3T1Y Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3T1Y_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_73535.1 | |
| HL_3T1Y_002 | 1/A/78:84 | No text annotation | homologous HL_4LFB_002 HL_46665.2 | |
| HL_3T1Y_004 | 1/A/186:191 | No text annotation | homologous HL_4LFB_004 HL_89167.2 | |
| HL_3T1Y_005 | 1/A/207:211 | Mini UNCG | homologous HL_4LFB_005 HL_90436.2 | |
| HL_3T1Y_006 | 1/A/254:262 | GNRA related | homologous HL_4LFB_006 HL_87268.1 | |
| HL_3T1Y_009 | 1/A/337:342 | UNCG | homologous HL_4LFB_009 HL_61337.2 | |
| HL_3T1Y_010 | 1/A/374:379 | GNRA | homologous HL_4LFB_010 HL_34789.2 | |
| HL_3T1Y_011 | 1/A/414:419 | UNCG | homologous HL_5J7L_011 NA | |
| HL_3T1Y_013 | 1/A/505:510 | No text annotation | geometric HL_4WF9_003 HL_75660.7 | |
| HL_3T1Y_014 | 1/A/600:606 | GNRA-like with tWH | homologous HL_4LFB_014 HL_86621.1 | |
| HL_3T1Y_015 | 1/A/672:681 | No text annotation | homologous HL_4LFB_015 HL_38491.2 | |
| HL_3T1Y_017 | 1/A/769:779 | No text annotation | homologous HL_4LFB_017 HL_38491.2 | |
| HL_3T1Y_034 | 1/A/821:825 | Mini UNCG | homologous HL_4LFB_018 HL_90436.2 | |
| HL_3T1Y_020 | 1/A/874:879 | GNRA | homologous HL_5J7L_020 NA | |
| HL_3T1Y_021 | 1/A/940:949 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_3T1Y_022 | 1/A/990:995 | GNRA | homologous HL_4LFB_022 HL_34789.2 | |
| HL_3T1Y_025 | 1/A/1071:1078 | T-loop related | homologous HL_4LFB_025 HL_63894.2 | |
| HL_3T1Y_035 | 1/A/1106:1131 | No text annotation | ||
| HL_3T1Y_026 | 1/A/1116:1122 | No text annotation | homologous HL_4LFB_026 HL_92935.1 | |
| HL_3T1Y_027 | 1/A/1147:1152 | GNRA | homologous HL_4LFB_027 HL_34789.2 | |
| HL_3T1Y_028 | 1/A/1246:1251 | GNRA | homologous HL_5J7L_027 NA | |
| HL_3T1Y_029 | 1/A/1295:1304 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_3T1Y_031 | 1/A/1429:1434 | UNCG | homologous HL_4LFB_031 HL_61337.2 | |
| HL_3T1Y_032 | 1/A/1492:1497 | GNRA | homologous HL_4LFB_032 HL_34789.2 | |
| HL_3T1Y_036 | 1/X/30:40 | Externally structured | geometric HL_8C3A_022 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3T1Y_003 | GNRA | ||
| HL_3T1Y_007 | GNRA | ||
| HL_3T1Y_008 | No text annotation | ||
| HL_3T1Y_012 | GNRA | ||
| HL_3T1Y_016 | GNRA | ||
| HL_3T1Y_018 | No text annotation | ||
| HL_3T1Y_019 | GNRA | ||
| HL_3T1Y_023 | No text annotation | ||
| HL_3T1Y_024 | GNRA | ||
| HL_3T1Y_030 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3T1Y_001 | 1/A/30:32, 1/A/535:536 | Single bulged G | homologous IL_4LFB_001 IL_28408.2 | |
| IL_3T1Y_002 | 1/A/44:45, 1/A/391:393 | Single bulged A | homologous IL_4LFB_002 IL_14190.2 | |
| IL_3T1Y_003 | 1/A/47:52, 1/A/354:356 | No text annotation | homologous IL_4LFB_003 IL_32983.2 | |
| IL_3T1Y_004 | 1/A/54:56, 1/A/351:352 | Minor groove platform | homologous IL_4LFB_004 IL_34520.2 | |
| IL_3T1Y_006 | 1/A/67:69, 1/A/93:95 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_01003.2 | |
| IL_3T1Y_007 | 1/A/122:125, 1/A/226:227 | Multiple bulged bases | homologous IL_4LFB_007 IL_75289.1 | |
| IL_3T1Y_008 | 1/A/126:130, 1/A/222:225 | No text annotation | homologous IL_4LFB_008 IL_60988.2 | |
| IL_3T1Y_009 | 1/A/142:147, 1/A/162:168 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_00680.1 | |
| IL_3T1Y_010 | 1/A/180:182, 1/A/195:197 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_01003.2 | |
| IL_3T1Y_011 | 1/A/237:242, 1/A/272:279 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_3T1Y_012 | 1/A/244:247, 1/A/269:270 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_3T1Y_013 | 1/A/287:288, 1/A/299:303 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_3T1Y_014 | 1/A/362:364, 1/A/387:388 | Single bulged U | homologous IL_4LFB_014 IL_97561.2 | |
| IL_3T1Y_015 | 1/A/366:370, 1/A/384:385 | C-loop | geometric IL_5J7L_018 NA | |
| IL_3T1Y_017 | 1/A/404:411, 1/A/422:428 | No text annotation | homologous IL_4LFB_017 IL_62329.1 | |
| IL_3T1Y_018 | 1/A/440:444, 1/A/467:472 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_82100.1 | |
| IL_3T1Y_019 | 1/A/444:449, 1/A/461:467 | No text annotation | homologous IL_4LFB_019 IL_31561.1 | |
| IL_3T1Y_021 | 1/A/498:504, 1/A/511:519 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_3T1Y_022 | 1/A/552:558, 1/A/857:858 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_3T1Y_023 | 1/A/563:567, 1/A/740:744 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_05821.1 | |
| IL_3T1Y_024 | 1/A/577:579, 1/A/627:628 | Major groove platform | homologous IL_4LFB_024 IL_48076.8 | |
| IL_3T1Y_025 | 1/A/580:581, 1/A/623:626 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_73108.2 | |
| IL_3T1Y_026 | 1/A/588:595, 1/A/611:616 | No text annotation | homologous IL_4LFB_026 IL_04211.1 | |
| IL_3T1Y_027 | 1/A/637:638, 1/A/734:737 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_74641.2 | |
| IL_3T1Y_028 | 1/A/640:641, 1/A/730:732 | Major groove platform | homologous IL_6CZR_140 NA | |
| IL_3T1Y_029 | 1/A/645:649, 1/A/723:726 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.2 | |
| IL_3T1Y_063 | 1/A/656:660, 1/A/696:700 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_3T1Y_031 | 1/A/666:671, 1/A/682:690 | Kink-turn | homologous IL_4LFB_031 IL_95727.1 | |
| IL_3T1Y_032 | 1/A/757:761, 1/A/787:788 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_3T1Y_034 | 1/A/864:871, 1/A/882:887 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_3T1Y_035 | 1/A/899:900, 1/A/1375:1377 | Single bulged A | homologous IL_4LFB_035 IL_14190.2 | |
| IL_3T1Y_036 | 1/A/902:904, 1/A/1372:1373 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_3T1Y_037 | 1/A/910:912, 1/A/1362:1366 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_3T1Y_039 | 1/A/970:974, 1/A/1026:1027 | Minor groove platform | homologous IL_4LFB_039 IL_61370.1 | |
| IL_3T1Y_042 | 1/A/1034:1038, 1/A/1185:1187 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_3T1Y_046 | 1/A/1106:1116, 1/A/1122:1131 | No text annotation | ||
| IL_3T1Y_047 | 1/A/1140:1143, 1/A/1156:1162 | No text annotation | homologous IL_5J7L_053 NA | |
| IL_3T1Y_048 | 1/A/1228:1234, 1/A/1265:1271 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_3T1Y_049 | 1/A/1236:1239, 1/A/1258:1263 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_3T1Y_064 | 1/A/1240:1243, 1/A/1254:1257 | Double sheared | homologous IL_4LFB_067 IL_58355.2 | |
| IL_3T1Y_051 | 1/A/1241:1243, 1/A/1254:1255 | Minor groove platform | homologous IL_4LFB_054 IL_34520.2 | |
| IL_3T1Y_052 | 1/A/1284:1289, 1/A/1310:1315 | No text annotation | geometric IL_4LFB_055 IL_57885.2 | |
| IL_3T1Y_054 | 1/A/1383:1386, 1/A/1474:1478 | No text annotation | geometric IL_4V88_464 NA | |
| IL_3T1Y_055 | 1/A/1387:1389, 1/A/1471:1473 | Isolated non-canonical cWW pair | geometric IL_3GM7_005 IL_01003.2 | |
| IL_3T1Y_056 | 1/A/1389:1391, 1/A/1468:1471 | Decoding loop related | geometric IL_3C3Z_002 IL_53541.1 | |
| IL_3T1Y_057 | 1/A/1394:1396, 1/A/1463:1465 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_01003.2 | |
| IL_3T1Y_066 | 1/A/1398:1401, 1/A/1458:1461 | Double sheared | homologous IL_4LFB_060 IL_58355.2 | |
| IL_3T1Y_060 | 1/A/1413:1417, 1/A/1443:1446 | UAA/GAN variation | homologous IL_4LFB_062 IL_77691.7 | |
| IL_3T1Y_061 | 1/A/1417:1419, 1/A/1441:1443 | Isolated non-canonical cWW pair | geometric IL_4LFB_063 IL_01003.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3T1Y_005 | Multiple bulged bases | ||
| IL_3T1Y_016 | Single bulged G | ||
| IL_3T1Y_020 | SSU/LSU pseudoknot | ||
| IL_3T1Y_030 | No text annotation | ||
| IL_3T1Y_033 | tSH-tHW-tHS | ||
| IL_3T1Y_038 | Minor groove platform | ||
| IL_3T1Y_040 | No text annotation | ||
| IL_3T1Y_041 | Single bulged U | ||
| IL_3T1Y_043 | Minor groove platform | ||
| IL_3T1Y_044 | Single bulged U | ||
| IL_3T1Y_045 | Isolated non-canonical cWW pair | ||
| IL_3T1Y_050 | Not an internal loop | ||
| IL_3T1Y_053 | No text annotation | ||
| IL_3T1Y_058 | Double sheared with non-canonical cWW | ||
| IL_3T1Y_065 | No text annotation | ||
| IL_3T1Y_059 | Isolated non-canonical cWW pair | ||
| IL_3T1Y_062 | Isolated basepair with bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3T1Y_010 | 1/A/46:47, 1/A/356:362, 1/A/388:390 | No text annotation | geometric J3_4LFB_010 J3_58657.1 | |
| J3_3T1Y_014 | 1/A/46:52, 1/A/354:362, 1/A/388:390 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_3T1Y_015 | 1/A/569:571, 1/A/634:638, 1/A/734:738 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_3T1Y_012 | 1/A/655:656, 1/A/700:708, 1/A/715:717 | No text annotation | homologous J3_4LFB_012 J3_74074.1 | |
| J3_3T1Y_001 | 1/A/809:812, 1/A/834:838, 1/A/845:851 | No text annotation | homologous J3_4LFB_001 J3_02285.1 | |
| J3_3T1Y_002 | 1/A/913:916, 1/A/1325:1331, 1/A/1354:1361 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_3T1Y_004 | 1/A/932:939, 1/A/950:961, 1/A/1202:1206 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_3T1Y_005 | 1/A/967:970, 1/A/1027:1029, 1/A/1191:1196 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_3T1Y_016 | 1/A/967:974, 1/A/1026:1029, 1/A/1191:1196 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_3T1Y_007 | 1/A/1045:1050, 1/A/1089:1095, 1/A/1168:1174 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_3T1Y_019 | 1/A/1055:1056, 1/A/1065:1068, 1/A/1081:1084 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_3T1Y_008 | 1/A/1098:1100, 1/A/1137:1140, 1/A/1162:1165 | No text annotation | homologous J3_4LFB_008 J3_82365.5 | |
| J3_3T1Y_018 | 1/A/1098:1100, 1/A/1137:1143, 1/A/1156:1165 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_3T1Y_009 | 1/A/1218:1222, 1/A/1277:1284, 1/A/1315:1318 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_3T1Y_001 | 1/A/108:115, 1/A/234:235, 1/A/281:284, 1/A/306:307 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_3T1Y_002 | 1/A/136:138, 1/A/172:177, 1/A/200:204, 1/A/214:216 | No text annotation | homologous J4_4LFB_002 J4_88771.1 | |
| J4_3T1Y_003 | 1/A/558:560, 1/A/747:752, 1/A/793:804, 1/A/856:857 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_3T1Y_001 | 1/A/36:39, 1/A/398:401, 1/A/431:436, 1/A/476:483, 1/A/528:531 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_3T1Y_002 | 1/A/58:61, 1/A/99:106, 1/A/309:311, 1/A/332:334, 1/A/345:349 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3T1Y_011 | No text annotation | ||
| J3_3T1Y_003 | No text annotation | ||
| J3_3T1Y_006 | No text annotation | ||
| J3_3T1Y_017 | No text annotation | ||
| J3_3T1Y_013 | No text annotation |
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