196:1200 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_7M4U_050 | 1/a/1057:1058, 1/a/1192:1194 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_7M4U_051 | 1/a/1058:1060, 1/a/1190:1192 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_7M4U_052 | 1/a/1120:1125, 1/a/1141:1147 | No text annotation | ||
| IL_7M4U_053 | 1/a/1126:1129, 1/a/1139:1140 | Minor groove platform | homologous IL_5J7L_052 NA | |
| IL_7M4U_054 | 1/a/1155:1158, 1/a/1172:1178 | No text annotation | geometric IL_5J7L_053 NA | |
| IL_7M4U_055 | 1/a/1244:1250, 1/a/1281:1287 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_7M4U_056 | 1/a/1252:1255, 1/a/1274:1279 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_7M4U_057 | 1/a/1256:1259, 1/a/1270:1273 | Tandem non-canonical cWW pairs | geometric IL_4V88_461 NA | |
| IL_7M4U_058 | 1/a/1300:1305, 1/a/1326:1331 | No text annotation | geometric IL_4LFB_055 IL_57885.2 | |
| IL_7M4U_059 | 1/a/1396:1398, 1/a/1498:1501 | No text annotation | geometric IL_5J7L_058 NA | |
| IL_7M4U_060 | 1/a/1398:1401, 1/a/1494:1498 | No text annotation | homologous IL_5J7L_059 NA | |
| IL_7M4U_061 | 1/a/1402:1404, 1/a/1491:1493 | Isolated non-canonical cWW pair | geometric IL_6IA2_005 IL_01003.4 | |
| IL_7M4U_062 | 1/a/1404:1406, 1/a/1488:1491 | No text annotation | geometric IL_6DME_003 IL_75527.2 | |
| IL_7M4U_063 | 1/a/1409:1411, 1/a/1483:1485 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_7M4U_064 | 1/a/1413:1416, 1/a/1478:1481 | Double sheared | homologous IL_4LFB_060 IL_58355.2 | |
| IL_7M4U_065 | 1/a/1418:1420, 1/a/1474:1476 | Isolated non-canonical cWW pair | geometric IL_4P3T_001 NA | |
| IL_7M4U_066 | 1/a/1427:1432, 1/a/1463:1467 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_7M4U_067 | 1/a/1437:1439, 1/a/1457:1458 | Major groove platform | geometric IL_4V9F_082 IL_48076.8 | |
| IL_7M4U_068 | 1/a/1442:1445, 1/a/1452:1454 | No text annotation | homologous IL_5J7L_065 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7M4U_034 | No text annotation | ||
| IL_7M4U_071 | No text annotation | ||
| IL_7M4U_047 | Isolated non-canonical cWW pair | ||
| IL_7M4U_072 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7M4U_001 | 1/a/48:49, 1/a/357:363, 1/a/389:391 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_7M4U_013 | 1/a/48:54, 1/a/355:363, 1/a/389:391 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_7M4U_002 | 1/a/583:585, 1/a/648:651, 1/a/751:752 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_7M4U_014 | 1/a/583:585, 1/a/648:652, 1/a/748:752 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_7M4U_003 | 1/a/669:670, 1/a/714:722, 1/a/729:731 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_7M4U_004 | 1/a/823:826, 1/a/854:858, 1/a/865:871 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_7M4U_015 | 1/a/933:936, 1/a/1341:1347, 1/a/1369:1376 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_7M4U_005 | 1/a/940:943, 1/a/1232:1234, 1/a/1334:1337 | No text annotation | homologous J3_4LFB_003 J3_44359.1 | |
| J3_7M4U_006 | 1/a/952:959, 1/a/970:981, 1/a/1218:1222 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_7M4U_007 | 1/a/987:990, 1/a/1042:1044, 1/a/1207:1212 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_7M4U_016 | 1/a/987:994, 1/a/1041:1044, 1/a/1207:1212 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_7M4U_008 | 1/a/999:1003, 1/a/1020:1024, 1/a/1031:1035 | No text annotation | ||
| J3_7M4U_009 | 1/a/1060:1065, 1/a/1104:1110, 1/a/1184:1190 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_7M4U_017 | 1/a/1070:1071, 1/a/1080:1083, 1/a/1096:1099 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_7M4U_011 | 1/a/1113:1115, 1/a/1152:1155, 1/a/1178:1181 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_7M4U_018 | 1/a/1113:1115, 1/a/1152:1158, 1/a/1172:1181 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_7M4U_012 | 1/a/1234:1238, 1/a/1293:1300, 1/a/1331:1334 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_7M4U_001 | 1/a/111:118, 1/a/235:236, 1/a/282:285, 1/a/307:308 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_7M4U_002 | 1/a/139:140, 1/a/174:180, 1/a/189:194, 1/a/215:216 | No text annotation | ||
| J4_7M4U_003 | 1/a/572:574, 1/a/761:766, 1/a/807:818, 1/a/876:877 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_7M4U_001 | 1/a/38:41, 1/a/399:402, 1/a/432:436, 1/a/494:497, 1/a/542:545 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_7M4U_002 | 1/a/38:41, 1/a/399:402, 1/a/432:438, 1/a/489:497, 1/a/542:545 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_7M4U_003 | 1/a/60:63, 1/a/102:109, 1/a/310:312, 1/a/333:335, 1/a/346:350 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_7M4U_010 | No text annotation |
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