2UXD Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_2UXD_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_2UXD_002 | 1/A/80:89 | No text annotation Not in a motif group | homologous HL_4LFB_002 HL_30784.2 | |
| HL_2UXD_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_2UXD_005 | 1/A/201:216 | No text annotation Not in a motif group | homologous HL_4LFB_005 HL_56691.2 | |
| HL_2UXD_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_4LFB_006 HL_69023.2 | |
| HL_2UXD_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_2UXD_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_4LFB_008 HL_81205.2 | |
| HL_2UXD_009 | 1/A/342:347 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
| HL_2UXD_010 | 1/A/379:384 | GNRA Not in a motif group | homologous HL_4LFB_010 HL_42097.1 | |
| HL_2UXD_013 | 1/A/522:527 | No text annotation Not in a motif group | geometric HL_5J7L_143 HL_75407.1 | |
| HL_2UXD_014 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
| HL_2UXD_015 | 1/A/689:698 | No text annotation Not in a motif group | homologous HL_5J7L_015 HL_12326.1 | |
| HL_2UXD_016 | 1/A/726:731 | Other HL Not in a motif group | homologous HL_4LFB_016 HL_87030.2 | |
| HL_2UXD_017 | 1/A/786:796 | No text annotation Not in a motif group | homologous HL_4LFB_017 HL_12326.1 | |
| HL_2UXD_019 | 1/A/862:867 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_2UXD_020 | 1/A/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_2UXD_021 | 1/A/963:972 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_2UXD_022 | 1/A/1012:1017 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_2UXD_023 | 1/A/1029:1032 | No text annotation Not in a motif group | geometric HL_7A0S_056 HL_84085.2 | |
| HL_2UXD_024 | 1/A/1076:1081 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_2UXD_025 | 1/A/1089:1096 | No text annotation Not in a motif group | homologous HL_5J7L_024 HL_71554.2 | |
| HL_2UXD_028 | 1/A/1265:1270 | Other HL Not in a motif group | homologous HL_4LFB_028 HL_42097.1 | |
| HL_2UXD_029 | 1/A/1314:1323 | No text annotation Not in a motif group | homologous HL_4LFB_029 HL_89380.2 | |
| HL_2UXD_030 | 1/A/1356:1366 | No text annotation Not in a motif group | ||
| HL_2UXD_032 | 1/A/1515:1520 | No text annotation Not in a motif group | homologous HL_4LFB_032 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_2UXD_004 | No text annotation | ||
| HL_2UXD_011 | UNCG | ||
| HL_2UXD_012 | No text annotation | ||
| HL_2UXD_018 | No text annotation | ||
| HL_2UXD_026 | No text annotation | ||
| HL_2UXD_027 | No text annotation | ||
| HL_2UXD_031 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_2UXD_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_4LFB_001 IL_00225.2 | |
| IL_2UXD_002 | 1/A/44:45, 1/A/396:398 | Single bulged A Not in a motif group | homologous IL_4LFB_002 IL_37497.2 | |
| IL_2UXD_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | homologous IL_4LFB_003 IL_11178.1 | |
| IL_2UXD_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_2UXD_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_005 IL_76389.1 | |
| IL_2UXD_006 | 1/A/67:69, 1/A/99:102 | No text annotation Not in a motif group | homologous IL_4LFB_006 IL_95997.1 | |
| IL_2UXD_009 | 1/A/132:136, 1/A/227:230 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_2UXD_010 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4LFB_009 IL_39753.1 | |
| IL_2UXD_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4LFB_011 IL_45067.2 | |
| IL_2UXD_012 | 1/A/249:252, 1/A/274:275 | No text annotation Not in a motif group | homologous IL_4LFB_012 IL_48100.2 | |
| IL_2UXD_013 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_2UXD_014 | 1/A/367:369, 1/A/392:393 | Single bulged U Not in a motif group | homologous IL_4LFB_014 IL_83039.13 | |
| IL_2UXD_015 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | geometric IL_4LFB_015 IL_75255.1 | |
| IL_2UXD_016 | 1/A/375:376, 1/A/387:389 | Single bulged G Not in a motif group | homologous IL_5J7L_019 IL_00225.2 | |
| IL_2UXD_017 | 1/A/408:416, 1/A/427:434 | No text annotation Not in a motif group | ||
| IL_2UXD_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_4LFB_018 IL_88269.3 | |
| IL_2UXD_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4LFB_020 IL_15861.7 | |
| IL_2UXD_021 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_2UXD_022 | 1/A/569:575, 1/A/880:881 | No text annotation Not in a motif group | homologous IL_4LFB_022 IL_69996.1 | |
| IL_2UXD_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_023 IL_17136.1 | |
| IL_2UXD_024 | 1/A/594:596, 1/A/644:645 | Major groove platform Not in a motif group | homologous IL_4LFB_024 IL_27635.1 | |
| IL_2UXD_025 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_4LFB_025 IL_09061.6 | |
| IL_2UXD_026 | 1/A/605:612, 1/A/628:633 | No text annotation Not in a motif group | homologous IL_4LFB_026 IL_78349.1 | |
| IL_2UXD_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4LFB_027 IL_50694.2 | |
| IL_2UXD_028 | 1/A/657:658, 1/A/747:749 | Major groove platform Not in a motif group | homologous IL_4LFB_028 IL_27635.1 | |
| IL_2UXD_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4LFB_029 IL_71110.1 | |
| IL_2UXD_030 | 1/A/673:678, 1/A/712:717 | No text annotation Not in a motif group | homologous IL_4LFB_030 IL_04668.1 | |
| IL_2UXD_031 | 1/A/683:688, 1/A/699:707 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_2UXD_032 | 1/A/774:778, 1/A/804:805 | Left turn Not in a motif group | homologous IL_4LFB_032 IL_29346.1 | |
| IL_2UXD_033 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_033 IL_17136.1 | |
| IL_2UXD_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4LFB_034 IL_24606.2 | |
| IL_2UXD_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A Not in a motif group | homologous IL_4LFB_035 IL_37497.2 | |
| IL_2UXD_036 | 1/A/925:927, 1/A/1390:1391 | Single bulged G Not in a motif group | homologous IL_4LFB_036 IL_00225.2 | |
| IL_2UXD_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform Not in a motif group | homologous IL_5J7L_041 IL_47078.1 | |
| IL_2UXD_038 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform Not in a motif group | homologous IL_4LFB_038 IL_42622.2 | |
| IL_2UXD_040 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U Not in a motif group | homologous IL_4LFB_042 IL_83039.13 | |
| IL_2UXD_041 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_2UXD_042 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform Not in a motif group | homologous IL_5J7L_048 IL_93353.1 | |
| IL_2UXD_043 | 1/A/1060:1063, 1/A/1193:1197 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_1D4R_001 IL_30621.2 | |
| IL_2UXD_044 | 1/A/1122:1128, 1/A/1143:1151 | No text annotation Not in a motif group | ||
| IL_2UXD_045 | 1/A/1128:1132, 1/A/1142:1143 | Minor groove platform Not in a motif group | geometric IL_4LFB_049 IL_15052.1 | |
| IL_2UXD_046 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation Not in a motif group | geometric IL_4LFB_050 IL_42032.1 | |
| IL_2UXD_047 | 1/A/1246:1253, 1/A/1284:1291 | No text annotation Not in a motif group | ||
| IL_2UXD_048 | 1/A/1255:1258, 1/A/1277:1282 | No text annotation Not in a motif group | homologous IL_4LFB_052 IL_84205.1 | |
| IL_2UXD_051 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation Not in a motif group | homologous IL_4LFB_055 IL_19954.2 | |
| IL_2UXD_052 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation Not in a motif group | geometric IL_4V88_463 IL_36143.3 | |
| IL_2UXD_053 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_2UXD_054 | 1/A/1405:1407, 1/A/1494:1496 | No text annotation Not in a motif group | geometric IL_4V9F_023 IL_95997.1 | |
| IL_2UXD_055 | 1/A/1407:1409, 1/A/1491:1494 | Decoding loop related Not in a motif group | geometric IL_3C3Z_002 IL_64417.1 | |
| IL_2UXD_056 | 1/A/1412:1414, 1/A/1486:1488 | No text annotation Not in a motif group | homologous IL_4LFB_059 IL_95997.1 | |
| IL_2UXD_057 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared Not in a motif group | homologous IL_4LFB_060 IL_09705.9 | |
| IL_2UXD_058 | 1/A/1431:1435, 1/A/1466:1469 | UAA/GAN variation Not in a motif group | geometric IL_4LFB_062 IL_07235.1 | |
| IL_2UXD_059 | 1/A/1435:1437, 1/A/1464:1466 | No text annotation Not in a motif group | homologous IL_4LFB_063 IL_95997.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_2UXD_007 | No text annotation | ||
| IL_2UXD_008 | Multiple bulged bases | ||
| IL_2UXD_019 | No text annotation | ||
| IL_2UXD_039 | No text annotation | ||
| IL_2UXD_049 | Not an internal loop | ||
| IL_2UXD_050 | Minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_2UXD_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation Not in a motif group | homologous J3_4LFB_001 NA | |
| J3_2UXD_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_2UXD_003 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation Not in a motif group | homologous J3_4LFB_003 NA | |
| J3_2UXD_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation Not in a motif group | ||
| J3_2UXD_005 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation Not in a motif group | ||
| J3_2UXD_006 | 1/A/1002:1006A, 1/A/1023:1027, 1/A/1034:1038 | No text annotation Not in a motif group | ||
| J3_2UXD_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation Not in a motif group | ||
| J3_2UXD_008 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation Not in a motif group | homologous J3_4LFB_008 NA | |
| J3_2UXD_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation Not in a motif group |
Problematic loops
No problematic loops
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