9ROT Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9ROT_001 | 1/A/654:664 | No text annotation | homologous HL_6CZR_072 NA | |
| HL_9ROT_002 | 1/A/701:708 | No text annotation | ||
| HL_9ROT_003 | 1/A/734:740 | No text annotation | ||
| HL_9ROT_004 | 1/A/768:773 | GNRA | geometric HL_5FJC_002 HL_34789.6 | |
| HL_9ROT_005 | 1/A/792:796 | No text annotation | geometric HL_6U8D_003 HL_01957.1 | |
| HL_9ROT_006 | 1/A/804:809 | No text annotation | ||
| HL_9ROT_007 | 1/A/842:847 | GNRA | homologous HL_6CZR_081 NA | |
| HL_9ROT_008 | 1/A/894:899 | GNRA variation | homologous HL_6CZR_216 NA | |
| HL_9ROT_009 | 1/A/989:998 | No text annotation | geometric HL_4LFB_015 HL_38491.4 | |
| HL_9ROT_010 | 1/A/1023:1028 | GNRA | geometric HL_6M0X_001 HL_34789.6 | |
| HL_9ROT_012 | 1/A/1115:1126 | No text annotation | ||
| HL_9ROT_013 | 1/A/1150:1155 | No text annotation | ||
| HL_9ROT_019 | 1/A/1516:1533 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9ROT_011 | No text annotation | ||
| HL_9ROT_014 | No text annotation | ||
| HL_9ROT_015 | No text annotation | ||
| HL_9ROT_016 | No text annotation | ||
| HL_9ROT_017 | No text annotation | ||
| HL_9ROT_018 | No text annotation | ||
| HL_9ROT_020 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9ROT_001 | 1/A/649:651, 1/A/667:668 | No text annotation | ||
| IL_9ROT_002 | 1/A/674:676, 1/A/921:923 | Isolated cWS basepair | geometric IL_5E81_401 IL_84227.1 | |
| IL_9ROT_003 | 1/A/685:686, 1/A/859:861 | Single bulged A | homologous IL_6CZR_114 NA | |
| IL_9ROT_004 | 1/A/690:692, 1/A/822:823 | Single bulged A | geometric IL_4R4V_004 IL_14190.4 | |
| IL_9ROT_005 | 1/A/694:696, 1/A/819:820 | Minor groove platform | homologous IL_6CZR_116 NA | |
| IL_9ROT_006 | 1/A/727:729, 1/A/744:747 | No text annotation | geometric IL_9DFE_030 IL_05502.2 | |
| IL_9ROT_007 | 1/A/729:732, 1/A/742:744 | No text annotation | geometric IL_9DFE_030 IL_05502.2 | |
| IL_9ROT_008 | 1/A/756:761, 1/A/779:786 | Kink-turn with non-sequential stacking | geometric IL_4LFB_011 IL_46174.6 | |
| IL_9ROT_009 | 1/A/762:765, 1/A/777:778 | Major groove platform; stack outside cWW | geometric IL_1NTA_003 IL_74641.4 | |
| IL_9ROT_010 | 1/A/762:766, 1/A/775:778 | No text annotation | ||
| IL_9ROT_011 | 1/A/765:766, 1/A/775:777 | No text annotation | ||
| IL_9ROT_012 | 1/A/830:832, 1/A/855:856 | Single bulged U | homologous IL_6CZR_126 NA | |
| IL_9ROT_013 | 1/A/834:838, 1/A/852:853 | C-loop | homologous IL_6CZR_127 NA | |
| IL_9ROT_014 | 1/A/838:839, 1/A/850:852 | Single bulged G | homologous IL_6CZR_358 NA | |
| IL_9ROT_015 | 1/A/876:885, 1/A/910:913 | No text annotation | ||
| IL_9ROT_016 | 1/A/887:893, 1/A/900:908 | Kink-turn related | homologous IL_6CZR_133 NA | |
| IL_9ROT_017 | 1/A/935:941, 1/A/1133:1134 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_9ROT_018 | 1/A/946:950, 1/A/1044:1049 | UAA/GAN | geometric IL_4V9F_052 IL_10133.1 | |
| IL_9ROT_019 | 1/A/952:968, 1/A/1036:1042 | No text annotation | ||
| IL_9ROT_020 | 1/A/974:980, 1/A/1008:1014 | No text annotation | ||
| IL_9ROT_021 | 1/A/982:984, 1/A/1004:1006 | Isolated non-canonical cWW pair | geometric IL_9AXU_020 IL_01003.6 | |
| IL_9ROT_022 | 1/A/986:988, 1/A/999:1002 | No text annotation | ||
| IL_9ROT_023 | 1/A/1062:1066, 1/A/1092:1093 | Left turn | homologous IL_6CZR_144 NA | |
| IL_9ROT_024 | 1/A/1067:1071, 1/A/1087:1091 | No text annotation | geometric IL_9H3G_204 IL_05821.3 | |
| IL_9ROT_025 | 1/A/1109:1111, 1/A/1130:1132 | Isolated non-canonical cWW pair | geometric IL_6OL3_002 IL_01003.6 | |
| IL_9ROT_026 | 1/A/1139:1147, 1/A/1158:1164 | No text annotation | ||
| IL_9ROT_027 | 1/A/1175:1177, 1/A/1476:1479 | Isolated non-canonical cWW with bulges | geometric IL_4PKD_001 IL_30722.1 | |
| IL_9ROT_028 | 1/A/1178:1192, 1/A/1462:1475 | No text annotation | ||
| IL_9ROT_034 | 1/A/1274:1277, 1/A/1298:1301 | Double sheared | geometric IL_8GLP_052 IL_58355.4 | |
| IL_9ROT_035 | 1/A/1278:1279, 1/A/1289:1297 | No text annotation | ||
| IL_9ROT_036 | 1/A/1489:1495, 1/A/1554:1561 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9ROT_029 | No text annotation | ||
| IL_9ROT_030 | Multiple bulged bases | ||
| IL_9ROT_031 | Minor groove platform | ||
| IL_9ROT_032 | Single bulged U | ||
| IL_9ROT_033 | Isolated non-canonical cWW pair | ||
| IL_9ROT_037 | No text annotation | ||
| IL_9ROT_038 | Tandem non-canonical cWW pairs | ||
| IL_9ROT_039 | No text annotation | ||
| IL_9ROT_040 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9ROT_001 | 1/A/677:680, 1/A/866:872, 1/A/917:920 | No text annotation | ||
| J3_9ROT_002 | 1/A/687:690, 1/A/823:830, 1/A/856:858 | No text annotation | ||
| J3_9ROT_003 | 1/A/973:974, 1/A/1014:1022, 1/A/1029:1031 | No text annotation | ||
| J4_9ROT_001 | 1/A/698:701, 1/A/708:715, 1/A/800:802, 1/A/811:817 | No text annotation | ||
| J4_9ROT_002 | 1/A/717:724, 1/A/750:753, 1/A/789:791, 1/A/797:798 | No text annotation | ||
| J4_9ROT_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_9ROT_004 | No text annotation | ||
| J3_9ROT_005 | No text annotation | ||
| J3_9ROT_006 | No text annotation |
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