6O9K Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6O9K_045 | 1/A/1777:1787 | No text annotation | homologous HL_7RQB_045 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6O9K_001 | No text annotation | ||
| HL_6O9K_002 | No text annotation | ||
| HL_6O9K_003 | No text annotation | ||
| HL_6O9K_004 | Mini UNCG | ||
| HL_6O9K_005 | No text annotation | ||
| HL_6O9K_006 | No text annotation | ||
| HL_6O9K_007 | No text annotation | ||
| HL_6O9K_008 | No text annotation | ||
| HL_6O9K_009 | T-loop with 1 bulged base | ||
| HL_6O9K_010 | No text annotation | ||
| HL_6O9K_011 | T-loop with unstacked turn | ||
| HL_6O9K_012 | No text annotation | ||
| HL_6O9K_013 | Pseudoknot geometry | ||
| HL_6O9K_014 | GNRA | ||
| HL_6O9K_015 | GNRA | ||
| HL_6O9K_016 | No text annotation | ||
| HL_6O9K_017 | T-loop with 2 stacked bulged bases | ||
| HL_6O9K_018 | No text annotation | ||
| HL_6O9K_019 | GNRA | ||
| HL_6O9K_020 | No text annotation | ||
| HL_6O9K_021 | GNRA wlth tandem sheared | ||
| HL_6O9K_022 | No text annotation | ||
| HL_6O9K_023 | No text annotation | ||
| HL_6O9K_024 | No text annotation | ||
| HL_6O9K_025 | No text annotation | ||
| HL_6O9K_026 | GNRA | ||
| HL_6O9K_027 | No text annotation | ||
| HL_6O9K_028 | No text annotation | ||
| HL_6O9K_029 | GNRA wlth tandem sheared | ||
| HL_6O9K_030 | No text annotation | ||
| HL_6O9K_031 | GNRA | ||
| HL_6O9K_032 | T-loop with 2 stacked bulged bases | ||
| HL_6O9K_033 | Pseudoknot geometry with 3' bulge | ||
| HL_6O9K_034 | GNRA | ||
| HL_6O9K_035 | No text annotation | ||
| HL_6O9K_036 | Mini UNCG with extended bulge | ||
| HL_6O9K_037 | Pseudoknot geometry with 3' bulge | ||
| HL_6O9K_038 | UNCG | ||
| HL_6O9K_039 | Mini UNCG | ||
| HL_6O9K_040 | No text annotation | ||
| HL_6O9K_041 | GNRA | ||
| HL_6O9K_042 | No text annotation | ||
| HL_6O9K_043 | No text annotation | ||
| HL_6O9K_044 | No text annotation | ||
| HL_6O9K_046 | GNRA related | ||
| HL_6O9K_047 | No text annotation | ||
| HL_6O9K_048 | No text annotation | ||
| HL_6O9K_049 | No text annotation | ||
| HL_6O9K_050 | No text annotation | ||
| HL_6O9K_107 | No text annotation | ||
| HL_6O9K_051 | No text annotation | ||
| HL_6O9K_052 | No text annotation | ||
| HL_6O9K_053 | No text annotation | ||
| HL_6O9K_054 | No text annotation | ||
| HL_6O9K_055 | No text annotation | ||
| HL_6O9K_111 | No text annotation | ||
| HL_6O9K_056 | Pseudoknot geometry | ||
| HL_6O9K_057 | GNRA | ||
| HL_6O9K_058 | GNRA | ||
| HL_6O9K_059 | No text annotation | ||
| HL_6O9K_060 | No text annotation | ||
| HL_6O9K_061 | GNRA variation | ||
| HL_6O9K_062 | No text annotation | ||
| HL_6O9K_063 | GNRA | ||
| HL_6O9K_064 | GNRA | ||
| HL_6O9K_065 | Ribsomal LSU H95 | ||
| HL_6O9K_066 | No text annotation | ||
| HL_6O9K_108 | UNCG variation | ||
| HL_6O9K_067 | Mini UNCG | ||
| HL_6O9K_068 | No text annotation | ||
| HL_6O9K_069 | GNRA | ||
| HL_6O9K_109 | No text annotation | ||
| HL_6O9K_070 | No text annotation | ||
| HL_6O9K_071 | Mini UNCG | ||
| HL_6O9K_072 | No text annotation | ||
| HL_6O9K_110 | No text annotation | ||
| HL_6O9K_112 | No text annotation | ||
| HL_6O9K_073 | No text annotation | ||
| HL_6O9K_074 | GNRA | ||
| HL_6O9K_075 | GNRA | ||
| HL_6O9K_076 | UNCG | ||
| HL_6O9K_077 | GNRA related | ||
| HL_6O9K_078 | GNRA | ||
| HL_6O9K_079 | No text annotation | ||
| HL_6O9K_080 | UNCG | ||
| HL_6O9K_081 | GNRA | ||
| HL_6O9K_082 | UNCG | ||
| HL_6O9K_083 | GNRA wlth extra near cWW | ||
| HL_6O9K_084 | No text annotation | ||
| HL_6O9K_085 | GNRA-like with tWH | ||
| HL_6O9K_086 | No text annotation | ||
| HL_6O9K_087 | GNRA | ||
| HL_6O9K_088 | No text annotation | ||
| HL_6O9K_089 | Externally structured | ||
| HL_6O9K_090 | GNRA | ||
| HL_6O9K_091 | GNRA | ||
| HL_6O9K_092 | No text annotation | ||
| HL_6O9K_093 | GNRA | ||
| HL_6O9K_094 | No text annotation | ||
| HL_6O9K_095 | GNRA | ||
| HL_6O9K_096 | T-loop related | ||
| HL_6O9K_097 | No text annotation | ||
| HL_6O9K_098 | GNRA | ||
| HL_6O9K_099 | GNRA | ||
| HL_6O9K_100 | T-loop with 3 stacked bulged bases | ||
| HL_6O9K_101 | No text annotation | ||
| HL_6O9K_102 | UNCG | ||
| HL_6O9K_103 | GNRA | ||
| HL_6O9K_104 | No text annotation | ||
| HL_6O9K_105 | tRNA anticodon loop | ||
| HL_6O9K_106 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6O9K_021 | 1/A/775:777, 1/A/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6O9K_001 | Triple sheared with non-canonical cWW | ||
| IL_6O9K_002 | Single bulged A | ||
| IL_6O9K_003 | Minor groove platform | ||
| IL_6O9K_004 | No text annotation | ||
| IL_6O9K_005 | Single stack bend | ||
| IL_6O9K_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6O9K_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6O9K_008 | No text annotation | ||
| IL_6O9K_173 | No text annotation | ||
| IL_6O9K_189 | No text annotation | ||
| IL_6O9K_009 | No text annotation | ||
| IL_6O9K_010 | No text annotation | ||
| IL_6O9K_011 | No text annotation | ||
| IL_6O9K_012 | Double sheared | ||
| IL_6O9K_013 | Isolated non-canonical cWW pair | ||
| IL_6O9K_014 | AAA cross-strand stack | ||
| IL_6O9K_015 | Isolated non-canonical cWW pair | ||
| IL_6O9K_016 | tHW-tHW cross-strand stack | ||
| IL_6O9K_017 | Single bulged A | ||
| IL_6O9K_018 | Single bulged G | ||
| IL_6O9K_019 | Triple sheared | ||
| IL_6O9K_020 | Major groove platform | ||
| IL_6O9K_022 | Single stack bend | ||
| IL_6O9K_023 | 90 degree turn | ||
| IL_6O9K_174 | No text annotation | ||
| IL_6O9K_024 | Stack outside cWW | ||
| IL_6O9K_025 | Single stack bend | ||
| IL_6O9K_026 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_6O9K_027 | Single bulged G | ||
| IL_6O9K_028 | C-loop with bulged stacked A's | ||
| IL_6O9K_029 | Isolated non-canonical cWW pair | ||
| IL_6O9K_175 | No text annotation | ||
| IL_6O9K_030 | Double sheared with non-canonical cWW | ||
| IL_6O9K_031 | No text annotation | ||
| IL_6O9K_176 | Tandem non-canonical cWW pairs | ||
| IL_6O9K_032 | Single bulged C | ||
| IL_6O9K_033 | UAA/GAN | ||
| IL_6O9K_034 | SSU/LSU pseudoknot | ||
| IL_6O9K_035 | Single bulged U | ||
| IL_6O9K_036 | Kink-turn related | ||
| IL_6O9K_037 | No text annotation | ||
| IL_6O9K_038 | Isolated non-canonical cWW pair | ||
| IL_6O9K_039 | Tandem non-canonical cWW pairs | ||
| IL_6O9K_040 | Kink-turn | ||
| IL_6O9K_041 | Major groove platform | ||
| IL_6O9K_177 | No text annotation | ||
| IL_6O9K_042 | Isolated cWS basepair | ||
| IL_6O9K_043 | No text annotation | ||
| IL_6O9K_044 | Kink-turn | ||
| IL_6O9K_045 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6O9K_046 | Major groove platform; stack outside cWW | ||
| IL_6O9K_047 | C-loop | ||
| IL_6O9K_048 | UAA/GAN | ||
| IL_6O9K_049 | tSH-tHW-tHS | ||
| IL_6O9K_050 | No text annotation | ||
| IL_6O9K_051 | UAA/GAN | ||
| IL_6O9K_052 | Tandem non-canonical cWW pairs | ||
| IL_6O9K_053 | tSH-tHW | ||
| IL_6O9K_054 | Single bulged U | ||
| IL_6O9K_055 | tSH-tHH-tHS | ||
| IL_6O9K_178 | No text annotation | ||
| IL_6O9K_179 | tSH-tHW-tHS | ||
| IL_6O9K_056 | No text annotation | ||
| IL_6O9K_057 | 180 degree turn | ||
| IL_6O9K_058 | Single bulged A | ||
| IL_6O9K_059 | UAA/GAN variation | ||
| IL_6O9K_060 | No text annotation | ||
| IL_6O9K_061 | Isolated tWW turn | ||
| IL_6O9K_062 | Major groove platform; stack outside cWW | ||
| IL_6O9K_180 | No text annotation | ||
| IL_6O9K_063 | Intercalated tWH | ||
| IL_6O9K_064 | tSH-tSH-tHH-tHS | ||
| IL_6O9K_065 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6O9K_066 | Quadruple sheared | ||
| IL_6O9K_181 | Triple sheared | ||
| IL_6O9K_067 | Single bulged A | ||
| IL_6O9K_068 | Kink-turn related | ||
| IL_6O9K_069 | Minor groove platform, major groove intercalation | ||
| IL_6O9K_070 | Major groove intercalation | ||
| IL_6O9K_182 | No text annotation | ||
| IL_6O9K_071 | Minor groove platform | ||
| IL_6O9K_183 | No text annotation | ||
| IL_6O9K_072 | Bulged stacked bases | ||
| IL_6O9K_073 | No text annotation | ||
| IL_6O9K_074 | Major groove platform | ||
| IL_6O9K_075 | No text annotation | ||
| IL_6O9K_076 | Single bulged U | ||
| IL_6O9K_077 | Minor groove platform | ||
| IL_6O9K_078 | Isolated tHS basepair with bulges | ||
| IL_6O9K_079 | Isolated non-canonical cWW pair | ||
| IL_6O9K_080 | Single bulged U | ||
| IL_6O9K_081 | Double sheared | ||
| IL_6O9K_082 | Major groove intercalation | ||
| IL_6O9K_083 | Major groove platform | ||
| IL_6O9K_084 | Major groove platform with extra pair | ||
| IL_6O9K_190 | Major groove platform | ||
| IL_6O9K_085 | Major groove minor groove platform with extra cWW | ||
| IL_6O9K_086 | Double sheared with non-canonical cWW | ||
| IL_6O9K_087 | Major groove platform | ||
| IL_6O9K_088 | Isolated non-canonical cWW with bulges | ||
| IL_6O9K_089 | No text annotation | ||
| IL_6O9K_090 | Major groove platform with intercalation | ||
| IL_6O9K_091 | Single bulged A | ||
| IL_6O9K_092 | tSH-tHS-tHW | ||
| IL_6O9K_093 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6O9K_094 | C-loop | ||
| IL_6O9K_095 | UAA/GAN related, with intercalation | ||
| IL_6O9K_096 | Multiple bulged bases | ||
| IL_6O9K_097 | UAA/GAN with extra cWW | ||
| IL_6O9K_098 | Single bulged A | ||
| IL_6O9K_099 | No text annotation | ||
| IL_6O9K_100 | Major groove intercalation | ||
| IL_6O9K_101 | Multiple bulged bases with non-canonical cWW | ||
| IL_6O9K_102 | tHS double platform | ||
| IL_6O9K_103 | Major groove intercalation | ||
| IL_6O9K_104 | No text annotation | ||
| IL_6O9K_105 | No text annotation | ||
| IL_6O9K_191 | No text annotation | ||
| IL_6O9K_106 | Symmetric double minor groove platform | ||
| IL_6O9K_107 | Bacterial 5S Loop E | ||
| IL_6O9K_108 | Single bulged G | ||
| IL_6O9K_109 | Single bulged A | ||
| IL_6O9K_110 | No text annotation | ||
| IL_6O9K_111 | Minor groove platform | ||
| IL_6O9K_112 | Multiple bulged bases | ||
| IL_6O9K_113 | Minor groove platform with extra cWW | ||
| IL_6O9K_114 | Minor groove platform | ||
| IL_6O9K_115 | Major groove intercalation | ||
| IL_6O9K_116 | Isolated non-canonical cWW pair | ||
| IL_6O9K_117 | Minor groove platform related | ||
| IL_6O9K_118 | Isolated cWH basepair | ||
| IL_6O9K_119 | tWH-tWH-tHW-tHW | ||
| IL_6O9K_120 | No text annotation | ||
| IL_6O9K_121 | Kink-turn with non-sequential stacking | ||
| IL_6O9K_192 | No text annotation | ||
| IL_6O9K_122 | No text annotation | ||
| IL_6O9K_123 | C-loop | ||
| IL_6O9K_124 | Single bulged U | ||
| IL_6O9K_125 | C-loop | ||
| IL_6O9K_126 | Single bulged G | ||
| IL_6O9K_127 | No text annotation | ||
| IL_6O9K_128 | No text annotation | ||
| IL_6O9K_129 | tSH-tHW-tWW | ||
| IL_6O9K_184 | No text annotation | ||
| IL_6O9K_130 | No text annotation | ||
| IL_6O9K_131 | SSU/LSU pseudoknot | ||
| IL_6O9K_132 | Kink-turn related | ||
| IL_6O9K_133 | No text annotation | ||
| IL_6O9K_134 | tSH-tHW-tHS | ||
| IL_6O9K_135 | Major groove platform | ||
| IL_6O9K_136 | Major groove minor groove platform; mini C-loop | ||
| IL_6O9K_137 | No text annotation | ||
| IL_6O9K_138 | Major groove platform; stack outside cWW | ||
| IL_6O9K_139 | Single stack bend | ||
| IL_6O9K_140 | Tandem non-canonical cWW pairs | ||
| IL_6O9K_185 | Triple non-canonical cWW pairs | ||
| IL_6O9K_141 | No text annotation | ||
| IL_6O9K_142 | Kink-turn | ||
| IL_6O9K_143 | Left turn | ||
| IL_6O9K_144 | tSH-tHW-tHS | ||
| IL_6O9K_145 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6O9K_146 | Single bulged A | ||
| IL_6O9K_147 | Single bulged G | ||
| IL_6O9K_148 | Minor groove platform | ||
| IL_6O9K_149 | No text annotation | ||
| IL_6O9K_150 | Minor groove platform | ||
| IL_6O9K_151 | Single stack bend | ||
| IL_6O9K_152 | Single bulged U | ||
| IL_6O9K_153 | Isolated cWS basepair | ||
| IL_6O9K_154 | Minor groove platform | ||
| IL_6O9K_155 | Single bulged U | ||
| IL_6O9K_156 | Isolated non-canonical cWW pair | ||
| IL_6O9K_157 | No text annotation | ||
| IL_6O9K_186 | No text annotation | ||
| IL_6O9K_187 | No text annotation | ||
| IL_6O9K_158 | Minor groove platform | ||
| IL_6O9K_159 | No text annotation | ||
| IL_6O9K_160 | No text annotation | ||
| IL_6O9K_161 | 180 degree turn | ||
| IL_6O9K_162 | Double sheared with non-canonical cWW | ||
| IL_6O9K_163 | No text annotation | ||
| IL_6O9K_164 | No text annotation | ||
| IL_6O9K_165 | No text annotation | ||
| IL_6O9K_166 | Isolated non-canonical cWW pair | ||
| IL_6O9K_167 | Isolated non-canonical cWW pair | ||
| IL_6O9K_188 | Isolated non-canonical cWW pair | ||
| IL_6O9K_168 | Tandem non-canonical cWW pairs | ||
| IL_6O9K_169 | Double sheared | ||
| IL_6O9K_170 | Triple sheared related | ||
| IL_6O9K_171 | Single bulged A | ||
| IL_6O9K_172 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6O9K_028 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_6O9K_003 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J4_6O9K_004 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6O9K_001 | No text annotation | ||
| J3_6O9K_027 | No text annotation | ||
| J3_6O9K_002 | No text annotation | ||
| J3_6O9K_004 | No text annotation | ||
| J3_6O9K_005 | No text annotation | ||
| J3_6O9K_029 | No text annotation | ||
| J3_6O9K_006 | No text annotation | ||
| J3_6O9K_007 | No text annotation | ||
| J3_6O9K_008 | No text annotation | ||
| J3_6O9K_030 | No text annotation | ||
| J3_6O9K_031 | No text annotation | ||
| J3_6O9K_009 | Kink-turn 3-way junction | ||
| J3_6O9K_032 | No text annotation | ||
| J3_6O9K_033 | No text annotation | ||
| J3_6O9K_010 | No text annotation | ||
| J3_6O9K_011 | No text annotation | ||
| J3_6O9K_012 | No text annotation | ||
| J3_6O9K_013 | No text annotation | ||
| J3_6O9K_014 | No text annotation | ||
| J3_6O9K_015 | No text annotation | ||
| J3_6O9K_034 | No text annotation | ||
| J3_6O9K_016 | No text annotation | ||
| J3_6O9K_035 | No text annotation | ||
| J3_6O9K_017 | No text annotation | ||
| J3_6O9K_018 | No text annotation | ||
| J3_6O9K_036 | No text annotation | ||
| J3_6O9K_019 | No text annotation | ||
| J3_6O9K_020 | No text annotation | ||
| J3_6O9K_021 | No text annotation | ||
| J3_6O9K_037 | No text annotation | ||
| J3_6O9K_022 | No text annotation | ||
| J3_6O9K_023 | No text annotation | ||
| J3_6O9K_024 | No text annotation | ||
| J3_6O9K_025 | No text annotation | ||
| J3_6O9K_038 | No text annotation | ||
| J3_6O9K_026 | No text annotation | ||
| J3_6O9K_039 | No text annotation | ||
| J4_6O9K_001 | No text annotation | ||
| J4_6O9K_002 | No text annotation | ||
| J4_6O9K_003 | No text annotation | ||
| J4_6O9K_016 | No text annotation | ||
| J4_6O9K_005 | No text annotation | ||
| J4_6O9K_017 | No text annotation | ||
| J4_6O9K_006 | No text annotation | ||
| J4_6O9K_007 | No text annotation | ||
| J4_6O9K_008 | No text annotation | ||
| J4_6O9K_009 | No text annotation | ||
| J4_6O9K_010 | No text annotation | ||
| J4_6O9K_011 | No text annotation | ||
| J4_6O9K_012 | No text annotation | ||
| J4_6O9K_013 | No text annotation | ||
| J4_6O9K_014 | No text annotation | ||
| J4_6O9K_018 | No text annotation | ||
| J4_6O9K_015 | No text annotation | ||
| J5_6O9K_001 | No text annotation | ||
| J5_6O9K_010 | No text annotation | ||
| J5_6O9K_002 | No text annotation | ||
| J5_6O9K_003 | No text annotation | ||
| J5_6O9K_004 | No text annotation | ||
| J5_6O9K_005 | No text annotation | ||
| J5_6O9K_006 | No text annotation | ||
| J5_6O9K_007 | No text annotation | ||
| J5_6O9K_008 | No text annotation | ||
| J5_6O9K_009 | No text annotation | ||
| J6_6O9K_001 | No text annotation | ||
| J6_6O9K_002 | No text annotation | ||
| J7_6O9K_001 | No text annotation | ||
| J7_6O9K_002 | No text annotation |
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