1XMO Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_1XMO_004 | 1/A/190B:190G | No text annotation Not in a motif group | homologous HL_4LFB_004 HL_10278.1 | |
| HL_1XMO_011 | 1/A/450:483 | No text annotation Not in a motif group | ||
| HL_1XMO_012 | 1/A/522:527 | No text annotation Not in a motif group | geometric HL_2Y8W_001 HL_01057.1 | |
| HL_1XMO_013 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
| HL_1XMO_014 | 1/A/689:698 | No text annotation Not in a motif group | homologous HL_4LFB_015 HL_12326.1 | |
| HL_1XMO_017 | 1/A/838:848 | No text annotation Not in a motif group | homologous HL_4LFB_018 HL_38927.2 | |
| HL_1XMO_020 | 1/A/963:972 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_1XMO_025 | 1/A/1124:1149 | No text annotation Not in a motif group | ||
| HL_1XMO_026 | 1/A/1165:1171 | GNRA Not in a motif group | homologous HL_4LFB_027 HL_42097.1 | |
| HL_1XMO_031 | 1/A/1515:1520 | No text annotation Not in a motif group | homologous HL_4LFB_032 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_1XMO_001 | No text annotation | ||
| HL_1XMO_002 | No text annotation | ||
| HL_1XMO_003 | GNRA | ||
| HL_1XMO_005 | No text annotation | ||
| HL_1XMO_006 | No text annotation | ||
| HL_1XMO_007 | GNRA | ||
| HL_1XMO_008 | No text annotation | ||
| HL_1XMO_009 | UNCG | ||
| HL_1XMO_010 | GNRA | ||
| HL_1XMO_015 | Other HL | ||
| HL_1XMO_016 | No text annotation | ||
| HL_1XMO_018 | GNRA | ||
| HL_1XMO_019 | GNRA | ||
| HL_1XMO_021 | GNRA | ||
| HL_1XMO_022 | No text annotation | ||
| HL_1XMO_023 | GNRA | ||
| HL_1XMO_024 | No text annotation | ||
| HL_1XMO_027 | Other HL | ||
| HL_1XMO_028 | No text annotation | ||
| HL_1XMO_029 | No text annotation | ||
| HL_1XMO_030 | UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_1XMO_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_4LFB_001 IL_00225.2 | |
| IL_1XMO_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | homologous IL_4LFB_003 IL_11178.1 | |
| IL_1XMO_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_1XMO_008 | 1/A/132:136, 1/A/227:230 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_1XMO_010 | 1/A/186:188, 1/A/190K:191 | No text annotation Not in a motif group | homologous IL_4LFB_010 IL_95997.1 | |
| IL_1XMO_011 | 1/A/189:190A, 1/A/190H:190J | Not an internal loop Not in a motif group | geometric IL_5VCI_005 IL_82842.2 | |
| IL_1XMO_012 | 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_1XMO_014 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_1XMO_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_4LFB_018 IL_88269.3 | |
| IL_1XMO_020 | 1/A/514:521, 1/A/528:537 | No text annotation Not in a motif group | ||
| IL_1XMO_025 | 1/A/605:612, 1/A/628:633 | No text annotation Not in a motif group | homologous IL_4LFB_026 IL_78349.1 | |
| IL_1XMO_028 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4LFB_029 IL_71110.1 | |
| IL_1XMO_035 | 1/A/925:927, 1/A/1390:1391 | Single bulged G Not in a motif group | homologous IL_4LFB_036 IL_00225.2 | |
| IL_1XMO_042 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_1XMO_043 | 1/A/1056:1058, 1/A/1199:1204 | No text annotation Not in a motif group | ||
| IL_1XMO_047 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation Not in a motif group | homologous IL_4LFB_051 IL_09129.1 | |
| IL_1XMO_048 | 1/A/1255:1258, 1/A/1277:1282 | No text annotation Not in a motif group | homologous IL_4LFB_052 IL_84205.1 | |
| IL_1XMO_051 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation Not in a motif group | geometric IL_4V88_463 IL_36143.3 | |
| IL_1XMO_052 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_1XMO_053 | 1/A/1405:1407, 1/A/1494:1496 | No text annotation Not in a motif group | geometric IL_5Z1I_004 IL_95997.1 | |
| IL_1XMO_054 | 1/A/1407:1409, 1/A/1491:1494 | Decoding loop related Not in a motif group | geometric IL_3C3Z_002 IL_64417.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_1XMO_002 | Single bulged A | ||
| IL_1XMO_005 | Multiple bulged bases | ||
| IL_1XMO_006 | No text annotation | ||
| IL_1XMO_007 | Multiple bulged bases | ||
| IL_1XMO_009 | tWH-tWH-tHW-tHW | ||
| IL_1XMO_013 | No text annotation | ||
| IL_1XMO_015 | Single bulged U | ||
| IL_1XMO_016 | C-loop | ||
| IL_1XMO_017 | Single bulged G | ||
| IL_1XMO_019 | SSU/LSU pseudoknot | ||
| IL_1XMO_021 | No text annotation | ||
| IL_1XMO_022 | tSH-tHW-tHS | ||
| IL_1XMO_023 | Major groove platform | ||
| IL_1XMO_024 | Major groove minor groove platform; mini C-loop | ||
| IL_1XMO_026 | Major groove platform; stack outside cWW | ||
| IL_1XMO_027 | Major groove platform | ||
| IL_1XMO_029 | No text annotation | ||
| IL_1XMO_030 | Kink-turn | ||
| IL_1XMO_031 | Left turn | ||
| IL_1XMO_032 | tSH-tHW-tHS | ||
| IL_1XMO_033 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_1XMO_034 | Single bulged A | ||
| IL_1XMO_036 | Minor groove platform | ||
| IL_1XMO_037 | Minor groove platform | ||
| IL_1XMO_038 | No text annotation | ||
| IL_1XMO_039 | No text annotation | ||
| IL_1XMO_040 | Tandem non-canonical cWW pairs | ||
| IL_1XMO_041 | Single bulged U | ||
| IL_1XMO_044 | Single bulged U | ||
| IL_1XMO_045 | No text annotation | ||
| IL_1XMO_046 | No text annotation | ||
| IL_1XMO_049 | Double sheared | ||
| IL_1XMO_050 | No text annotation | ||
| IL_1XMO_055 | No text annotation | ||
| IL_1XMO_056 | Double sheared | ||
| IL_1XMO_057 | UAA/GAN variation | ||
| IL_1XMO_058 | No text annotation | ||
| IL_1XMO_059 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_1XMO_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation Not in a motif group | homologous J3_4LFB_001 NA | |
| J3_1XMO_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_1XMO_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation Not in a motif group | ||
| J3_1XMO_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation Not in a motif group | ||
| J3_1XMO_008 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation Not in a motif group | ||
| J3_1XMO_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_1XMO_003 | No text annotation | ||
| J3_1XMO_005 | No text annotation | ||
| J3_1XMO_006 | No text annotation |
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