1XMO Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_1XMO_004 | 1/A/190B:190G | No text annotation | homologous HL_4LFB_004 HL_89167.1 | |
| HL_1XMO_011 | 1/A/450:483 | No text annotation | ||
| HL_1XMO_012 | 1/A/522:527 | No text annotation | geometric HL_2Y8W_001 NA | |
| HL_1XMO_013 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_1XMO_014 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_38491.1 | |
| HL_1XMO_017 | 1/A/838:848 | Mini UNCG | homologous HL_4LFB_018 HL_90436.1 | |
| HL_1XMO_020 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_1XMO_025 | 1/A/1124:1149 | No text annotation | ||
| HL_1XMO_026 | 1/A/1165:1171 | GNRA | homologous HL_4LFB_027 HL_34789.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_1XMO_001 | No text annotation | ||
| HL_1XMO_002 | No text annotation | ||
| HL_1XMO_033 | GNRA with extra near cWW | ||
| HL_1XMO_003 | GNRA | ||
| HL_1XMO_005 | No text annotation | ||
| HL_1XMO_035 | No text annotation | ||
| HL_1XMO_006 | GNRA related | ||
| HL_1XMO_007 | GNRA | ||
| HL_1XMO_008 | No text annotation | ||
| HL_1XMO_009 | UNCG | ||
| HL_1XMO_010 | GNRA | ||
| HL_1XMO_015 | GNRA | ||
| 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 | T-loop related | ||
| HL_1XMO_027 | GNRA | ||
| HL_1XMO_028 | T-loop with 3 stacked bulged bases | ||
| HL_1XMO_029 | No text annotation | ||
| HL_1XMO_030 | UNCG | ||
| HL_1XMO_031 | GNRA | ||
| HL_1XMO_034 | tRNA anticodon loop |
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 | homologous IL_4LFB_001 IL_28408.1 | |
| IL_1XMO_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_4LFB_003 IL_68149.1 | |
| IL_1XMO_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_34520.1 | |
| IL_1XMO_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_60988.1 | |
| IL_1XMO_010 | 1/A/186:188, 1/A/190K:191 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_01003.1 | |
| IL_1XMO_012 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_1XMO_014 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_1XMO_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_4LFB_018 IL_82100.1 | |
| IL_1XMO_063 | 1/A/515:521, 1/A/528:536 | Kink-turn related | homologous IL_5J7L_025 NA | |
| IL_1XMO_025 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_04211.1 | |
| IL_1XMO_028 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_1XMO_035 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_28408.1 | |
| IL_1XMO_042 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_1XMO_047 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_1XMO_048 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_1XMO_002 | Single bulged A | ||
| IL_1XMO_005 | Multiple bulged bases | ||
| IL_1XMO_006 | Isolated non-canonical cWW pair | ||
| IL_1XMO_007 | Multiple bulged bases | ||
| IL_1XMO_009 | tWH-tWH-tHW-tHW | ||
| IL_1XMO_011 | Not an internal loop | ||
| 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_060 | Single bulged G, near cWW | ||
| IL_1XMO_019 | SSU/LSU pseudoknot | ||
| IL_1XMO_020 | No text annotation | ||
| 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_061 | Triple non-canonical cWW pairs | ||
| 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 | Isolated non-canonical cWW pair | ||
| IL_1XMO_039 | Isolated non-canonical cWW pair | ||
| IL_1XMO_040 | Tandem non-canonical cWW pairs | ||
| IL_1XMO_041 | Single bulged U | ||
| IL_1XMO_043 | Minor groove platform with extra cWW | ||
| IL_1XMO_064 | Minor groove platform | ||
| IL_1XMO_062 | No text annotation | ||
| IL_1XMO_044 | Single bulged U | ||
| IL_1XMO_045 | Isolated non-canonical cWW pair | ||
| IL_1XMO_046 | No text annotation | ||
| IL_1XMO_049 | Double sheared | ||
| IL_1XMO_050 | No text annotation | ||
| IL_1XMO_051 | No text annotation | ||
| IL_1XMO_052 | No text annotation | ||
| IL_1XMO_053 | Isolated non-canonical cWW pair | ||
| IL_1XMO_054 | Decoding loop related | ||
| IL_1XMO_055 | Isolated non-canonical cWW pair | ||
| IL_1XMO_056 | Double sheared | ||
| IL_1XMO_057 | UAA/GAN variation | ||
| IL_1XMO_058 | Isolated non-canonical cWW pair | ||
| IL_1XMO_059 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_1XMO_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_1XMO_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_4LFB_001 J3_02285.1 | |
| J3_1XMO_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_1XMO_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_1XMO_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_1XMO_016 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_1XMO_008 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | homologous J3_4LFB_008 J3_82365.5 | |
| J3_1XMO_017 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_1XMO_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_1XMO_001 | 1/A/36:39, 1/A/403:442, 1/A/492:500, 1/A/545:548 | No text annotation | ||
| J4_1XMO_002 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_1XMO_003 | 1/A/142:144, 1/A/178:183, 1/A/194:198, 1/A/219:221 | No text annotation | homologous J4_4LFB_002 J4_88771.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_1XMO_010 | No text annotation | ||
| J3_1XMO_011 | No text annotation | ||
| J3_1XMO_015 | No text annotation | ||
| J3_1XMO_012 | No text annotation | ||
| J3_1XMO_003 | No text annotation | ||
| J3_1XMO_005 | No text annotation | ||
| J3_1XMO_006 | No text annotation | ||
| J4_1XMO_004 | No text annotation | ||
| J5_1XMO_001 | No text annotation |
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