9H3X Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H3X_014 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_9H3X_060 | 1/A/2819:2827 | No text annotation | homologous HL_5J7L_201 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H3X_001 | No text annotation | ||
| HL_9H3X_002 | No text annotation | ||
| HL_9H3X_003 | No text annotation | ||
| HL_9H3X_004 | Externally structured | ||
| HL_9H3X_005 | No text annotation | ||
| HL_9H3X_006 | No text annotation | ||
| HL_9H3X_007 | No text annotation | ||
| HL_9H3X_008 | No text annotation | ||
| HL_9H3X_009 | T-loop with 2 stacked bulged bases | ||
| HL_9H3X_010 | No text annotation | ||
| HL_9H3X_011 | T-loop with unstacked turn | ||
| HL_9H3X_012 | No text annotation | ||
| HL_9H3X_013 | Pseudoknot geometry | ||
| HL_9H3X_015 | GNRA | ||
| HL_9H3X_016 | No text annotation | ||
| HL_9H3X_017 | T-loop with 2 stacked bulged bases | ||
| HL_9H3X_018 | No text annotation | ||
| HL_9H3X_019 | GNRA | ||
| HL_9H3X_020 | Externally structured | ||
| HL_9H3X_021 | GNRA wlth tandem sheared | ||
| HL_9H3X_022 | No text annotation | ||
| HL_9H3X_023 | UNCG variation | ||
| HL_9H3X_024 | No text annotation | ||
| HL_9H3X_025 | GNRA | ||
| HL_9H3X_026 | No text annotation | ||
| HL_9H3X_027 | No text annotation | ||
| HL_9H3X_028 | GNRA | ||
| HL_9H3X_029 | T-loop with 2 stacked bulged bases | ||
| HL_9H3X_030 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3X_031 | GNRA | ||
| HL_9H3X_032 | No text annotation | ||
| HL_9H3X_033 | Mini UNCG with extended bulge | ||
| HL_9H3X_034 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3X_035 | UNCG | ||
| HL_9H3X_036 | Mini UNCG | ||
| HL_9H3X_037 | No text annotation | ||
| HL_9H3X_038 | GNRA | ||
| HL_9H3X_039 | UNCG | ||
| HL_9H3X_040 | No text annotation | ||
| HL_9H3X_041 | No text annotation | ||
| HL_9H3X_042 | No text annotation | ||
| HL_9H3X_043 | GNRA related | ||
| HL_9H3X_044 | GNRA variation | ||
| HL_9H3X_045 | No text annotation | ||
| HL_9H3X_046 | No text annotation | ||
| HL_9H3X_047 | UNCG | ||
| HL_9H3X_048 | No text annotation | ||
| HL_9H3X_049 | No text annotation | ||
| HL_9H3X_050 | No text annotation | ||
| HL_9H3X_051 | No text annotation | ||
| HL_9H3X_052 | Pseudoknot geometry | ||
| HL_9H3X_053 | GNRA | ||
| HL_9H3X_054 | GNRA | ||
| HL_9H3X_055 | No text annotation | ||
| HL_9H3X_056 | GNRA | ||
| HL_9H3X_057 | Ribsomal LSU H95 | ||
| HL_9H3X_058 | No text annotation | ||
| HL_9H3X_059 | No text annotation | ||
| HL_9H3X_061 | GNRA | ||
| HL_9H3X_062 | No text annotation | ||
| HL_9H3X_063 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H3X_014 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_7A0S_013 IL_66798.3 | |
| IL_9H3X_031 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_5J7L_277 NA | |
| IL_9H3X_032 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_9H3X_034 | 1/A/1018:1024, 1/A/1140:1144 | Kink-turn related | homologous IL_5J7L_280 NA | |
| IL_9H3X_041 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_9H3X_043 | 1/A/1319:1323, 1/A/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_9H3X_044 | 1/A/1349:1351, 1/A/1381:1382 | Single stack bend | geometric IL_8C3A_091 NA | |
| IL_9H3X_045 | 1/A/1353:1355, 1/A/1376:1379 | No text annotation | ||
| IL_9H3X_055 | 1/A/1489:1491, 1/A/1499:1500 | Single bulged A | homologous IL_5J7L_302 NA | |
| IL_9H3X_057 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation | homologous IL_7A0S_059 IL_12566.5 | |
| IL_9H3X_066 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_9H3X_067 | 1/A/1837:1840, 1/A/1902:1903 | No text annotation | homologous IL_4WF9_070 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H3X_001 | Single bulged A | ||
| IL_9H3X_002 | Minor groove platform with extra cWW | ||
| IL_9H3X_003 | No text annotation | ||
| IL_9H3X_004 | No text annotation | ||
| IL_9H3X_005 | Single stack bend | ||
| IL_9H3X_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9H3X_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_9H3X_008 | No text annotation | ||
| IL_9H3X_009 | No text annotation | ||
| IL_9H3X_010 | No text annotation | ||
| IL_9H3X_011 | No text annotation | ||
| IL_9H3X_012 | Double sheared | ||
| IL_9H3X_013 | Isolated non-canonical cWW pair | ||
| IL_9H3X_015 | Isolated non-canonical cWW pair | ||
| IL_9H3X_016 | tHW-tHW cross-strand stack | ||
| IL_9H3X_017 | Single bulged A | ||
| IL_9H3X_018 | No text annotation | ||
| IL_9H3X_019 | Decoding loop related | ||
| IL_9H3X_020 | No text annotation | ||
| IL_9H3X_021 | 90 degree turn | ||
| IL_9H3X_022 | No text annotation | ||
| IL_9H3X_023 | Stack outside cWW | ||
| IL_9H3X_024 | Single stack bend | ||
| IL_9H3X_025 | Single stack bend | ||
| IL_9H3X_026 | No text annotation | ||
| IL_9H3X_027 | Single bulged G | ||
| IL_9H3X_028 | C-loop with bulged stacked A's | ||
| IL_9H3X_029 | Isolated non-canonical cWW pair | ||
| IL_9H3X_030 | Single bulged C | ||
| IL_9H3X_033 | Single bulged U | ||
| IL_9H3X_035 | No text annotation | ||
| IL_9H3X_036 | Isolated non-canonical cWW pair | ||
| IL_9H3X_037 | Tandem non-canonical cWW pairs | ||
| IL_9H3X_038 | Isolated cWS basepair | ||
| IL_9H3X_039 | No text annotation | ||
| IL_9H3X_040 | Kink-turn | ||
| IL_9H3X_042 | Major groove platform; stack outside cWW | ||
| IL_9H3X_046 | tSH-tHW-tHS | ||
| IL_9H3X_047 | No text annotation | ||
| IL_9H3X_048 | UAA/GAN | ||
| IL_9H3X_049 | Tandem non-canonical cWW pairs | ||
| IL_9H3X_050 | tSH-tHW | ||
| IL_9H3X_051 | Single bulged U | ||
| IL_9H3X_052 | No text annotation | ||
| IL_9H3X_053 | tSH-tHW-tHS | ||
| IL_9H3X_054 | 180 degree turn | ||
| IL_9H3X_056 | UAA/GAN variation | ||
| IL_9H3X_058 | Isolated tWW turn | ||
| IL_9H3X_059 | Major groove platform; stack outside cWW | ||
| IL_9H3X_060 | No text annotation | ||
| IL_9H3X_061 | Intercalated tWH | ||
| IL_9H3X_062 | tSH-tSH-tHH-tHS | ||
| IL_9H3X_063 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_9H3X_064 | Triple sheared | ||
| IL_9H3X_065 | Single bulged A | ||
| IL_9H3X_068 | Major groove intercalation | ||
| IL_9H3X_069 | No text annotation | ||
| IL_9H3X_070 | No text annotation | ||
| IL_9H3X_071 | UAA/GAN variation | ||
| IL_9H3X_072 | Bulged stacked bases | ||
| IL_9H3X_073 | Major groove platform | ||
| IL_9H3X_074 | No text annotation | ||
| IL_9H3X_075 | Single bulged U | ||
| IL_9H3X_076 | Minor groove platform | ||
| IL_9H3X_077 | Isolated tHS basepair with bulges | ||
| IL_9H3X_078 | Isolated non-canonical cWW pair | ||
| IL_9H3X_079 | No text annotation | ||
| IL_9H3X_080 | Multiple bulged bases | ||
| IL_9H3X_081 | No text annotation | ||
| IL_9H3X_082 | No text annotation | ||
| IL_9H3X_083 | No text annotation | ||
| IL_9H3X_084 | No text annotation | ||
| IL_9H3X_085 | Single bulged U | ||
| IL_9H3X_086 | Double sheared | ||
| IL_9H3X_087 | No text annotation | ||
| IL_9H3X_088 | No text annotation | ||
| IL_9H3X_089 | No text annotation | ||
| IL_9H3X_090 | No text annotation | ||
| IL_9H3X_091 | C-loop | ||
| IL_9H3X_092 | No text annotation | ||
| IL_9H3X_093 | Multiple bulged bases | ||
| IL_9H3X_094 | No text annotation | ||
| IL_9H3X_095 | Single bulged A | ||
| IL_9H3X_096 | No text annotation | ||
| IL_9H3X_097 | Major groove intercalation | ||
| IL_9H3X_098 | Multiple bulged bases with non-canonical cWW | ||
| IL_9H3X_099 | tHS double platform | ||
| IL_9H3X_100 | Major groove intercalation | ||
| IL_9H3X_101 | No text annotation | ||
| IL_9H3X_102 | No text annotation | ||
| IL_9H3X_103 | Symmetric double minor groove platform | ||
| IL_9H3X_104 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H3X_004 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_7A0S_004 J3_46658.1 | |
| J3_9H3X_006 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_9H3X_007 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_9H3X_008 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_9H3X_009 | 1/A/1424:1429, 1/A/1564:1565, 1/A/1568:1574 | No text annotation | homologous J3_7A0S_019 J3_34864.3 | |
| J5_9H3X_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_9H3X_004 | 1/A/1674:1682, 1/A/1706:1707, 1/A/1751:1752, 1/A/1756:1764, 1/A/1988:1990 | No text annotation | homologous J5_5J7L_016 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9H3X_001 | No text annotation | ||
| J3_9H3X_002 | No text annotation | ||
| J3_9H3X_003 | No text annotation | ||
| J3_9H3X_005 | No text annotation | ||
| J3_9H3X_010 | Kink-turn 3-way junction | ||
| J3_9H3X_011 | No text annotation | ||
| J3_9H3X_012 | No text annotation | ||
| J3_9H3X_013 | No text annotation | ||
| J3_9H3X_014 | No text annotation | ||
| J4_9H3X_001 | No text annotation | ||
| J4_9H3X_002 | No text annotation | ||
| J4_9H3X_003 | No text annotation | ||
| J4_9H3X_004 | No text annotation | ||
| J4_9H3X_005 | No text annotation | ||
| J4_9H3X_006 | No text annotation | ||
| J4_9H3X_007 | No text annotation | ||
| J4_9H3X_008 | No text annotation | ||
| J4_9H3X_009 | No text annotation | ||
| J4_9H3X_010 | No text annotation | ||
| J4_9H3X_011 | No text annotation | ||
| J5_9H3X_001 | No text annotation | ||
| J5_9H3X_003 | No text annotation | ||
| J6_9H3X_001 | No text annotation | ||
| J6_9H3X_002 | No text annotation | ||
| J7_9H3X_001 | No text annotation | ||
| J7_9H3X_002 | No text annotation |
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