1N36 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_1N36_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_1N36_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_1N36_004 | 1/A/190A:190H | No text annotation Not in a motif group | ||
| HL_1N36_005 | 1/A/201:216 | No text annotation Not in a motif group | homologous HL_4LFB_005 HL_56691.2 | |
| HL_1N36_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_4LFB_006 HL_69023.2 | |
| HL_1N36_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_1N36_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_4LFB_008 HL_81205.2 | |
| HL_1N36_010 | 1/A/375:389 | No text annotation Not in a motif group | geometric HL_5J7L_022 HL_06285.2 | |
| HL_1N36_011 | 1/A/416:427 | No text annotation Not in a motif group | ||
| HL_1N36_012 | 1/A/458:474 | No text annotation Not in a motif group | ||
| HL_1N36_013 | 1/A/522:527 | No text annotation Not in a motif group | geometric HL_4WF9_003 HL_75407.1 | |
| HL_1N36_014 | 1/A/616:624 | No text annotation Not in a motif group | ||
| HL_1N36_015 | 1/A/689:698 | No text annotation Not in a motif group | homologous HL_5J7L_015 HL_12326.1 | |
| HL_1N36_016 | 1/A/726:731 | Other HL Not in a motif group | homologous HL_4LFB_016 HL_87030.2 | |
| HL_1N36_017 | 1/A/786:796 | No text annotation Not in a motif group | homologous HL_4LFB_017 HL_12326.1 | |
| HL_1N36_018 | 1/A/837:849 | No text annotation Not in a motif group | homologous HL_5J7L_018 HL_34168.2 | |
| HL_1N36_019 | 1/A/862:867 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_1N36_020 | 1/A/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_1N36_021 | 1/A/963:972 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_1N36_022 | 1/A/1012:1017 | GNRA Not in a motif group | geometric HL_4LFB_022 HL_42097.1 | |
| HL_1N36_024 | 1/A/1076:1081 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_1N36_025 | 1/A/1089:1096 | No text annotation Not in a motif group | homologous HL_5J7L_024 HL_71554.2 | |
| HL_1N36_026 | 1/A/1134:1140 | No text annotation Not in a motif group | geometric HL_4V9F_005 HL_03562.2 | |
| HL_1N36_027 | 1/A/1164:1172 | No text annotation Not in a motif group | geometric HL_7A0S_056 HL_84085.2 | |
| HL_1N36_029 | 1/A/1314:1323 | No text annotation Not in a motif group | homologous HL_5J7L_028 HL_89380.2 | |
| HL_1N36_031 | 1/A/1449:1454 | UNCG Not in a motif group | homologous HL_4LFB_031 HL_03562.2 | |
| HL_1N36_032 | 1/A/1515:1520 | No text annotation Not in a motif group | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_1N36_002 | tRNA anticodon loop | ||
| HL_1N36_009 | No text annotation | ||
| HL_1N36_023 | No text annotation | ||
| HL_1N36_028 | Other HL | ||
| HL_1N36_030 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_1N36_001 | 1/A/28:32, 1/A/552:555 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_1D4R_001 IL_30621.2 | |
| IL_1N36_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_1N36_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_1N36_004 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases Not in a motif group | homologous IL_5J7L_005 IL_76389.1 | |
| IL_1N36_005 | 1/A/67:69, 1/A/99:102 | No text annotation Not in a motif group | homologous IL_4LFB_006 IL_95997.1 | |
| IL_1N36_006 | 1/A/69:76, 1/A/93:99 | No text annotation Not in a motif group | geometric IL_6O5F_001 IL_04668.1 | |
| IL_1N36_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_007 IL_16396.2 | |
| IL_1N36_008 | 1/A/132:136, 1/A/227:230 | No text annotation Not in a motif group | geometric IL_4LFB_008 IL_58764.3 | |
| IL_1N36_010 | 1/A/147:153, 1/A/168:175 | No text annotation Not in a motif group | ||
| IL_1N36_011 | 1/A/186:188, 1/A/190K:191 | No text annotation Not in a motif group | homologous IL_4LFB_010 IL_95997.1 | |
| IL_1N36_012 | 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_1N36_013 | 1/A/249:253, 1/A/273:275 | No text annotation Not in a motif group | homologous IL_6CZR_124 IL_38684.1 | |
| IL_1N36_015 | 1/A/292:294, 1/A/303:308 | No text annotation Not in a motif group | ||
| IL_1N36_016 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | homologous IL_4LFB_015 IL_75255.1 | |
| IL_1N36_017 | 1/A/409:416, 1/A/427:433 | No text annotation Not in a motif group | homologous IL_4LFB_017 IL_28026.1 | |
| IL_1N36_018 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4LFB_020 IL_15861.7 | |
| IL_1N36_019 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_1N36_020 | 1/A/569:575, 1/A/880:881 | No text annotation Not in a motif group | ||
| IL_1N36_021 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_023 IL_17136.1 | |
| IL_1N36_023 | 1/A/594:596, 1/A/644:645 | Major groove platform Not in a motif group | homologous IL_4LFB_024 IL_27635.1 | |
| IL_1N36_024 | 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_1N36_025 | 1/A/603:605, 1/A/633:635 | No text annotation Not in a motif group | geometric IL_4KR9_002 IL_51629.2 | |
| IL_1N36_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_1N36_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_5J7L_031 IL_50694.2 | |
| IL_1N36_028 | 1/A/656:658, 1/A/747:750 | No text annotation Not in a motif group | geometric IL_6CZR_136 IL_05564.2 | |
| IL_1N36_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_1N36_030 | 1/A/673:679, 1/A/711:717 | No text annotation Not in a motif group | ||
| IL_1N36_031 | 1/A/683:688, 1/A/699:707 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_1N36_032 | 1/A/774:778, 1/A/804:805 | Left turn Not in a motif group | homologous IL_4LFB_032 IL_29346.1 | |
| IL_1N36_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_1N36_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_1N36_035 | 1/A/921:924, 1/A/1392:1396 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5EW4_001 IL_30621.2 | |
| IL_1N36_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_1N36_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_1N36_038 | 1/A/949:951, 1/A/1230:1232 | No text annotation Not in a motif group | geometric IL_1Z7F_002 IL_95997.1 | |
| IL_1N36_039 | 1/A/952:954, 1/A/1226:1229 | Minor groove platform with extra cWW Not in a motif group | geometric IL_4WF9_003 IL_65006.1 | |
| IL_1N36_040 | 1/A/1009:1012, 1/A/1017:1020 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_6JDV_002 IL_30621.2 | |
| IL_1N36_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_1N36_042 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform Not in a motif group | geometric IL_5J7L_048 IL_93353.1 | |
| IL_1N36_043 | 1/A/1058:1063, 1/A/1193:1199 | Tandem non-canonical cWW pairs with near WC pairs Not in a motif group | geometric IL_4EYA_005 IL_04668.1 | |
| IL_1N36_044 | 1/A/1120:1128, 1/A/1143:1153 | No text annotation Not in a motif group | ||
| IL_1N36_045 | 1/A/1128:1134, 1/A/1140:1143 | No text annotation Not in a motif group | ||
| IL_1N36_048 | 1/A/1246:1253, 1/A/1284:1291 | No text annotation Not in a motif group | ||
| IL_1N36_049 | 1/A/1253:1258, 1/A/1277:1284 | No text annotation Not in a motif group | ||
| IL_1N36_050 | 1/A/1258:1262, 1/A/1273:1277 | Triple sheared Not in a motif group | geometric IL_4V9F_085 IL_56467.8 | |
| IL_1N36_052 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation Not in a motif group | geometric IL_4LFB_055 IL_19954.2 | |
| IL_1N36_054 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation Not in a motif group | homologous IL_4LFB_056 NA | |
| IL_1N36_055 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation Not in a motif group | ||
| IL_1N36_056 | 1/A/1405:1407, 1/A/1494:1496 | No text annotation Not in a motif group | geometric IL_5MWI_001 IL_95997.1 | |
| IL_1N36_057 | 1/A/1407:1409, 1/A/1491:1494 | No text annotation Not in a motif group | ||
| IL_1N36_059 | 1/A/1412:1414, 1/A/1486:1488 | No text annotation Not in a motif group | homologous IL_5J7L_061 IL_95997.1 | |
| IL_1N36_060 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared Not in a motif group | geometric IL_5BTP_004 IL_09705.9 | |
| IL_1N36_061 | 1/A/1419:1422, 1/A/1479:1481 | No text annotation Not in a motif group | ||
| IL_1N36_062 | 1/A/1422:1423, 1/A/1477:1479 | Single stack bend Not in a motif group | geometric IL_4WF9_007 IL_76488.2 | |
| IL_1N36_064 | 1/A/1431:1435, 1/A/1466:1469 | UAA/GAN variation Not in a motif group | geometric IL_4LFB_062 IL_07235.1 | |
| IL_1N36_065 | 1/A/1435:1438, 1/A/1463:1466 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4K27_001 IL_30621.2 | |
| IL_1N36_066 | 1/A/1440:1447, 1/A/1459:1461 | No text annotation Not in a motif group | homologous IL_4LFB_064 IL_92788.2 | |
| IL_1N36_067 | 1/A/1512:1514, 1/A/1521:1523 | No text annotation Not in a motif group | geometric IL_3SZX_002 IL_95997.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_1N36_009 | CA cWW | ||
| IL_1N36_014 | Isolated cWH basepair | ||
| IL_1N36_022 | No text annotation | ||
| IL_1N36_046 | Tandem non-canonical cWW pairs | ||
| IL_1N36_047 | Tandem non-canonical cWW pairs | ||
| IL_1N36_051 | Tandem non-canonical cWW pairs | ||
| IL_1N36_053 | No text annotation | ||
| IL_1N36_058 | No text annotation | ||
| IL_1N36_063 | UG cWW |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_1N36_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_1N36_002 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation Not in a motif group | ||
| J3_1N36_003 | 1/A/955:962, 1/A/973:985, 1/A/1220:1225 | No text annotation Not in a motif group | ||
| J3_1N36_004 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation Not in a motif group | ||
| J3_1N36_005 | 1/A/1115:1118, 1/A/1155:1161, 1/A/1175:1185 | No text annotation Not in a motif group | ||
| J3_1N36_006 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation Not in a motif group | homologous J3_4LFB_009 NA |
Problematic loops
No problematic loops
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