5U4I Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/A/1910:1920 | geometric HL_5TBW_049 | NA HL_98248.1* | ||
| 1/B/38:44 | NA | NA | ||
| 1/B/86:90 | NA | NA | ||
| 1/a/12:22 | NA | NA | ||
| 1/a/80:89 | NA | NA | ||
| 1/a/158:163 | NA | NA | ||
| 1/a/186:191 | NA | NA | ||
| 1/a/202:215 | NA | NA | ||
| 1/a/259:267 | NA | NA | ||
| 1/a/296:301 | NA | NA | ||
| 1/a/320:333 | NA | NA | ||
| 1/a/342:347 | NA | NA | ||
| 1/a/379:384 | NA | NA | ||
| 1/a/419:424 | NA | NA | ||
| 1/a/462:470 | NA | NA | ||
| 1/a/521:528 | NA | NA | ||
| 1/a/617:623 | NA | NA | ||
| 1/a/689:698 | NA | NA | ||
| 1/a/726:731 | NA | NA | ||
| 1/a/786:796 | NA | NA | ||
| 1/a/839:847 | NA | NA | ||
| 1/a/862:867 | NA | NA | ||
| 1/a/897:902 | NA | NA | ||
| 1/a/963:972 | NA | NA | ||
| 1/a/1012:1017 | NA | NA | ||
| 1/a/1029:1033 | NA | NA | ||
| 1/a/1076:1081 | NA | NA | ||
| 1/a/1089:1096 | NA | NA | ||
| 1/a/1133:1141 | NA | NA | ||
| 1/a/1165:1171 | NA | NA | ||
| 1/a/1265:1270 | NA | NA | ||
| 1/a/1314:1323 | NA | NA | ||
| 1/a/1356:1366 | NA | NA | ||
| 1/a/1449:1454 | NA | NA | ||
| 1/a/1515:1520 | NA | NA | ||
| 1/x/12:22 | NA | NA | ||
| 1/x/31:39 | NA | NA | ||
| 1/x/53:61 | NA | NA | ||
| 1/y/12:22 | NA | NA | ||
| 1/y/31:39 | NA | NA | ||
| 1/y/53:61 | NA | NA |
Problematic loops
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/B/17:18, 1/B/65:67 | NA | NA | ||
| 1/B/23:28, 1/B/56:60 | NA | NA | ||
| 1/B/30:31, 1/B/51:54 | NA | NA | ||
| 1/B/34:38, 1/B/44:48 | NA | NA | ||
| 1/B/71:79, 1/B/97:105 | NA | NA | ||
| 1/a/30:33, 1/a/551:553 | NA | NA | ||
| 1/a/44:45, 1/a/396:398 | NA | NA | ||
| 1/a/47:52, 1/a/359:361 | NA | NA | ||
| 1/a/54:56, 1/a/356:357 | NA | NA | ||
| 1/a/63:66, 1/a/103:104 | NA | NA | ||
| 1/a/67:69, 1/a/99:102 | NA | NA | ||
| 1/a/70:73, 1/a/97:98 | NA | NA | ||
| 1/a/75:78, 1/a/91:95 | NA | NA | ||
| 1/a/128:131, 1/a/231:233 | NA | NA | ||
| 1/a/132:136, 1/a/227:230 | NA | NA | ||
| 1/a/144:146, 1/a/176:178 | NA | NA | ||
| 1/a/147:153, 1/a/168:175 | NA | NA | ||
| 1/a/242:247, 1/a/277:284 | NA | NA | ||
| 1/a/249:252, 1/a/274:275 | NA | NA | ||
| 1/a/291:293, 1/a/304:309 | NA | NA | ||
| 1/a/367:369, 1/a/392:393 | NA | NA | ||
| 1/a/370:375, 1/a/389:391 | NA | NA | ||
| 1/a/375:376, 1/a/387:389 | NA | NA | ||
| 1/a/409:416, 1/a/427:433 | NA | NA | ||
| 1/a/440:442, 1/a/492:497 | NA | NA | ||
| 1/a/446:450, 1/a/483:488 | NA | NA | ||
| 1/a/450:455, 1/a/477:483 | NA | NA | ||
| 1/a/504:511, 1/a/540:541 | NA | NA | ||
| 1/a/514:521, 1/a/528:537 | NA | NA | ||
| 1/a/569:575, 1/a/880:881 | NA | NA | ||
| 1/a/580:584, 1/a/757:761 | NA | NA | ||
| 1/a/594:596, 1/a/644:645 | NA | NA | ||
| 1/a/597:598, 1/a/640:643 | NA | NA | ||
| 1/a/604:613, 1/a/627:634 | NA | NA | ||
| 1/a/654:655, 1/a/751:754 | NA | NA | ||
| 1/a/658:659, 1/a/746:748 | NA | NA | ||
| 1/a/662:666, 1/a/740:743 | NA | NA | ||
| 1/a/673:678, 1/a/712:717 | NA | NA | ||
| 1/a/684:688, 1/a/699:706 | NA | NA | ||
| 1/a/774:778, 1/a/804:805 | NA | NA | ||
| 1/a/779:783, 1/a/799:803 | NA | NA | ||
| 1/a/887:894, 1/a/905:910 | NA | NA | ||
| 1/a/922:923, 1/a/1393:1395 | NA | NA | ||
| 1/a/925:927, 1/a/1390:1391 | NA | NA | ||
| 1/a/933:935, 1/a/1380:1384 | NA | NA | ||
| 1/a/953:954, 1/a/1226:1228 | NA | NA | ||
| 1/a/993:997, 1/a/1044:1045 | NA | NA | ||
| 1/a/998:1000, 1/a/1040:1043 | NA | NA | ||
| 1/a/1027:1029, 1/a/1033:1034 | NA | NA | ||
| 1/a/1048:1050, 1/a/1208:1209 | NA | NA | ||
| 1/a/1050:1052, 1/a/1206:1208 | NA | NA | ||
| 1/a/1052:1056, 1/a/1204:1206 | NA | NA | ||
| 1/a/1057:1058, 1/a/1199:1203 | NA | NA | ||
| 1/a/1060:1061, 1/a/1195:1197 | NA | NA | ||
| 1/a/1061:1063, 1/a/1193:1195 | NA | NA | ||
| 1/a/1124:1128, 1/a/1144:1149 | NA | NA | ||
| 1/a/1129:1132, 1/a/1142:1143 | NA | NA | ||
| 1/a/1158:1161, 1/a/1175:1181 | NA | NA | ||
| 1/a/1247:1253, 1/a/1284:1290 | NA | NA | ||
| 1/a/1255:1258, 1/a/1277:1282 | NA | NA | ||
| 1/a/1259:1263, 1/a/1272:1276 | NA | NA | ||
| 1/a/1303:1308, 1/a/1329:1334 | NA | NA | ||
| 1/a/1399:1401, 1/a/1501:1504 | NA | NA | ||
| 1/a/1401:1404, 1/a/1497:1501 | NA | NA | ||
| 1/a/1405:1409, 1/a/1491:1496 | NA | NA | ||
| 1/a/1412:1414, 1/a/1486:1488 | NA | NA | ||
| 1/a/1416:1419, 1/a/1481:1484 | NA | NA | ||
| 1/a/1430:1435, 1/a/1466:1470 | NA | NA | ||
| 1/a/1440:1442, 1/a/1460:1461 | NA | NA | ||
| 1/a/1445:1448, 1/a/1455:1457 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5U4I_001 | Triple sheared with non-canonical cWW homologous IL_7RQB_001 | ||
| IL_5U4I_002 | Single bulged A homologous IL_7RQB_002 | ||
| IL_5U4I_003 | Minor groove platform homologous IL_7RQB_003 | ||
| IL_5U4I_004 | Kink-turn homologous IL_7RQB_004 | ||
| IL_5U4I_005 | Single stack bend geometric IL_4WF9_007 | ||
| IL_5U4I_006 | Single stack bend geometric IL_5J7L_032 | ||
| IL_5U4I_007 | Single stack bend homologous IL_7RQB_005 | ||
| IL_5U4I_008 | 8x7 Sarcin-Ricin; G-bulge homologous IL_7RQB_006 | ||
| IL_5U4I_009 | 7x6 Sarcin-Ricin; G-bulge homologous IL_7RQB_007 | ||
| IL_5U4I_010 | geometric IL_5J7L_252 | ||
| IL_5U4I_011 | geometric IL_5J7L_253 | ||
| IL_5U4I_012 | homologous IL_7RQB_013 | ||
| IL_5U4I_013 | homologous IL_7RQB_014 | ||
| IL_5U4I_014 | Double sheared geometric IL_5J7L_256 | ||
| IL_5U4I_015 | homologous IL_7RQB_015 | ||
| IL_5U4I_016 | AAA cross-strand stack homologous IL_7RQB_016 | ||
| IL_5U4I_017 | homologous IL_7RQB_017 | ||
| IL_5U4I_018 | geometric IL_7RQB_018 | ||
| IL_5U4I_019 | Single bulged A geometric IL_4V9F_025 | ||
| IL_5U4I_020 | Single bulged G homologous IL_7RQB_020 | ||
| IL_5U4I_021 | Triple sheared geometric IL_4WF9_024 | ||
| IL_5U4I_022 | Major groove platform geometric IL_4WF9_026 | ||
| IL_5U4I_023 | Multiple bulged bases homologous IL_7RQB_023 | ||
| IL_5U4I_024 | NA | ||
| IL_5U4I_025 | Stack outside cWW geometric IL_5J7L_268 | ||
| IL_5U4I_026 | Single stack bend geometric IL_5J7L_032 | ||
| IL_5U4I_027 | 7x7 Sarcin-Ricin with intercalated A; G-bulge geometric IL_5J7L_270 | ||
| IL_5U4I_028 | Minor groove platform homologous IL_7RQB_028 | ||
| IL_5U4I_029 | C-loop homologous IL_7RQB_029 | ||
| IL_5U4I_030 | Tandem non-canonical cWW pairs geometric IL_5C5W_003 | ||
| IL_5U4I_031 | Triple sheared geometric IL_4V9F_085 | ||
| IL_5U4I_032 | Single bulged A homologous IL_7RQB_033 | ||
| IL_5U4I_033 | Single bulged C homologous IL_7RQB_035 | ||
| IL_5U4I_034 | UAA/GAN homologous IL_7RQB_036 | ||
| IL_5U4I_035 | SSU/LSU pseudoknot homologous IL_7RQB_037 | ||
| IL_5U4I_036 | Single bulged U geometric IL_4WF9_038 | ||
| IL_5U4I_037 | geometric IL_5J7L_280 | ||
| IL_5U4I_038 | geometric IL_5J7L_281 | ||
| IL_5U4I_039 | Isolated non-canonical cWW with bulges homologous IL_7RQB_041 | ||
| IL_5U4I_040 | Tandem non-canonical cWW pairs geometric IL_5J7L_283 | ||
| IL_5U4I_041 | Kink-turn homologous IL_7RQB_042 | ||
| IL_5U4I_042 | geometric IL_5D8H_002 | ||
| IL_5U4I_043 | Major groove platform geometric IL_4V9F_044 | ||
| IL_5U4I_044 | NA | ||
| IL_5U4I_045 | geometric IL_5J7L_287 | ||
| IL_5U4I_046 | Kink-turn homologous IL_7RQB_047 | ||
| IL_5U4I_047 | 8x7 Sarcin-Ricin; G-bulge homologous IL_7RQB_049 | ||
| IL_5U4I_048 | Major groove platform; stack outside cWW homologous IL_7RQB_050 | ||
| IL_5U4I_049 | C-loop homologous IL_7RQB_051 | ||
| IL_5U4I_050 | UAA/GAN geometric IL_5J7L_292 | ||
| IL_5U4I_051 | tSH-tHW-tHS homologous IL_7RQB_053 | ||
| IL_5U4I_052 | Single stack bend geometric IL_4LFB_041 | ||
| IL_5U4I_053 | geometric IL_5J7L_294 | ||
| IL_5U4I_054 | UAA/GAN homologous IL_7RQB_055 | ||
| IL_5U4I_055 | Tandem non-canonical cWW pairs geometric IL_5J7L_296 | ||
| IL_5U4I_056 | tSH-tHW homologous IL_7RQB_057 | ||
| IL_5U4I_057 | Single bulged U geometric IL_5TBW_130 | ||
| IL_5U4I_058 | geometric IL_3BNN_006 | ||
| IL_5U4I_059 | tSH-tHW-tHS geometric IL_5J7L_300 | ||
| IL_5U4I_060 | geometric IL_5J7L_301 | ||
| IL_5U4I_061 | Single bulged A geometric IL_5WWT_001 | ||
| IL_5U4I_062 | UAA/GAN variation geometric IL_6CZR_170 | ||
| IL_5U4I_063 | homologous IL_7RQB_064 | ||
| IL_5U4I_064 | Isolated tWW turn homologous IL_7RQB_065 | ||
| IL_5U4I_065 | Major groove platform; stack outside cWW geometric IL_7RQB_066 | ||
| IL_5U4I_066 | Intercalated tWH homologous IL_7RQB_067 | ||
| IL_5U4I_067 | tSH-tSH-tHH-tHS geometric IL_7RQB_068 | ||
| IL_5U4I_068 | NA | ||
| IL_5U4I_069 | NA | ||
| IL_5U4I_070 | Single bulged A homologous IL_7RQB_069 | ||
| IL_5U4I_071 | Kink-turn related homologous IL_7RQB_070 | ||
| IL_5U4I_072 | Major groove outside cWW, minor groove, intercalation pocket homologous IL_7RQB_071 | ||
| IL_5U4I_073 | Major groove outside cWW, minor groove, intercalation pocket homologous IL_7RQB_072 | ||
| IL_5U4I_074 | Major groove minor groove platform; mini C-loop geometric IL_5J7L_316 | ||
| IL_5U4I_075 | NA | ||
| IL_5U4I_076 | Multiple bulged bases geometric IL_7RQB_076 | ||
| IL_5U4I_077 | geometric IL_7A0S_072 | ||
| IL_5U4I_078 | Major groove platform homologous IL_7RQB_078 | ||
| IL_5U4I_079 | geometric IL_5J7L_321 | ||
| IL_5U4I_080 | geometric IL_6OL3_002 | ||
| IL_5U4I_081 | geometric IL_5H1K_001 | ||
| IL_5U4I_082 | Minor groove platform geometric IL_5J7L_324 | ||
| IL_5U4I_083 | Isolated tHS basepair with bulges homologous IL_7RQB_082 | ||
| IL_5U4I_084 | homologous IL_7RQB_083 | ||
| IL_5U4I_085 | geometric IL_5UNE_006 | ||
| IL_5U4I_086 | geometric IL_5TBW_121 | ||
| IL_5U4I_087 | NA | ||
| IL_5U4I_088 | NA | ||
| IL_5U4I_089 | Kink-turn geometric IL_5J7L_330 | ||
| IL_5U4I_090 | Tandem non-canonical cWW pairs geometric IL_4V88_429 | ||
| IL_5U4I_091 | Double sheared homologous IL_7RQB_089 | ||
| IL_5U4I_092 | NA | ||
| IL_5U4I_093 | NA | ||
| IL_5U4I_094 | Major groove platform with extra pair geometric IL_7RQB_093 | ||
| IL_5U4I_095 | Major groove minor groove platform with extra cWW homologous IL_7RQB_094 | ||
| IL_5U4I_096 | Triple sheared homologous IL_7RQB_095 | ||
| IL_5U4I_097 | Major groove platform with extra pair geometric IL_7RQB_093 | ||
| IL_5U4I_098 | Isolated non-canonical cWW with bulges geometric IL_5J7L_340 | ||
| IL_5U4I_099 | Multiple bulged bases homologous IL_7RQB_098 | ||
| IL_5U4I_100 | Minor groove platform with intercalation homologous IL_7RQB_099 | ||
| IL_5U4I_101 | homologous IL_7RQB_100 | ||
| IL_5U4I_102 | Single bulged A homologous IL_7RQB_101 | ||
| IL_5U4I_103 | tSH-tHS-tHW homologous IL_7RQB_102 | ||
| IL_5U4I_104 | 7x6 Sarcin-Ricin; G-bulge geometric IL_4V9F_106 | ||
| IL_5U4I_105 | C-loop homologous IL_7RQB_104 | ||
| IL_5U4I_106 | homologous IL_7RQB_105 | ||
| IL_5U4I_107 | Multiple bulged bases homologous IL_7RQB_106 | ||
| IL_5U4I_108 | UAA/GAN with extra cWW homologous IL_7RQB_107 | ||
| IL_5U4I_109 | geometric IL_5J7L_351 | ||
| IL_5U4I_110 | Isolated non-canonical cWW with bulges geometric IL_1U6B_001 | ||
| IL_5U4I_111 | Multiple bulged bases with non-canonical cWW geometric IL_5J7L_353 | ||
| IL_5U4I_112 | NA |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/B/10:16, 1/B/68:70, 1/B/106:110 | NA | NA | ||
| 1/a/46:47, 1/a/361:367, 1/a/393:395 | NA | NA | ||
| 1/a/586:588, 1/a/651:654, 1/a/754:755 | NA | NA | ||
| 1/a/672:673, 1/a/717:725, 1/a/732:734 | NA | NA | ||
| 1/a/826:829, 1/a/857:861, 1/a/868:874 | NA | NA | ||
| 1/a/936:939, 1/a/1344:1350, 1/a/1372:1379 | NA | NA | ||
| 1/a/943:946, 1/a/1235:1237, 1/a/1337:1340 | NA | NA | ||
| 1/a/955:962, 1/a/973:984, 1/a/1221:1225 | NA | NA | ||
| 1/a/990:993, 1/a/1045:1047, 1/a/1210:1215 | NA | NA | ||
| 1/a/1063:1068, 1/a/1107:1113, 1/a/1187:1193 | NA | NA | ||
| 1/a/1073:1074, 1/a/1083:1087, 1/a/1098:1102 | NA | NA | ||
| 1/a/1116:1118, 1/a/1155:1158, 1/a/1181:1184 | NA | NA | ||
| 1/a/1237:1241, 1/a/1296:1303, 1/a/1334:1337 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5U4I_001 | NA | ||
| J3_5U4I_002 | homologous J3_7RQB_002 | ||
| J3_5U4I_003 | NA | ||
| J3_5U4I_004 | homologous J3_7RQB_005 | ||
| J3_5U4I_005 | NA | ||
| J3_5U4I_006 | homologous J3_7RQB_007 | ||
| J3_5U4I_007 | homologous J3_7RQB_008 | ||
| J3_5U4I_008 | homologous J3_7RQB_009 | ||
| J3_5U4I_009 | homologous J3_7RQB_010 | ||
| J3_5U4I_010 | NA | ||
| J3_5U4I_011 | NA | ||
| J3_5U4I_012 | homologous J3_7RQB_012 | ||
| J3_5U4I_013 | NA | ||
| J3_5U4I_014 | NA |
Coloring options: