8C99 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8C99_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_8C99_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_8C99_003 | 1/A/123:128 | No text annotation | homologous HL_4WF9_003 HL_75660.7 | |
| HL_8C99_009 | 1/A/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_8C99_010 | 1/A/319:323 | No text annotation | homologous HL_5J7L_143 NA | |
| HL_8C99_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_8C99_014 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.2 | |
| HL_8C99_015 | 1/A/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_8C99_016 | 1/A/543:550 | No text annotation | homologous HL_5J7L_149 NA | |
| HL_8C99_017 | 1/A/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_8C99_024 | 1/A/978:985 | No text annotation | homologous HL_7A0S_027 HL_47171.1 | |
| HL_8C99_027 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8C99_004 | No text annotation | ||
| HL_8C99_005 | No text annotation | ||
| HL_8C99_006 | Ribsomal LSU H95 | ||
| HL_8C99_007 | No text annotation | ||
| HL_8C99_008 | No text annotation | ||
| HL_8C99_012 | No text annotation | ||
| HL_8C99_013 | Externally structured | ||
| HL_8C99_018 | GNRA | ||
| HL_8C99_019 | No text annotation | ||
| HL_8C99_020 | No text annotation | ||
| HL_8C99_021 | No text annotation | ||
| HL_8C99_022 | No text annotation | ||
| HL_8C99_023 | No text annotation | ||
| HL_8C99_025 | No text annotation | ||
| HL_8C99_026 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8C99_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_7RQB_001 NA | |
| IL_8C99_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_8C99_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_8C99_029 | 1/A/82:85, 1/A/97:104 | Kink-turn | geometric IL_1U63_003 IL_24134.1 | |
| IL_8C99_005 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_7A0S_005 IL_15011.2 | |
| IL_8C99_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.2 | |
| IL_8C99_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_7RQB_007 NA | |
| IL_8C99_011 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_8C99_014 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_8C99_015 | 1/A/536:539, 1/A/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_8C99_016 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_7RQB_016 NA | |
| IL_8C99_017 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.2 | |
| IL_8C99_018 | 1/A/674:678, 1/A/799:806 | No text annotation | ||
| IL_8C99_030 | 1/A/844:848, 1/A/930:934 | No text annotation | geometric IL_5J7L_399 NA | |
| IL_8C99_020 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_8C99_022 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_7RQB_035 NA | |
| IL_8C99_023 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_8C99_024 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | geometric IL_4WF9_037 IL_11411.1 | |
| IL_8C99_025 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_8C99_026 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_8C99_027 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_8C99_028 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8C99_004 | No text annotation | ||
| IL_8C99_008 | No text annotation | ||
| IL_8C99_009 | No text annotation | ||
| IL_8C99_010 | Not an internal loop | ||
| IL_8C99_012 | No text annotation | ||
| IL_8C99_013 | Single stack bend | ||
| IL_8C99_019 | 90 degree turn | ||
| IL_8C99_021 | Single stack bend |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8C99_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_5J7L_036 NA | |
| J3_8C99_003 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_8C99_002 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_8C99_004 | 1/A/297:301, 1/A/316:325, 1/A/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J4_8C99_002 | 1/A/297:301, 1/A/316:319, 1/A/323:325, 1/A/337:341 | No text annotation | homologous J4_5J7L_019 NA | |
| J4_8C99_003 | 1/A/601:604, 1/A/624:628, 1/A/635:640, 1/A/648:656 | No text annotation | homologous J4_7A0S_003 J4_98739.1 | |
| J5_8C99_003 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_8C99_002 | 1/A/584:589, 1/A/668:671, 1/A/809:812, 1/A/1195:1196, 1/A/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J6_8C99_002 | 1/A/45:46, 1/A/179:183, 1/A/214:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_8C99_001 | 1/A/817:822, 1/A/835:838, 1/A/940:946, 1/A/971:976, 1/A/987:991, 1/A/1163:1164, 1/A/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J4_8C99_001 | No text annotation | ||
| J5_8C99_001 | No text annotation | ||
| J6_8C99_001 | No text annotation |
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