6XDR Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6XDR_038 | 1/a/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_6XDR_070 | 1/a/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_6XDR_082 | 1/a/1777:1787 | No text annotation | homologous HL_5J7L_178 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6XDR_001 | No text annotation | ||
| HL_6XDR_002 | tRNA anticodon loop | ||
| HL_6XDR_003 | T-loop with 2 stacked bulged bases | ||
| HL_6XDR_004 | No text annotation | ||
| HL_6XDR_005 | No text annotation | ||
| HL_6XDR_006 | T-loop with 2 stacked bulged bases | ||
| HL_6XDR_007 | No text annotation | ||
| HL_6XDR_008 | No text annotation | ||
| HL_6XDR_009 | GNRA | ||
| HL_6XDR_010 | GNRA | ||
| HL_6XDR_109 | No text annotation | ||
| HL_6XDR_011 | UNCG | ||
| HL_6XDR_012 | GNRA related | ||
| HL_6XDR_013 | GNRA | ||
| HL_6XDR_014 | No text annotation | ||
| HL_6XDR_015 | UNCG | ||
| HL_6XDR_016 | GNRA | ||
| HL_6XDR_017 | UNCG | ||
| HL_6XDR_018 | GNRA wlth extra near cWW | ||
| HL_6XDR_019 | No text annotation | ||
| HL_6XDR_020 | GNRA-like with tWH | ||
| HL_6XDR_021 | No text annotation | ||
| HL_6XDR_022 | GNRA | ||
| HL_6XDR_023 | No text annotation | ||
| HL_6XDR_024 | No text annotation | ||
| HL_6XDR_025 | GNRA | ||
| HL_6XDR_026 | GNRA | ||
| HL_6XDR_027 | No text annotation | ||
| HL_6XDR_028 | GNRA | ||
| HL_6XDR_029 | GNRA | ||
| HL_6XDR_030 | T-loop related | ||
| HL_6XDR_110 | No text annotation | ||
| HL_6XDR_031 | No text annotation | ||
| HL_6XDR_032 | GNRA | ||
| HL_6XDR_033 | GNRA | ||
| HL_6XDR_034 | T-loop with 3 stacked bulged bases | ||
| HL_6XDR_035 | No text annotation | ||
| HL_6XDR_036 | UNCG | ||
| HL_6XDR_037 | GNRA | ||
| HL_6XDR_039 | No text annotation | ||
| HL_6XDR_040 | No text annotation | ||
| HL_6XDR_041 | UNCG | ||
| HL_6XDR_042 | No text annotation | ||
| HL_6XDR_043 | No text annotation | ||
| HL_6XDR_044 | No text annotation | ||
| HL_6XDR_045 | No text annotation | ||
| HL_6XDR_046 | T-loop with 2 stacked bulged bases | ||
| HL_6XDR_047 | No text annotation | ||
| HL_6XDR_048 | T-loop with unstacked turn | ||
| HL_6XDR_049 | No text annotation | ||
| HL_6XDR_050 | Pseudoknot geometry | ||
| HL_6XDR_051 | GNRA | ||
| HL_6XDR_052 | GNRA | ||
| HL_6XDR_053 | No text annotation | ||
| HL_6XDR_054 | T-loop with 2 stacked bulged bases | ||
| HL_6XDR_055 | No text annotation | ||
| HL_6XDR_056 | GNRA | ||
| HL_6XDR_057 | No text annotation | ||
| HL_6XDR_058 | GNRA wlth tandem sheared | ||
| HL_6XDR_059 | No text annotation | ||
| HL_6XDR_060 | No text annotation | ||
| HL_6XDR_061 | No text annotation | ||
| HL_6XDR_111 | No text annotation | ||
| HL_6XDR_062 | No text annotation | ||
| HL_6XDR_063 | No text annotation | ||
| HL_6XDR_064 | No text annotation | ||
| HL_6XDR_065 | No text annotation | ||
| HL_6XDR_066 | GNRA wlth tandem sheared | ||
| HL_6XDR_067 | No text annotation | ||
| HL_6XDR_068 | GNRA | ||
| HL_6XDR_069 | T-loop with 2 stacked bulged bases | ||
| HL_6XDR_071 | GNRA | ||
| HL_6XDR_072 | No text annotation | ||
| HL_6XDR_073 | Mini UNCG with extended bulge | ||
| HL_6XDR_074 | Pseudoknot geometry with 3' bulge | ||
| HL_6XDR_075 | UNCG | ||
| HL_6XDR_076 | Mini UNCG | ||
| HL_6XDR_077 | No text annotation | ||
| HL_6XDR_078 | GNRA | ||
| HL_6XDR_079 | UNCG | ||
| HL_6XDR_112 | No text annotation | ||
| HL_6XDR_080 | No text annotation | ||
| HL_6XDR_081 | No text annotation | ||
| HL_6XDR_083 | GNRA related | ||
| HL_6XDR_084 | GNRA variation | ||
| HL_6XDR_085 | No text annotation | ||
| HL_6XDR_086 | No text annotation | ||
| HL_6XDR_087 | No text annotation | ||
| HL_6XDR_088 | No text annotation | ||
| HL_6XDR_089 | No text annotation | ||
| HL_6XDR_090 | No text annotation | ||
| HL_6XDR_091 | No text annotation | ||
| HL_6XDR_092 | No text annotation | ||
| HL_6XDR_114 | No text annotation | ||
| HL_6XDR_093 | Pseudoknot geometry | ||
| HL_6XDR_094 | GNRA | ||
| HL_6XDR_095 | GNRA | ||
| HL_6XDR_096 | No text annotation | ||
| HL_6XDR_097 | No text annotation | ||
| HL_6XDR_098 | GNRA variation | ||
| HL_6XDR_099 | No text annotation | ||
| HL_6XDR_100 | GNRA | ||
| HL_6XDR_101 | GNRA | ||
| HL_6XDR_102 | Ribsomal LSU H95 | ||
| HL_6XDR_103 | No text annotation | ||
| HL_6XDR_104 | No text annotation | ||
| HL_6XDR_115 | UNCG variation | ||
| HL_6XDR_105 | No text annotation | ||
| HL_6XDR_106 | GNRA | ||
| HL_6XDR_113 | No text annotation | ||
| HL_6XDR_107 | No text annotation | ||
| HL_6XDR_108 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6XDR_077 | 1/a/481:484, 1/a/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_6XDR_130 | 1/a/1651:1656, 1/a/2004:2006 | No text annotation | homologous IL_5J7L_304 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6XDR_186 | No text annotation | ||
| IL_6XDR_187 | No text annotation | ||
| IL_6XDR_188 | No text annotation | ||
| IL_6XDR_001 | Single bulged G | ||
| IL_6XDR_002 | Single bulged A | ||
| IL_6XDR_003 | No text annotation | ||
| IL_6XDR_004 | Minor groove platform | ||
| IL_6XDR_005 | Multiple bulged bases | ||
| IL_6XDR_006 | Minor groove platform with extra cWW | ||
| IL_6XDR_007 | Minor groove platform | ||
| IL_6XDR_189 | Single bulged G | ||
| IL_6XDR_008 | Single bulged G, near cWW | ||
| IL_6XDR_009 | Isolated non-canonical cWW pair | ||
| IL_6XDR_010 | Minor groove platform related | ||
| IL_6XDR_011 | Isolated cWH basepair | ||
| IL_6XDR_190 | No text annotation | ||
| IL_6XDR_012 | tWH-tWH-tHW-tHW | ||
| IL_6XDR_013 | No text annotation | ||
| IL_6XDR_014 | Kink-turn with non-sequential stacking | ||
| IL_6XDR_015 | No text annotation | ||
| IL_6XDR_016 | C-loop | ||
| IL_6XDR_017 | Single bulged U | ||
| IL_6XDR_018 | C-loop | ||
| IL_6XDR_019 | Single bulged G | ||
| IL_6XDR_020 | No text annotation | ||
| IL_6XDR_021 | No text annotation | ||
| IL_6XDR_022 | tSH-tHW-tWW | ||
| IL_6XDR_023 | No text annotation | ||
| IL_6XDR_024 | SSU/LSU pseudoknot | ||
| IL_6XDR_025 | Kink-turn related | ||
| IL_6XDR_026 | No text annotation | ||
| IL_6XDR_027 | tSH-tHW-tHS | ||
| IL_6XDR_028 | Major groove platform | ||
| IL_6XDR_029 | Major groove minor groove platform; mini C-loop | ||
| IL_6XDR_030 | No text annotation | ||
| IL_6XDR_031 | Major groove platform; stack outside cWW | ||
| IL_6XDR_032 | Single stack bend | ||
| IL_6XDR_033 | Tandem non-canonical cWW pairs | ||
| IL_6XDR_034 | No text annotation | ||
| IL_6XDR_035 | Kink-turn | ||
| IL_6XDR_036 | Left turn | ||
| IL_6XDR_037 | tSH-tHW-tHS | ||
| IL_6XDR_038 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6XDR_039 | Single bulged A | ||
| IL_6XDR_040 | Single bulged G | ||
| IL_6XDR_041 | Minor groove platform | ||
| IL_6XDR_042 | No text annotation | ||
| IL_6XDR_043 | Minor groove platform | ||
| IL_6XDR_200 | Single stack bend | ||
| IL_6XDR_044 | No text annotation | ||
| IL_6XDR_045 | No text annotation | ||
| IL_6XDR_046 | Single bulged U | ||
| IL_6XDR_047 | Not an internal loop | ||
| IL_6XDR_048 | Isolated cWS basepair | ||
| IL_6XDR_049 | Minor groove platform | ||
| IL_6XDR_050 | Single bulged U | ||
| IL_6XDR_051 | Isolated non-canonical cWW pair | ||
| IL_6XDR_052 | No text annotation | ||
| IL_6XDR_053 | Minor groove platform | ||
| IL_6XDR_054 | No text annotation | ||
| IL_6XDR_055 | No text annotation | ||
| IL_6XDR_056 | 180 degree turn | ||
| IL_6XDR_191 | No text annotation | ||
| IL_6XDR_057 | Double sheared with non-canonical cWW | ||
| IL_6XDR_058 | No text annotation | ||
| IL_6XDR_059 | No text annotation | ||
| IL_6XDR_060 | No text annotation | ||
| IL_6XDR_061 | Partly complementary | ||
| IL_6XDR_062 | Isolated non-canonical cWW pair | ||
| IL_6XDR_063 | Double sheared | ||
| IL_6XDR_064 | Triple sheared related | ||
| IL_6XDR_065 | Single bulged A | ||
| IL_6XDR_066 | No text annotation | ||
| IL_6XDR_067 | Triple sheared with non-canonical cWW | ||
| IL_6XDR_068 | Single bulged A | ||
| IL_6XDR_069 | Minor groove platform | ||
| IL_6XDR_070 | No text annotation | ||
| IL_6XDR_071 | Single stack bend | ||
| IL_6XDR_072 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6XDR_073 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6XDR_074 | No text annotation | ||
| IL_6XDR_075 | No text annotation | ||
| IL_6XDR_076 | No text annotation | ||
| IL_6XDR_078 | Double sheared | ||
| IL_6XDR_079 | Isolated non-canonical cWW pair | ||
| IL_6XDR_080 | AAA cross-strand stack | ||
| IL_6XDR_081 | No text annotation | ||
| IL_6XDR_082 | tHW-tHW cross-strand stack | ||
| IL_6XDR_083 | Single bulged A | ||
| IL_6XDR_084 | Single bulged G | ||
| IL_6XDR_085 | Triple sheared | ||
| IL_6XDR_086 | Major groove platform | ||
| IL_6XDR_087 | Single stack bend | ||
| IL_6XDR_088 | Single stack bend | ||
| IL_6XDR_089 | Multiple bulged bases | ||
| IL_6XDR_090 | 90 degree turn | ||
| IL_6XDR_192 | No text annotation | ||
| IL_6XDR_091 | Stack outside cWW | ||
| IL_6XDR_092 | Single stack bend | ||
| IL_6XDR_193 | No text annotation | ||
| IL_6XDR_093 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_6XDR_094 | Single bulged G | ||
| IL_6XDR_095 | C-loop with bulged stacked A's | ||
| IL_6XDR_096 | Isolated non-canonical cWW pair | ||
| IL_6XDR_097 | Double sheared with non-canonical cWW | ||
| IL_6XDR_194 | No text annotation | ||
| IL_6XDR_098 | No text annotation | ||
| IL_6XDR_099 | Single bulged C | ||
| IL_6XDR_100 | UAA/GAN | ||
| IL_6XDR_101 | SSU/LSU pseudoknot | ||
| IL_6XDR_102 | Single bulged U | ||
| IL_6XDR_103 | Kink-turn related | ||
| IL_6XDR_104 | No text annotation | ||
| IL_6XDR_105 | Isolated non-canonical cWW pair | ||
| IL_6XDR_106 | Tandem non-canonical cWW pairs | ||
| IL_6XDR_107 | Kink-turn | ||
| IL_6XDR_195 | No text annotation | ||
| IL_6XDR_108 | No text annotation | ||
| IL_6XDR_109 | No text annotation | ||
| IL_6XDR_110 | Isolated cWS basepair | ||
| IL_6XDR_111 | No text annotation | ||
| IL_6XDR_112 | Kink-turn | ||
| IL_6XDR_113 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6XDR_114 | Major groove platform; stack outside cWW | ||
| IL_6XDR_115 | C-loop | ||
| IL_6XDR_116 | UAA/GAN | ||
| IL_6XDR_117 | tSH-tHW-tHS | ||
| IL_6XDR_118 | Single stack bend | ||
| IL_6XDR_119 | Single stack bend | ||
| IL_6XDR_196 | No text annotation | ||
| IL_6XDR_120 | No text annotation | ||
| IL_6XDR_121 | UAA/GAN | ||
| IL_6XDR_122 | Tandem non-canonical cWW pairs | ||
| IL_6XDR_123 | tSH-tHW | ||
| IL_6XDR_124 | Single bulged U | ||
| IL_6XDR_125 | No text annotation | ||
| IL_6XDR_126 | tSH-tHW-tHS | ||
| IL_6XDR_127 | No text annotation | ||
| IL_6XDR_201 | 180 degree turn | ||
| IL_6XDR_128 | Single bulged A | ||
| IL_6XDR_129 | UAA/GAN variation | ||
| IL_6XDR_131 | Isolated tWW turn | ||
| IL_6XDR_132 | Major groove platform; stack outside cWW | ||
| IL_6XDR_197 | No text annotation | ||
| IL_6XDR_133 | Intercalated tWH | ||
| IL_6XDR_134 | tSH-tSH-tHH-tHS | ||
| IL_6XDR_135 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6XDR_136 | Triple sheared | ||
| IL_6XDR_137 | Single bulged C | ||
| IL_6XDR_138 | Single bulged A | ||
| IL_6XDR_139 | Kink-turn related | ||
| IL_6XDR_140 | Minor groove platform, major groove intercalation | ||
| IL_6XDR_141 | Major groove intercalation | ||
| IL_6XDR_142 | Major groove minor groove platform; mini C-loop | ||
| IL_6XDR_198 | No text annotation | ||
| IL_6XDR_143 | UAA/GAN related | ||
| IL_6XDR_144 | Bulged stacked bases | ||
| IL_6XDR_145 | No text annotation | ||
| IL_6XDR_146 | Major groove platform | ||
| IL_6XDR_147 | No text annotation | ||
| IL_6XDR_148 | No text annotation | ||
| IL_6XDR_149 | Not an internal loop | ||
| IL_6XDR_150 | Minor groove platform | ||
| IL_6XDR_151 | Isolated tHS basepair with bulges | ||
| IL_6XDR_152 | Isolated non-canonical cWW pair | ||
| IL_6XDR_153 | Isolated non-canonical cWW pair | ||
| IL_6XDR_154 | Isolated non-canonical cWW pair | ||
| IL_6XDR_155 | Isolated non-canonical cWW pair | ||
| IL_6XDR_156 | No text annotation | ||
| IL_6XDR_199 | No text annotation | ||
| IL_6XDR_157 | Kink-turn | ||
| IL_6XDR_158 | Single bulged U | ||
| IL_6XDR_159 | Double sheared | ||
| IL_6XDR_160 | No text annotation | ||
| IL_6XDR_161 | No text annotation | ||
| IL_6XDR_162 | No text annotation | ||
| IL_6XDR_163 | Major groove minor groove platform with extra cWW | ||
| IL_6XDR_164 | Double sheared with non-canonical cWW | ||
| IL_6XDR_165 | No text annotation | ||
| IL_6XDR_166 | Isolated non-canonical cWW with bulges | ||
| IL_6XDR_167 | No text annotation | ||
| IL_6XDR_168 | Major groove platform with intercalation | ||
| IL_6XDR_169 | No text annotation | ||
| IL_6XDR_170 | Single bulged A | ||
| IL_6XDR_171 | tSH-tHS-tHW | ||
| IL_6XDR_172 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6XDR_173 | C-loop | ||
| IL_6XDR_174 | UAA/GAN related, with intercalation | ||
| IL_6XDR_175 | Multiple bulged bases | ||
| IL_6XDR_176 | UAA/GAN with extra cWW | ||
| IL_6XDR_177 | No text annotation | ||
| IL_6XDR_178 | Major groove intercalation | ||
| IL_6XDR_179 | Multiple bulged bases with non-canonical cWW | ||
| IL_6XDR_180 | tHS double platform | ||
| IL_6XDR_181 | Major groove intercalation | ||
| IL_6XDR_182 | No text annotation | ||
| IL_6XDR_183 | Major groove minor groove platform; mini C-loop | ||
| IL_6XDR_184 | Symmetric double minor groove platform | ||
| IL_6XDR_185 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6XDR_032 | 1/a/30:31, 1/a/474:484, 1/a/496:510 | No text annotation | homologous J3_9DFE_002 J3_17917.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6XDR_001 | No text annotation | ||
| J3_6XDR_027 | No text annotation | ||
| J3_6XDR_002 | No text annotation | ||
| J3_6XDR_028 | No text annotation | ||
| J3_6XDR_003 | No text annotation | ||
| J3_6XDR_004 | No text annotation | ||
| J3_6XDR_005 | No text annotation | ||
| J3_6XDR_006 | No text annotation | ||
| J3_6XDR_029 | No text annotation | ||
| J3_6XDR_007 | No text annotation | ||
| J3_6XDR_008 | No text annotation | ||
| J3_6XDR_030 | No text annotation | ||
| J3_6XDR_009 | No text annotation | ||
| J3_6XDR_010 | No text annotation | ||
| J3_6XDR_011 | No text annotation | ||
| J3_6XDR_031 | No text annotation | ||
| J3_6XDR_012 | No text annotation | ||
| J3_6XDR_013 | No text annotation | ||
| J3_6XDR_033 | No text annotation | ||
| J3_6XDR_014 | No text annotation | ||
| J3_6XDR_034 | No text annotation | ||
| J3_6XDR_015 | No text annotation | ||
| J3_6XDR_016 | No text annotation | ||
| J3_6XDR_017 | No text annotation | ||
| J3_6XDR_018 | No text annotation | ||
| J3_6XDR_019 | No text annotation | ||
| J3_6XDR_020 | No text annotation | ||
| J3_6XDR_035 | No text annotation | ||
| J3_6XDR_021 | Kink-turn 3-way junction | ||
| J3_6XDR_036 | No text annotation | ||
| J3_6XDR_022 | No text annotation | ||
| J3_6XDR_023 | No text annotation | ||
| J3_6XDR_024 | No text annotation | ||
| J3_6XDR_025 | No text annotation | ||
| J3_6XDR_026 | No text annotation | ||
| J4_6XDR_001 | tRNA junction | ||
| J4_6XDR_002 | tRNA junction | ||
| J4_6XDR_003 | No text annotation | ||
| J4_6XDR_004 | No text annotation | ||
| J4_6XDR_005 | No text annotation | ||
| J4_6XDR_006 | No text annotation | ||
| J4_6XDR_007 | No text annotation | ||
| J4_6XDR_008 | No text annotation | ||
| J4_6XDR_009 | No text annotation | ||
| J4_6XDR_010 | No text annotation | ||
| J4_6XDR_011 | No text annotation | ||
| J4_6XDR_012 | No text annotation | ||
| J4_6XDR_013 | No text annotation | ||
| J4_6XDR_014 | No text annotation | ||
| J4_6XDR_015 | No text annotation | ||
| J5_6XDR_001 | No text annotation | ||
| J5_6XDR_002 | No text annotation | ||
| J5_6XDR_003 | No text annotation | ||
| J5_6XDR_004 | No text annotation | ||
| J5_6XDR_005 | No text annotation | ||
| J5_6XDR_006 | No text annotation | ||
| J5_6XDR_007 | No text annotation | ||
| J6_6XDR_001 | No text annotation | ||
| J7_6XDR_001 | No text annotation | ||
| J7_6XDR_002 | No text annotation |
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