5O5J Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5O5J_001 | 1/A/16:26 | No text annotation Not in a motif group | homologous HL_5J7L_001 HL_89881.2 | |
| HL_5O5J_003 | 1/A/155:160 | GNRA Not in a motif group | homologous HL_5J7L_003 HL_42097.1 | |
| HL_5O5J_004 | 1/A/191:196 | No text annotation Not in a motif group | ||
| HL_5O5J_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_4LFB_006 HL_69023.2 | |
| HL_5O5J_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_5O5J_008 | 1/A/320:333 | No text annotation Not in a motif group | ||
| HL_5O5J_009 | 1/A/342:347 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
| HL_5O5J_010 | 1/A/379:384 | GNRA Not in a motif group | homologous HL_4LFB_010 HL_42097.1 | |
| HL_5O5J_013 | 1/A/502:507 | No text annotation Not in a motif group | geometric HL_5J7L_143 HL_75407.1 | |
| HL_5O5J_014 | 1/A/597:603 | No text annotation Not in a motif group | homologous HL_5J7L_014 HL_26881.1 | |
| HL_5O5J_015 | 1/A/669:678 | No text annotation Not in a motif group | homologous HL_4LFB_015 HL_12326.1 | |
| HL_5O5J_016 | 1/A/706:711 | Other HL Not in a motif group | homologous HL_5J7L_016 HL_87030.2 | |
| HL_5O5J_017 | 1/A/766:776 | No text annotation Not in a motif group | homologous HL_5J7L_017 HL_12326.1 | |
| HL_5O5J_019 | 1/A/844:849 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_5O5J_020 | 1/A/879:884 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_5O5J_021 | 1/A/945:954 | No text annotation Not in a motif group | homologous HL_5J7L_021 NA | |
| HL_5O5J_022 | 1/A/995:1000 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_5O5J_024 | 1/A/1056:1061 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_5O5J_028 | 1/A/1246:1251 | Other HL Not in a motif group | homologous HL_4LFB_028 HL_42097.1 | |
| HL_5O5J_029 | 1/A/1296:1305 | No text annotation Not in a motif group | homologous HL_4LFB_029 HL_89380.2 | |
| HL_5O5J_030 | 1/A/1338:1349 | No text annotation Not in a motif group | homologous HL_4LFB_030 HL_96366.1 | |
| HL_5O5J_032 | 1/A/1499:1504 | No text annotation Not in a motif group | homologous HL_4LFB_032 NA | |
| HL_5O5J_033 | 1/W/31:39 | tRNA anticodon loop Not in a motif group | geometric HL_4TUE_034 HL_53597.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5O5J_002 | No text annotation | ||
| HL_5O5J_005 | No text annotation | ||
| HL_5O5J_011 | UNCG | ||
| HL_5O5J_012 | No text annotation | ||
| HL_5O5J_018 | No text annotation | ||
| HL_5O5J_023 | No text annotation | ||
| HL_5O5J_025 | No text annotation | ||
| HL_5O5J_026 | No text annotation | ||
| HL_5O5J_027 | GNRA | ||
| HL_5O5J_031 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5O5J_001 | 1/A/34:36, 1/A/532:533 | Single bulged G Not in a motif group | homologous IL_6CZR_113 IL_00225.2 | |
| IL_5O5J_002 | 1/A/48:49, 1/A/396:398 | Single bulged A Not in a motif group | homologous IL_4LFB_002 IL_37497.2 | |
| IL_5O5J_003 | 1/A/51:56, 1/A/359:361 | No text annotation Not in a motif group | geometric IL_5J7L_003 IL_11178.1 | |
| IL_5O5J_004 | 1/A/58:60, 1/A/356:357 | Minor groove platform Not in a motif group | homologous IL_5J7L_004 IL_93353.1 | |
| IL_5O5J_005 | 1/A/67:70, 1/A/99:100 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_005 IL_76389.1 | |
| IL_5O5J_006 | 1/A/71:73, 1/A/95:98 | Minor groove platform with extra cWW Not in a motif group | homologous IL_5J7L_006 IL_65006.1 | |
| IL_5O5J_009 | 1/A/125:128, 1/A/231:232 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_007 IL_16396.2 | |
| IL_5O5J_010 | 1/A/129:133, 1/A/227:230 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_5O5J_011 | 1/A/144:150, 1/A/165:172 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_5J7L_012 IL_80604.2 | |
| IL_5O5J_012 | 1/A/187:188, 1/A/199:201 | No text annotation Not in a motif group | ||
| IL_5O5J_013 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_5J7L_014 IL_45067.2 | |
| IL_5O5J_014 | 1/A/249:252, 1/A/274:275 | No text annotation Not in a motif group | homologous IL_4LFB_012 IL_48100.2 | |
| IL_5O5J_015 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_5O5J_016 | 1/A/367:369, 1/A/392:393 | Single bulged U Not in a motif group | geometric IL_4LFB_014 IL_83039.13 | |
| IL_5O5J_017 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | homologous IL_5J7L_018 IL_75255.1 | |
| IL_5O5J_018 | 1/A/375:376, 1/A/387:389 | Single bulged G Not in a motif group | geometric IL_4LFB_016 IL_00225.2 | |
| IL_5O5J_019 | 1/A/409:416, 1/A/427:433 | No text annotation Not in a motif group | homologous IL_4LFB_017 IL_28026.1 | |
| IL_5O5J_020 | 1/A/440:442, 1/A/472:477 | No text annotation Not in a motif group | homologous IL_5J7L_021 IL_22248.1 | |
| IL_5O5J_021 | 1/A/446:450, 1/A/463:468 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_4LFB_018 IL_88269.3 | |
| IL_5O5J_023 | 1/A/484:491, 1/A/520:521 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4LFB_020 IL_15861.7 | |
| IL_5O5J_024 | 1/A/495:501, 1/A/508:516 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_5O5J_025 | 1/A/549:555, 1/A/862:863 | No text annotation Not in a motif group | homologous IL_4LFB_022 IL_69996.1 | |
| IL_5O5J_026 | 1/A/560:564, 1/A/737:741 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_027 IL_17136.1 | |
| IL_5O5J_027 | 1/A/574:576, 1/A/624:625 | Major groove platform Not in a motif group | homologous IL_4LFB_024 IL_27635.1 | |
| IL_5O5J_028 | 1/A/577:578, 1/A/620:623 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_4LFB_025 IL_09061.6 | |
| IL_5O5J_029 | 1/A/585:591, 1/A/609:613 | No text annotation Not in a motif group | ||
| IL_5O5J_030 | 1/A/634:635, 1/A/731:734 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_5J7L_031 IL_50694.2 | |
| IL_5O5J_031 | 1/A/637:638, 1/A/727:729 | Major groove platform Not in a motif group | homologous IL_4LFB_028 IL_27635.1 | |
| IL_5O5J_032 | 1/A/642:646, 1/A/720:723 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_5J7L_033 IL_71110.1 | |
| IL_5O5J_033 | 1/A/653:658, 1/A/692:697 | No text annotation Not in a motif group | homologous IL_4LFB_030 IL_04668.1 | |
| IL_5O5J_034 | 1/A/664:668, 1/A/679:686 | Kink-turn Not in a motif group | homologous IL_5J7L_035 IL_45067.2 | |
| IL_5O5J_035 | 1/A/754:758, 1/A/784:785 | Left turn Not in a motif group | homologous IL_5J7L_036 IL_29346.1 | |
| IL_5O5J_036 | 1/A/759:763, 1/A/779:783 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_033 IL_17136.1 | |
| IL_5O5J_037 | 1/A/869:876, 1/A/887:892 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_5J7L_038 IL_24606.2 | |
| IL_5O5J_038 | 1/A/904:905, 1/A/1376:1378 | Single bulged A Not in a motif group | homologous IL_4LFB_035 IL_37497.2 | |
| IL_5O5J_039 | 1/A/907:909, 1/A/1373:1374 | Single bulged G Not in a motif group | homologous IL_4LFB_036 IL_00225.2 | |
| IL_5O5J_040 | 1/A/915:917, 1/A/1363:1367 | Minor groove platform Not in a motif group | homologous IL_5J7L_041 IL_47078.1 | |
| IL_5O5J_041 | 1/A/935:936, 1/A/1207:1209 | Minor groove platform Not in a motif group | homologous IL_4LFB_038 IL_42622.2 | |
| IL_5O5J_042 | 1/A/975:979, 1/A/1024:1025 | Minor groove platform Not in a motif group | homologous IL_4LFB_039 IL_47078.1 | |
| IL_5O5J_044 | 1/A/1028:1030, 1/A/1189:1190 | Single bulged U Not in a motif group | homologous IL_5J7L_046 IL_83039.13 | |
| IL_5O5J_045 | 1/A/1032:1036, 1/A/1185:1187 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_5O5J_046 | 1/A/1037:1038, 1/A/1180:1184 | Minor groove platform Not in a motif group | homologous IL_5J7L_048 IL_93353.1 | |
| IL_5O5J_047 | 1/A/1040:1041, 1/A/1176:1178 | Single bulged A Not in a motif group | geometric IL_5J7L_049 IL_37497.2 | |
| IL_5O5J_048 | 1/A/1041:1043, 1/A/1174:1176 | No text annotation Not in a motif group | homologous IL_5J7L_050 IL_95997.1 | |
| IL_5O5J_049 | 1/A/1104:1108, 1/A/1125:1130 | No text annotation Not in a motif group | homologous IL_5J7L_051 IL_93211.1 | |
| IL_5O5J_050 | 1/A/1109:1112, 1/A/1123:1124 | Minor groove platform Not in a motif group | homologous IL_5J7L_052 IL_15052.1 | |
| IL_5O5J_051 | 1/A/1139:1142, 1/A/1156:1162 | No text annotation Not in a motif group | homologous IL_5J7L_053 IL_42032.1 | |
| IL_5O5J_052 | 1/A/1228:1234, 1/A/1265:1272 | No text annotation Not in a motif group | homologous IL_5J7L_054 IL_09129.1 | |
| IL_5O5J_053 | 1/A/1236:1239, 1/A/1258:1263 | No text annotation Not in a motif group | homologous IL_4LFB_052 IL_84205.1 | |
| IL_5O5J_054 | 1/A/1240:1244, 1/A/1253:1257 | Triple sheared Not in a motif group | homologous IL_5J7L_056 IL_56467.8 | |
| IL_5O5J_055 | 1/A/1285:1290, 1/A/1311:1316 | No text annotation Not in a motif group | homologous IL_4LFB_055 IL_19954.2 | |
| IL_5O5J_056 | 1/A/1382:1384, 1/A/1485:1488 | No text annotation Not in a motif group | geometric IL_4V88_463 IL_36143.3 | |
| IL_5O5J_057 | 1/A/1384:1387, 1/A/1481:1485 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_5O5J_058 | 1/A/1388:1390, 1/A/1478:1480 | No text annotation Not in a motif group | geometric IL_4WF9_020 IL_95997.1 | |
| IL_5O5J_059 | 1/A/1390:1392, 1/A/1475:1478 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_3TD0_005 IL_82068.2 | |
| IL_5O5J_060 | 1/A/1395:1397, 1/A/1470:1472 | No text annotation Not in a motif group | homologous IL_5J7L_061 IL_95997.1 | |
| IL_5O5J_061 | 1/A/1399:1402, 1/A/1465:1468 | Double sheared Not in a motif group | homologous IL_5J7L_062 IL_09705.9 | |
| IL_5O5J_062 | 1/A/1407:1410, 1/A/1457:1460 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5TBW_100 IL_30621.2 | |
| IL_5O5J_063 | 1/A/1413:1418, 1/A/1450:1454 | Triple sheared related Not in a motif group | homologous IL_5J7L_063 IL_64879.2 | |
| IL_5O5J_064 | 1/A/1418:1420, 1/A/1448:1450 | No text annotation Not in a motif group | geometric IL_4LFB_063 IL_95997.1 | |
| IL_5O5J_065 | 1/A/1423:1426, 1/A/1443:1445 | Isolated tHS basepair with bulges Not in a motif group | geometric IL_7RQB_082 IL_38958.7 | |
| IL_5O5J_066 | 1/A/1428:1431, 1/A/1439:1441 | No text annotation Not in a motif group | homologous IL_5J7L_065 IL_02284.5 | |
| IL_5O5J_067 | 1/A/1432:1433, 1/A/1436:1438 | No text annotation Not in a motif group | ||
| IL_5O5J_068 | 1/W/26:27, 1/W/43:44 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5O5J_007 | Minor groove platform | ||
| IL_5O5J_008 | Major groove platform | ||
| IL_5O5J_022 | No text annotation | ||
| IL_5O5J_043 | Single stack bend |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5O5J_001 | 1/A/50:51, 1/A/361:367, 1/A/393:395 | No text annotation Not in a motif group | homologous J3_5J7L_001 NA | |
| J3_5O5J_002 | 1/A/566:568, 1/A/631:634, 1/A/734:735 | No text annotation Not in a motif group | ||
| J3_5O5J_003 | 1/A/652:653, 1/A/697:705, 1/A/712:714 | No text annotation Not in a motif group | ||
| J3_5O5J_004 | 1/A/806:809, 1/A/839:843, 1/A/850:856 | No text annotation Not in a motif group | homologous J3_5J7L_004 NA | |
| J3_5O5J_005 | 1/A/918:921, 1/A/1326:1332, 1/A/1355:1362 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_5O5J_006 | 1/A/925:928, 1/A/1216:1218, 1/A/1319:1322 | No text annotation Not in a motif group | homologous J3_4LFB_003 NA | |
| J3_5O5J_007 | 1/A/937:944, 1/A/955:966, 1/A/1202:1206 | No text annotation Not in a motif group | ||
| J3_5O5J_008 | 1/A/972:975, 1/A/1025:1027, 1/A/1191:1196 | No text annotation Not in a motif group | ||
| J3_5O5J_010 | 1/A/1043:1048, 1/A/1087:1093, 1/A/1168:1174 | No text annotation Not in a motif group | ||
| J3_5O5J_011 | 1/A/1053:1054, 1/A/1063:1067, 1/A/1078:1082 | No text annotation Not in a motif group | homologous J3_5J7L_009 NA | |
| J3_5O5J_012 | 1/A/1096:1098, 1/A/1136:1139, 1/A/1162:1165 | No text annotation Not in a motif group | ||
| J3_5O5J_013 | 1/A/1218:1222, 1/A/1278:1285, 1/A/1316:1319 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5O5J_009 | No text annotation |
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