9RPF Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9RPF_001 | 1/A/654:664 | No text annotation | homologous HL_6CZR_072 NA | |
| HL_9RPF_002 | 1/A/701:708 | No text annotation | ||
| HL_9RPF_004 | 1/A/768:773 | GNRA | geometric HL_6N2V_003 HL_34789.6 | |
| HL_9RPF_007 | 1/A/842:847 | GNRA | homologous HL_6CZR_081 NA | |
| HL_9RPF_008 | 1/A/894:899 | GNRA variation | homologous HL_6CZR_216 NA | |
| HL_9RPF_010 | 1/A/1023:1028 | GNRA | geometric HL_6M0X_001 HL_34789.6 | |
| HL_9RPF_011 | 1/A/1074:1084 | No text annotation | homologous HL_6CZR_088 NA | |
| HL_9RPF_012 | 1/A/1115:1126 | No text annotation | ||
| HL_9RPF_014 | 1/A/1217:1226 | No text annotation | homologous HL_6CZR_092 NA | |
| HL_9RPF_015 | 1/A/1281:1287 | GNRA related | geometric HL_8G9Z_003 HL_37569.4 | |
| HL_9RPF_016 | 1/A/1310:1315 | No text annotation | ||
| HL_9RPF_021 | 1/A/1580:1585 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9RPF_003 | No text annotation | ||
| HL_9RPF_005 | No text annotation | ||
| HL_9RPF_006 | No text annotation | ||
| HL_9RPF_009 | No text annotation | ||
| HL_9RPF_013 | No text annotation | ||
| HL_9RPF_017 | No text annotation | ||
| HL_9RPF_018 | No text annotation | ||
| HL_9RPF_019 | No text annotation | ||
| HL_9RPF_020 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9RPF_001 | 1/A/649:651, 1/A/667:668 | No text annotation | ||
| IL_9RPF_002 | 1/A/674:676, 1/A/921:923 | No text annotation | geometric IL_8GLP_063 IL_71625.5 | |
| IL_9RPF_003 | 1/A/685:686, 1/A/859:861 | Single bulged A | homologous IL_6CZR_114 NA | |
| IL_9RPF_005 | 1/A/694:696, 1/A/819:820 | Minor groove platform | homologous IL_6CZR_116 NA | |
| IL_9RPF_008 | 1/A/756:761, 1/A/779:786 | Kink-turn with non-sequential stacking | geometric IL_4LFB_011 IL_46174.6 | |
| IL_9RPF_012 | 1/A/830:832, 1/A/855:856 | Single bulged U | homologous IL_6CZR_126 NA | |
| IL_9RPF_013 | 1/A/834:838, 1/A/852:853 | C-loop | homologous IL_6CZR_127 NA | |
| IL_9RPF_015 | 1/A/876:885, 1/A/910:913 | No text annotation | ||
| IL_9RPF_016 | 1/A/887:893, 1/A/900:908 | Kink-turn related | homologous IL_6CZR_133 NA | |
| IL_9RPF_017 | 1/A/935:941, 1/A/1133:1134 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_9RPF_018 | 1/A/946:950, 1/A/1044:1049 | No text annotation | ||
| IL_9RPF_019 | 1/A/952:968, 1/A/1036:1042 | No text annotation | ||
| IL_9RPF_020 | 1/A/974:980, 1/A/1008:1014 | No text annotation | ||
| IL_9RPF_023 | 1/A/1020:1022, 1/A/1029:1030 | No text annotation | ||
| IL_9RPF_025 | 1/A/1067:1071, 1/A/1087:1091 | No text annotation | geometric IL_9H3G_204 IL_05821.3 | |
| IL_9RPF_026 | 1/A/1109:1111, 1/A/1130:1132 | Isolated non-canonical cWW pair | geometric IL_5CCB_001 IL_01003.6 | |
| IL_9RPF_027 | 1/A/1139:1147, 1/A/1158:1164 | No text annotation | ||
| IL_9RPF_028 | 1/A/1175:1176, 1/A/1477:1479 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_9RPF_029 | 1/A/1178:1180, 1/A/1474:1475 | Single bulged G | homologous IL_6CZR_148 NA | |
| IL_9RPF_030 | 1/A/1186:1190, 1/A/1464:1468 | No text annotation | ||
| IL_9RPF_032 | 1/A/1244:1252, 1/A/1340:1345 | No text annotation | ||
| IL_9RPF_033 | 1/A/1253:1255, 1/A/1338:1339 | No text annotation | homologous IL_6CZR_152 NA | |
| IL_9RPF_034 | 1/A/1257:1261, 1/A/1334:1336 | No text annotation | homologous IL_6CZR_154 NA | |
| IL_9RPF_035 | 1/A/1262:1263, 1/A/1329:1333 | Minor groove platform | homologous IL_6CZR_155 NA | |
| IL_9RPF_036 | 1/A/1265:1266, 1/A/1325:1327 | Single bulged U | homologous IL_6CZR_156 NA | |
| IL_9RPF_037 | 1/A/1266:1268, 1/A/1323:1325 | Isolated non-canonical cWW pair | homologous IL_6CZR_157 NA | |
| IL_9RPF_038 | 1/A/1274:1277, 1/A/1298:1301 | Double sheared | geometric IL_8GLP_052 IL_58355.4 | |
| IL_9RPF_039 | 1/A/1278:1279, 1/A/1289:1297 | No text annotation | ||
| IL_9RPF_041 | 1/A/1483:1485, 1/A/1566:1569 | No text annotation | homologous IL_6CZR_165 NA | |
| IL_9RPF_042 | 1/A/1485:1488, 1/A/1562:1566 | No text annotation | homologous IL_6CZR_368 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9RPF_004 | Single bulged A | ||
| IL_9RPF_006 | No text annotation | ||
| IL_9RPF_007 | No text annotation | ||
| IL_9RPF_009 | Major groove platform; stack outside cWW | ||
| IL_9RPF_010 | No text annotation | ||
| IL_9RPF_011 | No text annotation | ||
| IL_9RPF_014 | Single bulged G | ||
| IL_9RPF_021 | Isolated non-canonical cWW pair | ||
| IL_9RPF_022 | No text annotation | ||
| IL_9RPF_024 | Left turn | ||
| IL_9RPF_031 | Minor groove platform | ||
| IL_9RPF_040 | No text annotation | ||
| IL_9RPF_043 | No text annotation | ||
| IL_9RPF_044 | UAA/GAN related | ||
| IL_9RPF_045 | Tandem non-canonical cWW pairs | ||
| IL_9RPF_046 | No text annotation | ||
| IL_9RPF_047 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9RPF_001 | 1/A/677:680, 1/A/866:872, 1/A/917:920 | No text annotation | ||
| J3_9RPF_002 | 1/A/687:690, 1/A/823:830, 1/A/856:858 | No text annotation | ||
| J3_9RPF_003 | 1/A/973:974, 1/A/1014:1020, 1/A/1030:1031 | No text annotation | ||
| J3_9RPF_004 | 1/A/1192:1194, 1/A/1428:1434, 1/A/1456:1462 | No text annotation | ||
| J3_9RPF_006 | 1/A/1210:1216, 1/A/1227:1238, 1/A/1351:1354 | No text annotation | ||
| J3_9RPF_007 | 1/A/1268:1273, 1/A/1302:1308, 1/A/1317:1323 | No text annotation | ||
| J4_9RPF_001 | 1/A/698:701, 1/A/708:715, 1/A/800:802, 1/A/811:817 | No text annotation | ||
| J4_9RPF_002 | 1/A/717:724, 1/A/750:753, 1/A/789:791, 1/A/797:798 | No text annotation | ||
| J4_9RPF_003 | 1/A/941:943, 1/A/1052:1057, 1/A/1098:1109, 1/A/1132:1133 | No text annotation | homologous J4_6CZR_013 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9RPF_005 | No text annotation | ||
| J3_9RPF_008 | No text annotation |
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