4JYA Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_4JYA_001 | 1/A/13:23 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_4JYA_002 | 1/A/78:86 | No text annotation Not in a motif group | ||
| HL_4JYA_003 | 1/A/153:158 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_4JYA_004 | 1/A/187:192 | No text annotation Not in a motif group | homologous HL_4LFB_004 HL_10278.1 | |
| HL_4JYA_005 | 1/A/208:212 | No text annotation Not in a motif group | ||
| HL_4JYA_006 | 1/A/255:263 | No text annotation Not in a motif group | homologous HL_4LFB_006 HL_69023.2 | |
| HL_4JYA_007 | 1/A/292:297 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_4JYA_008 | 1/A/316:329 | No text annotation Not in a motif group | homologous HL_4LFB_008 HL_81205.2 | |
| HL_4JYA_009 | 1/A/338:343 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
| HL_4JYA_010 | 1/A/375:380 | GNRA Not in a motif group | homologous HL_4LFB_010 HL_42097.1 | |
| HL_4JYA_011 | 1/A/415:420 | No text annotation Not in a motif group | homologous HL_6CZR_082 HL_03562.2 | |
| HL_4JYA_012 | 1/A/453:459 | No text annotation Not in a motif group | homologous HL_4LFB_012 HL_43656.2 | |
| HL_4JYA_013 | 1/A/506:511 | No text annotation Not in a motif group | geometric HL_2Y8W_001 HL_01057.1 | |
| HL_4JYA_014 | 1/A/601:607 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
| HL_4JYA_015 | 1/A/673:682 | No text annotation Not in a motif group | homologous HL_4LFB_015 HL_12326.1 | |
| HL_4JYA_016 | 1/A/710:715 | Other HL Not in a motif group | homologous HL_4LFB_016 HL_87030.2 | |
| HL_4JYA_017 | 1/A/770:780 | No text annotation Not in a motif group | homologous HL_4LFB_017 HL_12326.1 | |
| HL_4JYA_018 | 1/A/822:826 | No text annotation Not in a motif group | homologous HL_4LFB_018 HL_38927.2 | |
| HL_4JYA_019 | 1/A/840:845 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_4JYA_020 | 1/A/875:880 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_4JYA_021 | 1/A/941:950 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_4JYA_022 | 1/A/991:996 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_4JYA_023 | 1/A/1059:1064 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_4JYA_024 | 1/A/1072:1079 | No text annotation Not in a motif group | homologous HL_4LFB_025 HL_71554.2 | |
| HL_4JYA_025 | 1/A/1111:1126 | No text annotation Not in a motif group | ||
| HL_4JYA_026 | 1/A/1148:1153 | GNRA Not in a motif group | homologous HL_4LFB_027 HL_42097.1 | |
| HL_4JYA_027 | 1/A/1247:1252 | Other HL Not in a motif group | homologous HL_4LFB_028 HL_42097.1 | |
| HL_4JYA_028 | 1/A/1296:1305 | No text annotation Not in a motif group | homologous HL_4LFB_029 HL_89380.2 | |
| HL_4JYA_029 | 1/A/1338:1349 | No text annotation Not in a motif group | ||
| HL_4JYA_030 | 1/A/1430:1435 | UNCG Not in a motif group | homologous HL_4LFB_031 HL_03562.2 | |
| HL_4JYA_031 | 1/A/1493:1498 | 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_4JYA_001 | 1/A/31:33, 1/A/536:537 | Single bulged G Not in a motif group | homologous IL_4LFB_001 IL_00225.2 | |
| IL_4JYA_002 | 1/A/45:46, 1/A/392:394 | Single bulged A Not in a motif group | homologous IL_4LFB_002 IL_37497.2 | |
| IL_4JYA_003 | 1/A/48:53, 1/A/355:357 | No text annotation Not in a motif group | homologous IL_4LFB_003 IL_11178.1 | |
| IL_4JYA_004 | 1/A/55:57, 1/A/352:353 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_4JYA_005 | 1/A/64:67, 1/A/97:98 | Multiple bulged bases Not in a motif group | homologous IL_5J7L_005 IL_76389.1 | |
| IL_4JYA_006 | 1/A/68:70, 1/A/94:96 | No text annotation Not in a motif group | homologous IL_4LFB_006 IL_95997.1 | |
| IL_4JYA_007 | 1/A/76:78, 1/A/86:88 | No text annotation Not in a motif group | geometric IL_4E48_005 IL_95997.1 | |
| IL_4JYA_008 | 1/A/123:126, 1/A/227:228 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_007 IL_16396.2 | |
| IL_4JYA_009 | 1/A/127:131, 1/A/223:226 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_4JYA_010 | 1/A/143:148, 1/A/163:169 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4LFB_009 IL_39753.1 | |
| IL_4JYA_011 | 1/A/181:183, 1/A/196:198 | No text annotation Not in a motif group | homologous IL_4LFB_010 IL_95997.1 | |
| IL_4JYA_012 | 1/A/238:243, 1/A/273:280 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4LFB_011 IL_45067.2 | |
| IL_4JYA_013 | 1/A/245:248, 1/A/270:271 | No text annotation Not in a motif group | homologous IL_4LFB_012 IL_48100.2 | |
| IL_4JYA_014 | 1/A/288:289, 1/A/300:304 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_4JYA_015 | 1/A/363:365, 1/A/388:389 | Single bulged U Not in a motif group | homologous IL_4LFB_014 IL_83039.13 | |
| IL_4JYA_016 | 1/A/367:371, 1/A/385:386 | C-loop Not in a motif group | geometric IL_5J7L_018 IL_75255.1 | |
| IL_4JYA_017 | 1/A/371:372, 1/A/383:385 | Single bulged G Not in a motif group | homologous IL_4LFB_016 IL_00225.2 | |
| IL_4JYA_018 | 1/A/405:412, 1/A/423:429 | No text annotation Not in a motif group | homologous IL_4LFB_017 IL_28026.1 | |
| IL_4JYA_019 | 1/A/441:445, 1/A/468:473 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_4LFB_018 IL_88269.3 | |
| IL_4JYA_020 | 1/A/445:450, 1/A/462:468 | No text annotation Not in a motif group | homologous IL_4LFB_019 IL_11882.1 | |
| IL_4JYA_021 | 1/A/488:495, 1/A/524:525 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4LFB_020 IL_15861.7 | |
| IL_4JYA_022 | 1/A/499:505, 1/A/512:520 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_4JYA_023 | 1/A/553:559, 1/A/858:859 | No text annotation Not in a motif group | homologous IL_4LFB_022 IL_69996.1 | |
| IL_4JYA_024 | 1/A/564:568, 1/A/741:745 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_023 IL_17136.1 | |
| IL_4JYA_025 | 1/A/578:580, 1/A/628:629 | Major groove platform Not in a motif group | homologous IL_4LFB_024 IL_27635.1 | |
| IL_4JYA_026 | 1/A/581:582, 1/A/624:627 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_4LFB_025 IL_09061.6 | |
| IL_4JYA_027 | 1/A/589:596, 1/A/612:617 | No text annotation Not in a motif group | homologous IL_4LFB_026 IL_78349.1 | |
| IL_4JYA_028 | 1/A/638:639, 1/A/735:738 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_5J7L_031 IL_50694.2 | |
| IL_4JYA_029 | 1/A/641:642, 1/A/731:733 | Major groove platform Not in a motif group | homologous IL_4LFB_028 IL_27635.1 | |
| IL_4JYA_030 | 1/A/646:650, 1/A/724:727 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4LFB_029 IL_71110.1 | |
| IL_4JYA_031 | 1/A/657:662, 1/A/696:701 | No text annotation Not in a motif group | homologous IL_4LFB_030 IL_04668.1 | |
| IL_4JYA_032 | 1/A/667:672, 1/A/683:691 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_4JYA_033 | 1/A/758:762, 1/A/788:789 | Left turn Not in a motif group | homologous IL_4LFB_032 IL_29346.1 | |
| IL_4JYA_034 | 1/A/763:767, 1/A/783:787 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_033 IL_17136.1 | |
| IL_4JYA_035 | 1/A/865:872, 1/A/883:888 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4LFB_034 IL_24606.2 | |
| IL_4JYA_036 | 1/A/900:901, 1/A/1376:1378 | Single bulged A Not in a motif group | homologous IL_4LFB_035 IL_37497.2 | |
| IL_4JYA_037 | 1/A/903:905, 1/A/1373:1374 | Single bulged G Not in a motif group | homologous IL_4LFB_036 IL_00225.2 | |
| IL_4JYA_038 | 1/A/911:913, 1/A/1363:1367 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_4JYA_039 | 1/A/931:932, 1/A/1208:1210 | Minor groove platform Not in a motif group | homologous IL_4LFB_038 IL_42622.2 | |
| IL_4JYA_040 | 1/A/971:975, 1/A/1027:1028 | Minor groove platform Not in a motif group | homologous IL_4LFB_039 IL_47078.1 | |
| IL_4JYA_041 | 1/A/978:985, 1/A/1002:1024 | No text annotation Not in a motif group | ||
| IL_4JYA_042 | 1/A/986:988, 1/A/999:1001 | No text annotation Not in a motif group | geometric IL_4V88_417 IL_95997.1 | |
| IL_4JYA_043 | 1/A/1031:1033, 1/A/1190:1191 | Single bulged U Not in a motif group | homologous IL_4LFB_042 IL_83039.13 | |
| IL_4JYA_044 | 1/A/1035:1039, 1/A/1186:1188 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_4JYA_045 | 1/A/1040:1041, 1/A/1181:1185 | Minor groove platform Not in a motif group | homologous IL_5J7L_048 IL_93353.1 | |
| IL_4JYA_046 | 1/A/1043:1044, 1/A/1177:1179 | Single bulged U Not in a motif group | geometric IL_2PN3_003 IL_83039.13 | |
| IL_4JYA_047 | 1/A/1044:1046, 1/A/1175:1177 | No text annotation Not in a motif group | homologous IL_4LFB_047 IL_95997.1 | |
| IL_4JYA_048 | 1/A/1106:1111, 1/A/1126:1133 | No text annotation Not in a motif group | ||
| IL_4JYA_049 | 1/A/1141:1144, 1/A/1157:1163 | No text annotation Not in a motif group | homologous IL_5J7L_053 IL_42032.1 | |
| IL_4JYA_050 | 1/A/1228:1235, 1/A/1266:1273 | No text annotation Not in a motif group | ||
| IL_4JYA_051 | 1/A/1237:1240, 1/A/1259:1264 | No text annotation Not in a motif group | homologous IL_6CZR_161 IL_75461.4 | |
| IL_4JYA_052 | 1/A/1241:1242, 1/A/1256:1258 | Not an internal loop Not in a motif group | homologous IL_4LFB_053 IL_93353.1 | |
| IL_4JYA_053 | 1/A/1242:1244, 1/A/1255:1256 | Minor groove platform Not in a motif group | geometric IL_4LFB_054 IL_93353.1 | |
| IL_4JYA_054 | 1/A/1285:1290, 1/A/1311:1316 | No text annotation Not in a motif group | geometric IL_4LFB_055 IL_19954.2 | |
| IL_4JYA_055 | 1/A/1332:1336, 1/A/1351:1355 | No text annotation Not in a motif group | geometric IL_5TBW_121 IL_05145.2 | |
| IL_4JYA_056 | 1/A/1382:1384, 1/A/1479:1482 | No text annotation Not in a motif group | homologous IL_4LFB_056 NA | |
| IL_4JYA_057 | 1/A/1384:1387, 1/A/1475:1479 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_4JYA_058 | 1/A/1388:1390, 1/A/1472:1474 | No text annotation Not in a motif group | geometric IL_3GM7_005 IL_95997.1 | |
| IL_4JYA_059 | 1/A/1390:1392, 1/A/1469:1472 | Decoding loop related Not in a motif group | geometric IL_3C3Z_002 IL_64417.1 | |
| IL_4JYA_060 | 1/A/1395:1397, 1/A/1464:1466 | No text annotation Not in a motif group | homologous IL_4LFB_059 IL_95997.1 | |
| IL_4JYA_061 | 1/A/1399:1402, 1/A/1459:1462 | Double sheared Not in a motif group | homologous IL_4LFB_060 IL_09705.9 | |
| IL_4JYA_063 | 1/A/1414:1418, 1/A/1444:1447 | UAA/GAN variation Not in a motif group | geometric IL_4LFB_062 IL_07235.1 | |
| IL_4JYA_064 | 1/A/1418:1420, 1/A/1442:1444 | No text annotation Not in a motif group | homologous IL_4LFB_063 IL_95997.1 | |
| IL_4JYA_065 | 1/A/1423:1428, 1/A/1437:1439 | No text annotation Not in a motif group | homologous IL_4LFB_064 IL_92788.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_4JYA_062 | Isolated cWH basepair |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_4JYA_001 | 1/A/810:813, 1/A/835:839, 1/A/846:852 | No text annotation Not in a motif group | homologous J3_4LFB_001 NA | |
| J3_4JYA_002 | 1/A/914:917, 1/A/1326:1332, 1/A/1355:1362 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_4JYA_003 | 1/A/921:924, 1/A/1217:1219, 1/A/1319:1322 | No text annotation Not in a motif group | ||
| J3_4JYA_004 | 1/A/933:940, 1/A/951:962, 1/A/1203:1207 | No text annotation Not in a motif group | ||
| J3_4JYA_005 | 1/A/968:971, 1/A/1028:1030, 1/A/1192:1197 | No text annotation Not in a motif group | ||
| J3_4JYA_006 | 1/A/1046:1051, 1/A/1090:1096, 1/A/1169:1175 | No text annotation Not in a motif group | ||
| J3_4JYA_007 | 1/A/1099:1101, 1/A/1138:1141, 1/A/1163:1166 | No text annotation Not in a motif group | ||
| J3_4JYA_008 | 1/A/1219:1223, 1/A/1278:1285, 1/A/1316:1319 | No text annotation Not in a motif group | homologous J3_4LFB_009 NA |
Problematic loops
No problematic loops
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