6XGF Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6XGF_007 | 1/D/12:22 | No text annotation | homologous HL_4LFB_001 HL_73535.1 | |
| HL_6XGF_082 | 1/a/1777:1787 | No text annotation | homologous HL_5J7L_178 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6XGF_001 | No text annotation | ||
| HL_6XGF_002 | tRNA anticodon loop | ||
| HL_6XGF_003 | T-loop with 2 stacked bulged bases | ||
| HL_6XGF_004 | No text annotation | ||
| HL_6XGF_005 | No text annotation | ||
| HL_6XGF_006 | T-loop with 2 stacked bulged bases | ||
| HL_6XGF_008 | No text annotation | ||
| HL_6XGF_009 | GNRA | ||
| HL_6XGF_010 | GNRA | ||
| HL_6XGF_109 | No text annotation | ||
| HL_6XGF_011 | UNCG | ||
| HL_6XGF_012 | GNRA related | ||
| HL_6XGF_013 | GNRA | ||
| HL_6XGF_014 | No text annotation | ||
| HL_6XGF_015 | UNCG | ||
| HL_6XGF_016 | GNRA | ||
| HL_6XGF_017 | UNCG | ||
| HL_6XGF_018 | GNRA wlth extra near cWW | ||
| HL_6XGF_019 | No text annotation | ||
| HL_6XGF_020 | GNRA-like with tWH | ||
| HL_6XGF_021 | No text annotation | ||
| HL_6XGF_022 | GNRA | ||
| HL_6XGF_023 | No text annotation | ||
| HL_6XGF_024 | No text annotation | ||
| HL_6XGF_025 | GNRA | ||
| HL_6XGF_026 | GNRA | ||
| HL_6XGF_027 | No text annotation | ||
| HL_6XGF_028 | GNRA | ||
| HL_6XGF_029 | GNRA | ||
| HL_6XGF_030 | T-loop related | ||
| HL_6XGF_110 | No text annotation | ||
| HL_6XGF_031 | No text annotation | ||
| HL_6XGF_032 | GNRA | ||
| HL_6XGF_033 | GNRA | ||
| HL_6XGF_034 | T-loop with 3 stacked bulged bases | ||
| HL_6XGF_035 | No text annotation | ||
| HL_6XGF_036 | UNCG | ||
| HL_6XGF_037 | GNRA | ||
| HL_6XGF_038 | No text annotation | ||
| HL_6XGF_039 | No text annotation | ||
| HL_6XGF_040 | No text annotation | ||
| HL_6XGF_041 | UNCG | ||
| HL_6XGF_042 | No text annotation | ||
| HL_6XGF_043 | No text annotation | ||
| HL_6XGF_044 | No text annotation | ||
| HL_6XGF_045 | No text annotation | ||
| HL_6XGF_046 | T-loop with 2 stacked bulged bases | ||
| HL_6XGF_047 | No text annotation | ||
| HL_6XGF_048 | T-loop with unstacked turn | ||
| HL_6XGF_049 | No text annotation | ||
| HL_6XGF_050 | Pseudoknot geometry | ||
| HL_6XGF_051 | GNRA | ||
| HL_6XGF_052 | GNRA | ||
| HL_6XGF_053 | No text annotation | ||
| HL_6XGF_054 | T-loop with 2 stacked bulged bases | ||
| HL_6XGF_055 | No text annotation | ||
| HL_6XGF_056 | GNRA | ||
| HL_6XGF_057 | No text annotation | ||
| HL_6XGF_058 | GNRA wlth tandem sheared | ||
| HL_6XGF_059 | No text annotation | ||
| HL_6XGF_060 | No text annotation | ||
| HL_6XGF_061 | No text annotation | ||
| HL_6XGF_111 | No text annotation | ||
| HL_6XGF_062 | No text annotation | ||
| HL_6XGF_063 | No text annotation | ||
| HL_6XGF_064 | No text annotation | ||
| HL_6XGF_065 | No text annotation | ||
| HL_6XGF_066 | GNRA wlth tandem sheared | ||
| HL_6XGF_067 | No text annotation | ||
| HL_6XGF_068 | GNRA | ||
| HL_6XGF_069 | T-loop with 2 stacked bulged bases | ||
| HL_6XGF_070 | Pseudoknot geometry with 3' bulge | ||
| HL_6XGF_071 | GNRA | ||
| HL_6XGF_072 | No text annotation | ||
| HL_6XGF_073 | Mini UNCG with extended bulge | ||
| HL_6XGF_074 | Pseudoknot geometry with 3' bulge | ||
| HL_6XGF_075 | UNCG | ||
| HL_6XGF_076 | Mini UNCG | ||
| HL_6XGF_077 | No text annotation | ||
| HL_6XGF_078 | GNRA | ||
| HL_6XGF_079 | UNCG | ||
| HL_6XGF_112 | No text annotation | ||
| HL_6XGF_080 | No text annotation | ||
| HL_6XGF_081 | No text annotation | ||
| HL_6XGF_083 | GNRA related | ||
| HL_6XGF_084 | GNRA variation | ||
| HL_6XGF_085 | No text annotation | ||
| HL_6XGF_086 | No text annotation | ||
| HL_6XGF_087 | No text annotation | ||
| HL_6XGF_088 | No text annotation | ||
| HL_6XGF_089 | No text annotation | ||
| HL_6XGF_090 | No text annotation | ||
| HL_6XGF_091 | No text annotation | ||
| HL_6XGF_092 | No text annotation | ||
| HL_6XGF_114 | No text annotation | ||
| HL_6XGF_093 | Pseudoknot geometry | ||
| HL_6XGF_094 | GNRA | ||
| HL_6XGF_095 | GNRA | ||
| HL_6XGF_096 | No text annotation | ||
| HL_6XGF_097 | No text annotation | ||
| HL_6XGF_098 | GNRA variation | ||
| HL_6XGF_099 | No text annotation | ||
| HL_6XGF_100 | GNRA | ||
| HL_6XGF_101 | GNRA | ||
| HL_6XGF_102 | Ribsomal LSU H95 | ||
| HL_6XGF_103 | No text annotation | ||
| HL_6XGF_104 | No text annotation | ||
| HL_6XGF_115 | UNCG variation | ||
| HL_6XGF_105 | No text annotation | ||
| HL_6XGF_106 | GNRA | ||
| HL_6XGF_113 | No text annotation | ||
| HL_6XGF_107 | No text annotation | ||
| HL_6XGF_108 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6XGF_026 | 1/D/569:575, 1/D/880:881 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_6XGF_039 | 1/D/922:923, 1/D/1393:1395 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_6XGF_059 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | homologous IL_5J7L_058 NA | |
| IL_6XGF_110 | 1/a/1196:1198, 1/a/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_6XGF_147 | 1/a/2054:2056, 1/a/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6XGF_170 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6XGF_186 | No text annotation | ||
| IL_6XGF_187 | No text annotation | ||
| IL_6XGF_188 | No text annotation | ||
| IL_6XGF_001 | Single bulged G | ||
| IL_6XGF_002 | Single bulged A | ||
| IL_6XGF_003 | No text annotation | ||
| IL_6XGF_004 | Minor groove platform | ||
| IL_6XGF_005 | Multiple bulged bases | ||
| IL_6XGF_006 | Minor groove platform with extra cWW | ||
| IL_6XGF_007 | Minor groove platform | ||
| IL_6XGF_189 | Single bulged G | ||
| IL_6XGF_008 | Single bulged G, near cWW | ||
| IL_6XGF_009 | Isolated non-canonical cWW pair | ||
| IL_6XGF_010 | Minor groove platform related | ||
| IL_6XGF_011 | Isolated cWH basepair | ||
| IL_6XGF_190 | No text annotation | ||
| IL_6XGF_012 | tWH-tWH-tHW-tHW | ||
| IL_6XGF_013 | No text annotation | ||
| IL_6XGF_014 | Kink-turn with non-sequential stacking | ||
| IL_6XGF_015 | No text annotation | ||
| IL_6XGF_016 | C-loop | ||
| IL_6XGF_017 | Single bulged U | ||
| IL_6XGF_018 | C-loop | ||
| IL_6XGF_019 | Single bulged G | ||
| IL_6XGF_020 | No text annotation | ||
| IL_6XGF_021 | No text annotation | ||
| IL_6XGF_022 | tSH-tHW-tWW | ||
| IL_6XGF_023 | No text annotation | ||
| IL_6XGF_024 | SSU/LSU pseudoknot | ||
| IL_6XGF_025 | Kink-turn related | ||
| IL_6XGF_027 | tSH-tHW-tHS | ||
| IL_6XGF_028 | Major groove platform | ||
| IL_6XGF_029 | Major groove minor groove platform; mini C-loop | ||
| IL_6XGF_030 | No text annotation | ||
| IL_6XGF_031 | Major groove platform; stack outside cWW | ||
| IL_6XGF_032 | Single stack bend | ||
| IL_6XGF_033 | Tandem non-canonical cWW pairs | ||
| IL_6XGF_034 | No text annotation | ||
| IL_6XGF_035 | Kink-turn | ||
| IL_6XGF_036 | Left turn | ||
| IL_6XGF_037 | tSH-tHW-tHS | ||
| IL_6XGF_038 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6XGF_040 | Single bulged G | ||
| IL_6XGF_041 | Minor groove platform | ||
| IL_6XGF_042 | No text annotation | ||
| IL_6XGF_043 | Minor groove platform | ||
| IL_6XGF_200 | Single stack bend | ||
| IL_6XGF_044 | No text annotation | ||
| IL_6XGF_045 | No text annotation | ||
| IL_6XGF_046 | Single bulged U | ||
| IL_6XGF_047 | Not an internal loop | ||
| IL_6XGF_048 | Isolated cWS basepair | ||
| IL_6XGF_049 | Minor groove platform | ||
| IL_6XGF_050 | Single bulged A | ||
| IL_6XGF_051 | Isolated non-canonical cWW pair | ||
| IL_6XGF_052 | No text annotation | ||
| IL_6XGF_053 | Minor groove platform | ||
| IL_6XGF_054 | No text annotation | ||
| IL_6XGF_055 | No text annotation | ||
| IL_6XGF_056 | 180 degree turn | ||
| IL_6XGF_191 | No text annotation | ||
| IL_6XGF_057 | Double sheared with non-canonical cWW | ||
| IL_6XGF_058 | No text annotation | ||
| IL_6XGF_060 | No text annotation | ||
| IL_6XGF_061 | No text annotation | ||
| IL_6XGF_062 | Isolated non-canonical cWW pair | ||
| IL_6XGF_063 | Double sheared | ||
| IL_6XGF_064 | Triple sheared related | ||
| IL_6XGF_065 | Single bulged A | ||
| IL_6XGF_066 | No text annotation | ||
| IL_6XGF_067 | Triple sheared with non-canonical cWW | ||
| IL_6XGF_068 | Single bulged A | ||
| IL_6XGF_069 | Minor groove platform | ||
| IL_6XGF_070 | No text annotation | ||
| IL_6XGF_071 | Single stack bend | ||
| IL_6XGF_072 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6XGF_073 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6XGF_074 | No text annotation | ||
| IL_6XGF_075 | No text annotation | ||
| IL_6XGF_076 | No text annotation | ||
| IL_6XGF_077 | No text annotation | ||
| IL_6XGF_078 | Double sheared | ||
| IL_6XGF_079 | Isolated non-canonical cWW pair | ||
| IL_6XGF_080 | AAA cross-strand stack | ||
| IL_6XGF_081 | No text annotation | ||
| IL_6XGF_082 | tHW-tHW cross-strand stack | ||
| IL_6XGF_083 | Single bulged A | ||
| IL_6XGF_084 | Single bulged G | ||
| IL_6XGF_085 | Triple sheared | ||
| IL_6XGF_086 | Major groove platform | ||
| IL_6XGF_087 | Single stack bend | ||
| IL_6XGF_088 | Single stack bend | ||
| IL_6XGF_089 | Multiple bulged bases | ||
| IL_6XGF_090 | 90 degree turn | ||
| IL_6XGF_192 | No text annotation | ||
| IL_6XGF_091 | Stack outside cWW | ||
| IL_6XGF_092 | Single stack bend | ||
| IL_6XGF_193 | No text annotation | ||
| IL_6XGF_093 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_6XGF_094 | Single bulged G | ||
| IL_6XGF_095 | C-loop with bulged stacked A's | ||
| IL_6XGF_096 | Isolated non-canonical cWW pair | ||
| IL_6XGF_097 | Double sheared with non-canonical cWW | ||
| IL_6XGF_194 | No text annotation | ||
| IL_6XGF_098 | No text annotation | ||
| IL_6XGF_099 | Single bulged C | ||
| IL_6XGF_100 | UAA/GAN | ||
| IL_6XGF_101 | SSU/LSU pseudoknot | ||
| IL_6XGF_102 | Single bulged U | ||
| IL_6XGF_103 | Kink-turn related | ||
| IL_6XGF_104 | No text annotation | ||
| IL_6XGF_105 | Isolated non-canonical cWW pair | ||
| IL_6XGF_106 | Tandem non-canonical cWW pairs | ||
| IL_6XGF_107 | Kink-turn | ||
| IL_6XGF_195 | No text annotation | ||
| IL_6XGF_108 | No text annotation | ||
| IL_6XGF_109 | Major groove platform | ||
| IL_6XGF_111 | No text annotation | ||
| IL_6XGF_112 | Kink-turn | ||
| IL_6XGF_113 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6XGF_114 | Major groove platform; stack outside cWW | ||
| IL_6XGF_115 | C-loop | ||
| IL_6XGF_116 | UAA/GAN | ||
| IL_6XGF_117 | tSH-tHW-tHS | ||
| IL_6XGF_118 | Single stack bend | ||
| IL_6XGF_119 | Single stack bend | ||
| IL_6XGF_196 | No text annotation | ||
| IL_6XGF_120 | No text annotation | ||
| IL_6XGF_121 | UAA/GAN | ||
| IL_6XGF_122 | Tandem non-canonical cWW pairs | ||
| IL_6XGF_123 | tSH-tHW | ||
| IL_6XGF_124 | Single bulged U | ||
| IL_6XGF_125 | No text annotation | ||
| IL_6XGF_126 | tSH-tHW-tHS | ||
| IL_6XGF_127 | No text annotation | ||
| IL_6XGF_201 | 180 degree turn | ||
| IL_6XGF_128 | Single bulged A | ||
| IL_6XGF_129 | UAA/GAN variation | ||
| IL_6XGF_130 | No text annotation | ||
| IL_6XGF_131 | Isolated tWW turn | ||
| IL_6XGF_132 | Major groove platform; stack outside cWW | ||
| IL_6XGF_197 | No text annotation | ||
| IL_6XGF_133 | Intercalated tWH | ||
| IL_6XGF_134 | tSH-tSH-tHH-tHS | ||
| IL_6XGF_135 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6XGF_136 | Triple sheared | ||
| IL_6XGF_137 | Single bulged C | ||
| IL_6XGF_138 | Single bulged A | ||
| IL_6XGF_139 | Kink-turn related | ||
| IL_6XGF_140 | Minor groove platform, major groove intercalation | ||
| IL_6XGF_141 | Major groove intercalation | ||
| IL_6XGF_142 | Major groove minor groove platform; mini C-loop | ||
| IL_6XGF_198 | No text annotation | ||
| IL_6XGF_143 | UAA/GAN related | ||
| IL_6XGF_144 | Bulged stacked bases | ||
| IL_6XGF_145 | No text annotation | ||
| IL_6XGF_146 | Major groove platform | ||
| IL_6XGF_148 | No text annotation | ||
| IL_6XGF_149 | No text annotation | ||
| IL_6XGF_150 | Minor groove platform | ||
| IL_6XGF_151 | Isolated tHS basepair with bulges | ||
| IL_6XGF_152 | Isolated non-canonical cWW pair | ||
| IL_6XGF_153 | Isolated non-canonical cWW pair | ||
| IL_6XGF_154 | Isolated non-canonical cWW pair | ||
| IL_6XGF_155 | Isolated non-canonical cWW pair | ||
| IL_6XGF_156 | No text annotation | ||
| IL_6XGF_199 | No text annotation | ||
| IL_6XGF_157 | Kink-turn | ||
| IL_6XGF_158 | Single bulged U | ||
| IL_6XGF_159 | Double sheared | ||
| IL_6XGF_160 | No text annotation | ||
| IL_6XGF_161 | No text annotation | ||
| IL_6XGF_162 | No text annotation | ||
| IL_6XGF_163 | Major groove minor groove platform with extra cWW | ||
| IL_6XGF_164 | Double sheared with non-canonical cWW | ||
| IL_6XGF_165 | No text annotation | ||
| IL_6XGF_166 | Isolated non-canonical cWW with bulges | ||
| IL_6XGF_167 | No text annotation | ||
| IL_6XGF_168 | Major groove platform with intercalation | ||
| IL_6XGF_169 | No text annotation | ||
| IL_6XGF_171 | tSH-tHS-tHW | ||
| IL_6XGF_172 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6XGF_173 | C-loop | ||
| IL_6XGF_174 | UAA/GAN related, with intercalation | ||
| IL_6XGF_175 | Multiple bulged bases | ||
| IL_6XGF_176 | UAA/GAN with extra cWW | ||
| IL_6XGF_177 | No text annotation | ||
| IL_6XGF_178 | Major groove intercalation | ||
| IL_6XGF_179 | Multiple bulged bases with non-canonical cWW | ||
| IL_6XGF_180 | tHS double platform | ||
| IL_6XGF_181 | Major groove intercalation | ||
| IL_6XGF_182 | No text annotation | ||
| IL_6XGF_183 | Major groove minor groove platform; mini C-loop | ||
| IL_6XGF_184 | Symmetric double minor groove platform | ||
| IL_6XGF_185 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J4_6XGF_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_6XGF_005 | 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 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6XGF_001 | No text annotation | ||
| J3_6XGF_027 | No text annotation | ||
| J3_6XGF_002 | No text annotation | ||
| J3_6XGF_028 | No text annotation | ||
| J3_6XGF_003 | No text annotation | ||
| J3_6XGF_004 | No text annotation | ||
| J3_6XGF_005 | No text annotation | ||
| J3_6XGF_006 | No text annotation | ||
| J3_6XGF_029 | No text annotation | ||
| J3_6XGF_007 | No text annotation | ||
| J3_6XGF_008 | No text annotation | ||
| J3_6XGF_030 | No text annotation | ||
| J3_6XGF_009 | No text annotation | ||
| J3_6XGF_010 | No text annotation | ||
| J3_6XGF_011 | No text annotation | ||
| J3_6XGF_031 | No text annotation | ||
| J3_6XGF_012 | No text annotation | ||
| J3_6XGF_013 | No text annotation | ||
| J3_6XGF_032 | No text annotation | ||
| J3_6XGF_033 | No text annotation | ||
| J3_6XGF_014 | No text annotation | ||
| J3_6XGF_034 | No text annotation | ||
| J3_6XGF_015 | No text annotation | ||
| J3_6XGF_016 | No text annotation | ||
| J3_6XGF_017 | No text annotation | ||
| J3_6XGF_018 | No text annotation | ||
| J3_6XGF_019 | No text annotation | ||
| J3_6XGF_020 | No text annotation | ||
| J3_6XGF_035 | No text annotation | ||
| J3_6XGF_021 | Kink-turn 3-way junction | ||
| J3_6XGF_036 | No text annotation | ||
| J3_6XGF_022 | No text annotation | ||
| J3_6XGF_023 | No text annotation | ||
| J3_6XGF_024 | No text annotation | ||
| J3_6XGF_025 | No text annotation | ||
| J3_6XGF_026 | No text annotation | ||
| J4_6XGF_001 | tRNA junction | ||
| J4_6XGF_002 | tRNA junction | ||
| J4_6XGF_003 | No text annotation | ||
| J4_6XGF_004 | No text annotation | ||
| J4_6XGF_006 | No text annotation | ||
| J4_6XGF_007 | No text annotation | ||
| J4_6XGF_008 | No text annotation | ||
| J4_6XGF_009 | No text annotation | ||
| J4_6XGF_010 | No text annotation | ||
| J4_6XGF_011 | No text annotation | ||
| J4_6XGF_012 | No text annotation | ||
| J4_6XGF_013 | No text annotation | ||
| J4_6XGF_014 | No text annotation | ||
| J4_6XGF_015 | No text annotation | ||
| J5_6XGF_001 | No text annotation | ||
| J5_6XGF_002 | No text annotation | ||
| J5_6XGF_003 | No text annotation | ||
| J5_6XGF_004 | No text annotation | ||
| J5_6XGF_006 | No text annotation | ||
| J5_6XGF_007 | No text annotation | ||
| J6_6XGF_001 | No text annotation | ||
| J7_6XGF_001 | No text annotation | ||
| J7_6XGF_002 | No text annotation |
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