3J2D Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3J2D_001 | 1/N/12:22 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_3J2D_002 | 1/N/82:87 | No text annotation Not in a motif group | ||
| HL_3J2D_003 | 1/N/158:163 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_3J2D_004 | 1/N/186:191 | GNRA Not in a motif group | homologous HL_5J7L_004 HL_42097.1 | |
| HL_3J2D_005 | 1/N/207:212 | No text annotation Not in a motif group | ||
| HL_3J2D_006 | 1/N/258:268 | No text annotation Not in a motif group | ||
| HL_3J2D_007 | 1/N/296:301 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_3J2D_008 | 1/N/320:333 | No text annotation Not in a motif group | homologous HL_5J7L_008 HL_81205.2 | |
| HL_3J2D_009 | 1/N/342:347 | No text annotation Not in a motif group | homologous HL_6CZR_080 HL_03562.2 | |
| HL_3J2D_010 | 1/N/379:384 | GNRA Not in a motif group | homologous HL_5J7L_010 HL_42097.1 | |
| HL_3J2D_011 | 1/N/419:424 | UNCG Not in a motif group | homologous HL_5J7L_011 HL_03562.2 | |
| HL_3J2D_012 | 1/N/459:472 | No text annotation Not in a motif group | ||
| HL_3J2D_013 | 1/N/522:527 | No text annotation Not in a motif group | geometric HL_4YAZ_004 HL_56691.2 | |
| HL_3J2D_014 | 1/N/617:623 | No text annotation Not in a motif group | homologous HL_5J7L_014 HL_26881.1 | |
| HL_3J2D_015 | 1/N/689:698 | No text annotation Not in a motif group | homologous HL_4LFB_015 HL_12326.1 | |
| HL_3J2D_016 | 1/N/726:731 | Other HL Not in a motif group | homologous HL_5J7L_016 HL_87030.2 | |
| HL_3J2D_017 | 1/N/786:796 | No text annotation Not in a motif group | ||
| HL_3J2D_018 | 1/N/840:846 | No text annotation Not in a motif group | ||
| HL_3J2D_019 | 1/N/862:867 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_3J2D_020 | 1/N/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_3J2D_021 | 1/N/963:972 | No text annotation Not in a motif group | ||
| HL_3J2D_022 | 1/N/1012:1017 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_3J2D_023 | 1/N/1028:1033 | No text annotation Not in a motif group | geometric HL_5U3G_001 HL_87030.2 | |
| HL_3J2D_024 | 1/N/1076:1081 | Other HL Not in a motif group | geometric HL_1P6V_001 HL_03562.2 | |
| HL_3J2D_025 | 1/N/1089:1096 | No text annotation Not in a motif group | ||
| HL_3J2D_026 | 1/N/1134:1140 | No text annotation Not in a motif group | homologous HL_5J7L_025 HL_03562.2 | |
| HL_3J2D_027 | 1/N/1165:1171 | No text annotation Not in a motif group | homologous HL_5J7L_026 HL_90617.2 | |
| HL_3J2D_028 | 1/N/1265:1270 | Other HL Not in a motif group | homologous HL_4LFB_028 HL_42097.1 | |
| HL_3J2D_029 | 1/N/1314:1323 | No text annotation Not in a motif group | homologous HL_5J7L_028 HL_89380.2 | |
| HL_3J2D_030 | 1/N/1356:1366 | No text annotation Not in a motif group | ||
| HL_3J2D_031 | 1/N/1444:1458 | No text annotation Not in a motif group | ||
| HL_3J2D_032 | 1/N/1515:1520 | No text annotation Not in a motif group | homologous HL_4LFB_032 NA |
Problematic loops
No problematic loops
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3J2D_001 | 1/N/30:32, 1/N/552:553 | Single bulged G Not in a motif group | homologous IL_6CZR_113 IL_00225.2 | |
| IL_3J2D_002 | 1/N/44:45, 1/N/396:398 | Single bulged A Not in a motif group | homologous IL_5J7L_002 IL_37497.2 | |
| IL_3J2D_003 | 1/N/54:56, 1/N/356:357 | Minor groove platform Not in a motif group | homologous IL_5J7L_004 IL_93353.1 | |
| IL_3J2D_004 | 1/N/61:63, 1/N/104:106 | No text annotation Not in a motif group | geometric IL_7A0S_026 IL_51629.2 | |
| IL_3J2D_005 | 1/N/63:66, 1/N/103:104 | Multiple bulged bases Not in a motif group | geometric IL_1FUF_002 IL_16396.2 | |
| IL_3J2D_006 | 1/N/67:69, 1/N/99:102 | Minor groove platform with extra cWW Not in a motif group | homologous IL_5J7L_006 IL_65006.1 | |
| IL_3J2D_007 | 1/N/70:73, 1/N/97:98 | Minor groove platform Not in a motif group | homologous IL_5J7L_007 IL_15052.1 | |
| IL_3J2D_008 | 1/N/75:82, 1/N/87:95 | No text annotation Not in a motif group | ||
| IL_3J2D_009 | 1/N/128:136, 1/N/227:233 | No text annotation Not in a motif group | ||
| IL_3J2D_011 | 1/N/144:146, 1/N/176:178 | Isolated cWH basepair Not in a motif group | homologous IL_5J7L_011 IL_51629.2 | |
| IL_3J2D_012 | 1/N/147:153, 1/N/168:175 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_5J7L_012 IL_80604.2 | |
| IL_3J2D_014 | 1/N/200:202, 1/N/215:217 | No text annotation Not in a motif group | geometric IL_7A0S_026 IL_51629.2 | |
| IL_3J2D_015 | 1/N/202:207, 1/N/212:215 | No text annotation Not in a motif group | ||
| IL_3J2D_016 | 1/N/242:247, 1/N/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_5J7L_014 IL_45067.2 | |
| IL_3J2D_017 | 1/N/248:253, 1/N/273:276 | No text annotation Not in a motif group | ||
| IL_3J2D_018 | 1/N/292:293, 1/N/304:308 | No text annotation Not in a motif group | ||
| IL_3J2D_019 | 1/N/367:369, 1/N/392:393 | Single bulged U Not in a motif group | geometric IL_5TBW_130 IL_83039.13 | |
| IL_3J2D_020 | 1/N/370:375, 1/N/389:391 | No text annotation Not in a motif group | ||
| IL_3J2D_021 | 1/N/375:376, 1/N/387:389 | Single bulged G Not in a motif group | homologous IL_5J7L_019 IL_00225.2 | |
| IL_3J2D_023 | 1/N/408:416, 1/N/427:434 | No text annotation Not in a motif group | ||
| IL_3J2D_024 | 1/N/440:442, 1/N/492:497 | No text annotation Not in a motif group | homologous IL_5J7L_021 IL_22248.1 | |
| IL_3J2D_025 | 1/N/446:450, 1/N/483:488 | tSH-tHW-tWW Not in a motif group | homologous IL_5J7L_022 IL_88269.3 | |
| IL_3J2D_026 | 1/N/450:455, 1/N/477:483 | No text annotation Not in a motif group | ||
| IL_3J2D_028 | 1/N/457:459, 1/N/472:475 | No text annotation Not in a motif group | ||
| IL_3J2D_029 | 1/N/504:511, 1/N/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_024 IL_15861.7 | |
| IL_3J2D_030 | 1/N/515:521, 1/N/528:536 | No text annotation Not in a motif group | ||
| IL_3J2D_031 | 1/N/569:575, 1/N/880:881 | No text annotation Not in a motif group | homologous IL_4LFB_022 IL_69996.1 | |
| IL_3J2D_032 | 1/N/580:584, 1/N/757:761 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_027 IL_17136.1 | |
| IL_3J2D_034 | 1/N/594:596, 1/N/644:645 | Major groove platform Not in a motif group | homologous IL_5J7L_028 IL_27635.1 | |
| IL_3J2D_035 | 1/N/597:598, 1/N/640:643 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_5J7L_029 IL_09061.6 | |
| IL_3J2D_037 | 1/N/605:612, 1/N/628:633 | No text annotation Not in a motif group | ||
| IL_3J2D_038 | 1/N/654:655, 1/N/751:754 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_5J7L_031 IL_50694.2 | |
| IL_3J2D_040 | 1/N/658:659, 1/N/746:748 | Single stack bend Not in a motif group | homologous IL_5J7L_032 IL_76488.2 | |
| IL_3J2D_042 | 1/N/662:666, 1/N/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4LFB_029 IL_71110.1 | |
| IL_3J2D_043 | 1/N/683:688, 1/N/699:707 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_3J2D_044 | 1/N/773:779, 1/N/803:806 | No text annotation Not in a motif group | ||
| IL_3J2D_045 | 1/N/779:783, 1/N/799:803 | tSH-tHW-tHS Not in a motif group | geometric IL_4LFB_033 IL_17136.1 | |
| IL_3J2D_046 | 1/N/831:833, 1/N/853:855 | No text annotation Not in a motif group | geometric IL_3R1D_012 IL_51629.2 | |
| IL_3J2D_047 | 1/N/887:894, 1/N/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4LFB_034 IL_24606.2 | |
| IL_3J2D_048 | 1/N/922:924, 1/N/1392:1395 | No text annotation Not in a motif group | geometric IL_4P3U_007 IL_95997.1 | |
| IL_3J2D_049 | 1/N/924:927, 1/N/1390:1392 | No text annotation Not in a motif group | ||
| IL_3J2D_050 | 1/N/933:935, 1/N/1380:1384 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_3J2D_052 | 1/N/993:997, 1/N/1044:1045 | Minor groove platform Not in a motif group | homologous IL_5J7L_043 IL_47078.1 | |
| IL_3J2D_053 | 1/N/998:999, 1/N/1041:1043 | Single stack bend Not in a motif group | homologous IL_5J7L_044 IL_76488.2 | |
| IL_3J2D_054 | 1/N/1048:1050, 1/N/1208:1209 | Single bulged U Not in a motif group | homologous IL_4LFB_042 IL_83039.13 | |
| IL_3J2D_055 | 1/N/1052:1056, 1/N/1204:1206 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_3J2D_056 | 1/N/1056:1059, 1/N/1198:1204 | No text annotation Not in a motif group | ||
| IL_3J2D_058 | 1/N/1121:1128, 1/N/1144:1152 | No text annotation Not in a motif group | ||
| IL_3J2D_059 | 1/N/1129:1132, 1/N/1142:1143 | Minor groove platform Not in a motif group | homologous IL_5J7L_052 IL_15052.1 | |
| IL_3J2D_060 | 1/N/1158:1161, 1/N/1175:1181 | No text annotation Not in a motif group | geometric IL_5J7L_053 IL_42032.1 | |
| IL_3J2D_061 | 1/N/1247:1253, 1/N/1284:1290 | No text annotation Not in a motif group | ||
| IL_3J2D_063 | 1/N/1255:1258, 1/N/1277:1282 | No text annotation Not in a motif group | geometric IL_5J7L_055 IL_75461.4 | |
| IL_3J2D_064 | 1/N/1259:1263, 1/N/1272:1276 | Triple sheared Not in a motif group | homologous IL_5J7L_056 IL_56467.8 | |
| IL_3J2D_065 | 1/N/1303:1308, 1/N/1329:1334 | No text annotation Not in a motif group | geometric IL_5J7L_057 IL_19954.2 | |
| IL_3J2D_067 | 1/N/1401:1404, 1/N/1497:1501 | No text annotation Not in a motif group | ||
| IL_3J2D_068 | 1/N/1405:1407, 1/N/1494:1496 | No text annotation Not in a motif group | geometric IL_4ZC7_001 IL_95997.1 | |
| IL_3J2D_069 | 1/N/1407:1409, 1/N/1491:1494 | No text annotation Not in a motif group | ||
| IL_3J2D_071 | 1/N/1412:1414, 1/N/1486:1488 | Isolated near basepair Not in a motif group | geometric IL_3NJ7_004 IL_52767.2 | |
| IL_3J2D_072 | 1/N/1414:1416, 1/N/1484:1486 | No text annotation Not in a motif group | geometric IL_1L9A_003 IL_51629.2 | |
| IL_3J2D_073 | 1/N/1416:1419, 1/N/1481:1484 | Double sheared Not in a motif group | homologous IL_4LFB_060 IL_09705.9 | |
| IL_3J2D_074 | 1/N/1430:1435, 1/N/1466:1470 | Triple sheared related Not in a motif group | homologous IL_5J7L_063 IL_64879.2 | |
| IL_3J2D_075 | 1/N/1437:1439, 1/N/1462:1464 | No text annotation Not in a motif group | geometric IL_6IA2_004 IL_95997.1 | |
| IL_3J2D_076 | 1/N/1439:1443, 1/N/1459:1462 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3J2D_010 | UU cWW | ||
| IL_3J2D_013 | No text annotation | ||
| IL_3J2D_022 | Isolated cWH basepair | ||
| IL_3J2D_027 | No text annotation | ||
| IL_3J2D_033 | No text annotation | ||
| IL_3J2D_036 | Stack and bulge | ||
| IL_3J2D_039 | No text annotation | ||
| IL_3J2D_041 | No text annotation | ||
| IL_3J2D_051 | No text annotation | ||
| IL_3J2D_057 | Isolated cWS basepair | ||
| IL_3J2D_062 | No text annotation | ||
| IL_3J2D_066 | UU cWW | ||
| IL_3J2D_070 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3J2D_001 | 1/N/46:52, 1/N/359:367, 1/N/393:395 | No text annotation Not in a motif group | ||
| J3_3J2D_002 | 1/N/826:829, 1/N/857:861, 1/N/868:874 | No text annotation Not in a motif group | homologous J3_5J7L_004 NA | |
| J3_3J2D_003 | 1/N/936:939, 1/N/1344:1350, 1/N/1372:1379 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_3J2D_004 | 1/N/941:947, 1/N/1234:1237, 1/N/1337:1342 | No text annotation Not in a motif group | ||
| J3_3J2D_005 | 1/N/953:962, 1/N/973:984, 1/N/1221:1228 | No text annotation Not in a motif group | ||
| J3_3J2D_006 | 1/N/990:993, 1/N/1045:1047, 1/N/1210:1215 | No text annotation Not in a motif group | ||
| J3_3J2D_007 | 1/N/1002:1006, 1/N/1023:1027, 1/N/1034:1038 | No text annotation Not in a motif group | ||
| J3_3J2D_008 | 1/N/1060:1068, 1/N/1107:1114, 1/N/1186:1197 | No text annotation Not in a motif group | ||
| J3_3J2D_009 | 1/N/1116:1118, 1/N/1155:1158, 1/N/1181:1184 | No text annotation Not in a motif group | homologous J3_5J7L_010 NA | |
| J3_3J2D_010 | 1/N/1237:1241, 1/N/1296:1303, 1/N/1334:1337 | No text annotation Not in a motif group | homologous J3_5J7L_011 NA |
Problematic loops
No problematic loops
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