9H3N Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H3N_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_9H3N_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9H3N_010 | 1/A/319:323 | No text annotation | homologous HL_7A0S_011 HL_75660.6 | |
| HL_9H3N_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9H3N_014 | 1/A/462:467 | GNRA | homologous HL_7A0S_015 HL_34789.1 | |
| HL_9H3N_017 | 1/A/564:577 | No text annotation | ||
| HL_9H3N_026 | 1/A/978:985 | No text annotation | homologous HL_9DFE_026 HL_47171.1 | |
| HL_9H3N_028 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_9H3N_029 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_4WF9_032 HL_33597.1 | |
| HL_9H3N_032 | 1/A/1389:1398 | No text annotation | homologous HL_9DFE_034 HL_77449.1 | |
| HL_9H3N_033 | 1/A/1451:1459 | Mini UNCG with extended bulge | homologous HL_5J7L_169 NA | |
| HL_9H3N_039 | 1/A/2027:2036 | No text annotation | homologous HL_5J7L_183 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H3N_002 | No text annotation | ||
| HL_9H3N_004 | No text annotation | ||
| HL_9H3N_005 | No text annotation | ||
| HL_9H3N_006 | No text annotation | ||
| HL_9H3N_007 | No text annotation | ||
| HL_9H3N_008 | No text annotation | ||
| HL_9H3N_009 | T-loop with 2 stacked bulged bases | ||
| HL_9H3N_012 | No text annotation | ||
| HL_9H3N_013 | No text annotation | ||
| HL_9H3N_015 | GNRA | ||
| HL_9H3N_016 | No text annotation | ||
| HL_9H3N_018 | No text annotation | ||
| HL_9H3N_019 | No text annotation | ||
| HL_9H3N_020 | No text annotation | ||
| HL_9H3N_021 | GNRA wlth tandem sheared | ||
| HL_9H3N_022 | No text annotation | ||
| HL_9H3N_023 | No text annotation | ||
| HL_9H3N_024 | Mini UNCG | ||
| HL_9H3N_025 | Mini UNCG | ||
| HL_9H3N_027 | Externally structured | ||
| HL_9H3N_030 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3N_031 | GNRA | ||
| HL_9H3N_034 | Externally structured | ||
| HL_9H3N_035 | UNCG | ||
| HL_9H3N_036 | Mini UNCG | ||
| HL_9H3N_037 | No text annotation | ||
| HL_9H3N_038 | GNRA | ||
| HL_9H3N_040 | No text annotation | ||
| HL_9H3N_041 | Externally structured | ||
| HL_9H3N_042 | GNRA | ||
| HL_9H3N_043 | GNRA | ||
| HL_9H3N_044 | Ribsomal LSU H95 | ||
| HL_9H3N_045 | No text annotation | ||
| HL_9H3N_046 | Mini UNCG | ||
| HL_9H3N_047 | No text annotation | ||
| HL_9H3N_048 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H3N_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_7A0S_001 IL_22311.1 | |
| IL_9H3N_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7A0S_002 IL_14190.1 | |
| IL_9H3N_004 | 1/A/82:85, 1/A/97:104 | No text annotation | ||
| IL_9H3N_007 | 1/A/236:238, 1/A/260:261 | Single stack bend | geometric IL_5J7L_391 NA | |
| IL_9H3N_011 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9H3N_012 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_9H3N_015 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.1 | |
| IL_9H3N_025 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.1 | |
| IL_9H3N_026 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_9H3N_027 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_9H3N_028 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_9H3N_030 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.4 | |
| IL_9H3N_031 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_9H3N_032 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_9H3N_034 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | geometric IL_6CZR_139 NA | |
| IL_9H3N_035 | 1/A/1319:1323, 1/A/1331:1333 | No text annotation | geometric IL_8CRE_126 NA | |
| IL_9H3N_044 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_9H3N_055 | 1/A/2636:2640, 1/A/2774:2782 | No text annotation | homologous IL_9DFE_101 IL_04638.4 | |
| IL_9H3N_060 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_9H3N_066 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H3N_003 | Minor groove platform | ||
| IL_9H3N_005 | No text annotation | ||
| IL_9H3N_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9H3N_008 | No text annotation | ||
| IL_9H3N_009 | No text annotation | ||
| IL_9H3N_010 | No text annotation | ||
| IL_9H3N_013 | Double sheared | ||
| IL_9H3N_014 | AAA cross-strand stack | ||
| IL_9H3N_016 | No text annotation | ||
| IL_9H3N_017 | Single bulged A | ||
| IL_9H3N_018 | No text annotation | ||
| IL_9H3N_019 | No text annotation | ||
| IL_9H3N_020 | Multiple bulged bases | ||
| IL_9H3N_021 | 90 degree turn | ||
| IL_9H3N_022 | No text annotation | ||
| IL_9H3N_023 | Stack outside cWW | ||
| IL_9H3N_024 | Single stack bend | ||
| IL_9H3N_029 | No text annotation | ||
| IL_9H3N_033 | No text annotation | ||
| IL_9H3N_036 | UAA/GAN | ||
| IL_9H3N_037 | tSH-tHW-tHS | ||
| IL_9H3N_038 | No text annotation | ||
| IL_9H3N_039 | No text annotation | ||
| IL_9H3N_040 | Single stack bend | ||
| IL_9H3N_041 | Tandem non-canonical cWW pairs | ||
| IL_9H3N_042 | tSH-tHW | ||
| IL_9H3N_043 | Single bulged U | ||
| IL_9H3N_045 | tSH-tHW-tHS | ||
| IL_9H3N_046 | 180 degree turn | ||
| IL_9H3N_047 | Single bulged A | ||
| IL_9H3N_048 | UAA/GAN variation | ||
| IL_9H3N_049 | No text annotation | ||
| IL_9H3N_050 | Isolated tWW turn | ||
| IL_9H3N_051 | No text annotation | ||
| IL_9H3N_052 | No text annotation | ||
| IL_9H3N_053 | No text annotation | ||
| IL_9H3N_054 | No text annotation | ||
| IL_9H3N_056 | Single stack bend | ||
| IL_9H3N_057 | Single stack bend | ||
| IL_9H3N_058 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9H3N_059 | C-loop | ||
| IL_9H3N_061 | Multiple bulged bases | ||
| IL_9H3N_062 | UAA/GAN with extra cWW | ||
| IL_9H3N_063 | Single bulged A | ||
| IL_9H3N_064 | No text annotation | ||
| IL_9H3N_065 | Major groove intercalation | ||
| IL_9H3N_067 | tHS double platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H3N_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9H3N_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_9H3N_006 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_9H3N_007 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_9H3N_008 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_9H3N_012 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_9H3N_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_9H3N_005 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_9H3N_006 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J5_9H3N_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:152, 1/A/174:178 | No text annotation | ||
| J5_9H3N_002 | 1/A/531:533, 1/A/560:564, 1/A/577:579, 1/A/1261:1262, 1/A/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_9H3N_003 | 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_4WF9_004 J5_74302.6 | |
| J6_9H3N_001 | 1/A/45:46, 1/A/179:183, 1/A/215:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9H3N_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2630, 1/A/2788:2789, 1/A/2894:2895 | No text annotation | ||
| J7_9H3N_002 | 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 |
|---|---|---|---|
| J3_9H3N_001 | No text annotation | ||
| J3_9H3N_004 | No text annotation | ||
| J3_9H3N_005 | No text annotation | ||
| J3_9H3N_009 | No text annotation | ||
| J3_9H3N_010 | No text annotation | ||
| J3_9H3N_011 | No text annotation | ||
| J4_9H3N_001 | No text annotation | ||
| J4_9H3N_003 | No text annotation | ||
| J4_9H3N_004 | No text annotation | ||
| J4_9H3N_007 | No text annotation | ||
| J4_9H3N_008 | No text annotation |
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