9H3T Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H3T_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9H3T_013 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_9H3T_029 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_9H3T_031 | 1/A/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_9H3T_037 | 1/A/1630:1636 | GNRA | homologous HL_5J7L_174 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H3T_001 | No text annotation | ||
| HL_9H3T_002 | No text annotation | ||
| HL_9H3T_004 | No text annotation | ||
| HL_9H3T_005 | No text annotation | ||
| HL_9H3T_006 | No text annotation | ||
| HL_9H3T_007 | No text annotation | ||
| HL_9H3T_008 | No text annotation | ||
| HL_9H3T_009 | T-loop with 2 stacked bulged bases | ||
| HL_9H3T_010 | T-loop with unstacked turn | ||
| HL_9H3T_011 | No text annotation | ||
| HL_9H3T_012 | Pseudoknot geometry | ||
| HL_9H3T_014 | GNRA | ||
| HL_9H3T_015 | Mini UNCG with extended bulge | ||
| HL_9H3T_016 | T-loop with 2 stacked bulged bases | ||
| HL_9H3T_017 | No text annotation | ||
| HL_9H3T_018 | GNRA | ||
| HL_9H3T_019 | No text annotation | ||
| HL_9H3T_020 | GNRA wlth tandem sheared | ||
| HL_9H3T_021 | No text annotation | ||
| HL_9H3T_022 | No text annotation | ||
| HL_9H3T_023 | No text annotation | ||
| HL_9H3T_024 | GNRA | ||
| HL_9H3T_025 | No text annotation | ||
| HL_9H3T_026 | No text annotation | ||
| HL_9H3T_027 | GNRA | ||
| HL_9H3T_028 | T-loop with 2 stacked bulged bases | ||
| HL_9H3T_030 | GNRA | ||
| HL_9H3T_032 | Mini UNCG with extended bulge | ||
| HL_9H3T_033 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3T_034 | UNCG | ||
| HL_9H3T_035 | Mini UNCG | ||
| HL_9H3T_036 | No text annotation | ||
| HL_9H3T_038 | UNCG | ||
| HL_9H3T_039 | No text annotation | ||
| HL_9H3T_040 | No text annotation | ||
| HL_9H3T_041 | No text annotation | ||
| HL_9H3T_042 | GNRA related | ||
| HL_9H3T_043 | No text annotation | ||
| HL_9H3T_044 | No text annotation | ||
| HL_9H3T_045 | No text annotation | ||
| HL_9H3T_046 | GNRA variation | ||
| HL_9H3T_047 | GNRA | ||
| HL_9H3T_048 | Ribsomal LSU H95 | ||
| HL_9H3T_049 | No text annotation | ||
| HL_9H3T_050 | Mini UNCG | ||
| HL_9H3T_051 | No text annotation | ||
| HL_9H3T_052 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H3T_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9H3T_036 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | geometric IL_4V9F_008 IL_74641.1 | |
| IL_9H3T_038 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_7A0S_048 IL_89021.3 | |
| IL_9H3T_043 | 1/A/1437:1440, 1/A/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_9H3T_045 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_9H3T_051 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_9H3T_072 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H3T_001 | Triple sheared with non-canonical cWW | ||
| IL_9H3T_002 | Single bulged A | ||
| IL_9H3T_003 | Minor groove platform | ||
| IL_9H3T_004 | No text annotation | ||
| IL_9H3T_005 | Single stack bend | ||
| IL_9H3T_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9H3T_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_9H3T_008 | No text annotation | ||
| IL_9H3T_009 | No text annotation | ||
| IL_9H3T_011 | No text annotation | ||
| IL_9H3T_012 | Double sheared | ||
| IL_9H3T_013 | Isolated non-canonical cWW pair | ||
| IL_9H3T_014 | AAA cross-strand stack | ||
| IL_9H3T_015 | Isolated non-canonical cWW pair | ||
| IL_9H3T_016 | tHW-tHW cross-strand stack | ||
| IL_9H3T_017 | Single bulged A | ||
| IL_9H3T_018 | No text annotation | ||
| IL_9H3T_019 | Major groove platform | ||
| IL_9H3T_020 | Multiple bulged bases | ||
| IL_9H3T_021 | 90 degree turn | ||
| IL_9H3T_022 | Stack outside cWW | ||
| IL_9H3T_023 | Single stack bend | ||
| IL_9H3T_024 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_9H3T_025 | Single bulged C | ||
| IL_9H3T_026 | UAA/GAN | ||
| IL_9H3T_027 | SSU/LSU pseudoknot | ||
| IL_9H3T_028 | Single bulged U | ||
| IL_9H3T_029 | Kink-turn related | ||
| IL_9H3T_030 | No text annotation | ||
| IL_9H3T_031 | Isolated non-canonical cWW pair | ||
| IL_9H3T_032 | Isolated cWS basepair | ||
| IL_9H3T_033 | No text annotation | ||
| IL_9H3T_034 | Kink-turn | ||
| IL_9H3T_035 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9H3T_037 | Major groove minor groove platform with tHH | ||
| IL_9H3T_039 | tSH-tHW-tHS | ||
| IL_9H3T_040 | No text annotation | ||
| IL_9H3T_041 | UAA/GAN | ||
| IL_9H3T_042 | Tandem non-canonical cWW pairs | ||
| IL_9H3T_044 | Single bulged U | ||
| IL_9H3T_046 | tSH-tHW-tHS | ||
| IL_9H3T_047 | 180 degree turn | ||
| IL_9H3T_048 | Single bulged A | ||
| IL_9H3T_049 | UAA/GAN variation | ||
| IL_9H3T_050 | No text annotation | ||
| IL_9H3T_052 | Major groove platform; stack outside cWW | ||
| IL_9H3T_053 | No text annotation | ||
| IL_9H3T_054 | Intercalated tWH | ||
| IL_9H3T_055 | tSH-tSH-tHH-tHS | ||
| IL_9H3T_056 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_9H3T_057 | Triple sheared | ||
| IL_9H3T_058 | Single bulged A | ||
| IL_9H3T_059 | Kink-turn related | ||
| IL_9H3T_060 | Major groove platform | ||
| IL_9H3T_061 | No text annotation | ||
| IL_9H3T_062 | Isolated tHS basepair with bulges | ||
| IL_9H3T_063 | Isolated non-canonical cWW pair | ||
| IL_9H3T_064 | Single bulged U | ||
| IL_9H3T_065 | No text annotation | ||
| IL_9H3T_066 | Isolated non-canonical cWW with bulges | ||
| IL_9H3T_067 | Multiple bulged bases | ||
| IL_9H3T_068 | Major groove platform with intercalation | ||
| IL_9H3T_069 | tSH-tHS-tHW | ||
| IL_9H3T_070 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9H3T_071 | C-loop | ||
| IL_9H3T_073 | Multiple bulged bases | ||
| IL_9H3T_074 | UAA/GAN with extra cWW | ||
| IL_9H3T_075 | Single bulged A | ||
| IL_9H3T_076 | No text annotation | ||
| IL_9H3T_077 | Major groove intercalation | ||
| IL_9H3T_078 | Multiple bulged bases with non-canonical cWW | ||
| IL_9H3T_079 | tHS double platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H3T_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9H3T_006 | 1/A/698:700, 1/A/732:736, 1/A/760:763 | No text annotation | homologous J3_4WF9_003 J3_69816.1 | |
| J3_9H3T_007 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_7A0S_006 J3_32852.7 | |
| J3_9H3T_008 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_9H3T_009 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_9H3T_010 | 1/A/1424:1429, 1/A/1564:1565, 1/A/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_9H3T_013 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_9H3T_003 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_9H3T_004 | 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_9H3T_005 | 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_9H3T_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_5J7L_015 NA | |
| J7_9H3T_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 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9H3T_001 | No text annotation | ||
| J3_9H3T_003 | No text annotation | ||
| J3_9H3T_004 | No text annotation | ||
| J3_9H3T_005 | No text annotation | ||
| J3_9H3T_011 | Kink-turn 3-way junction | ||
| J3_9H3T_012 | No text annotation | ||
| J4_9H3T_001 | No text annotation | ||
| J4_9H3T_002 | No text annotation | ||
| J4_9H3T_006 | No text annotation | ||
| J4_9H3T_007 | No text annotation | ||
| J4_9H3T_008 | No text annotation | ||
| J5_9H3T_001 | No text annotation | ||
| J5_9H3T_002 | No text annotation | ||
| J5_9H3T_004 | No text annotation | ||
| J6_9H3T_001 | No text annotation | ||
| J7_9H3T_002 | No text annotation |
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