6X9Q Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6X9Q_026 | 1/D/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.8 | |
| HL_6X9Q_054 | 1/a/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 HL_28252.9 | |
| HL_6X9Q_060 | 1/a/779:785 | No text annotation | homologous HL_5J7L_156 HL_87954.2 | |
| HL_6X9Q_082 | 1/a/1777:1787 | No text annotation | homologous HL_5J7L_178 HL_01962.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6X9Q_001 | No text annotation | ||
| HL_6X9Q_002 | tRNA anticodon loop | ||
| HL_6X9Q_003 | T-loop with 2 stacked bulged bases | ||
| HL_6X9Q_004 | No text annotation | ||
| HL_6X9Q_005 | No text annotation | ||
| HL_6X9Q_006 | T-loop with 2 stacked bulged bases | ||
| HL_6X9Q_007 | No text annotation | ||
| HL_6X9Q_008 | No text annotation | ||
| HL_6X9Q_009 | GNRA | ||
| HL_6X9Q_010 | GNRA | ||
| HL_6X9Q_109 | No text annotation | ||
| HL_6X9Q_011 | UNCG | ||
| HL_6X9Q_012 | GNRA related | ||
| HL_6X9Q_013 | GNRA | ||
| HL_6X9Q_014 | No text annotation | ||
| HL_6X9Q_015 | UNCG | ||
| HL_6X9Q_016 | GNRA | ||
| HL_6X9Q_017 | UNCG | ||
| HL_6X9Q_018 | GNRA wlth extra near cWW | ||
| HL_6X9Q_019 | No text annotation | ||
| HL_6X9Q_020 | GNRA-like with tWH | ||
| HL_6X9Q_021 | No text annotation | ||
| HL_6X9Q_022 | GNRA | ||
| HL_6X9Q_023 | No text annotation | ||
| HL_6X9Q_024 | No text annotation | ||
| HL_6X9Q_025 | GNRA | ||
| HL_6X9Q_027 | No text annotation | ||
| HL_6X9Q_028 | GNRA | ||
| HL_6X9Q_029 | GNRA | ||
| HL_6X9Q_030 | T-loop related | ||
| HL_6X9Q_110 | No text annotation | ||
| HL_6X9Q_031 | No text annotation | ||
| HL_6X9Q_032 | GNRA | ||
| HL_6X9Q_033 | GNRA | ||
| HL_6X9Q_034 | T-loop with 3 stacked bulged bases | ||
| HL_6X9Q_035 | No text annotation | ||
| HL_6X9Q_036 | UNCG | ||
| HL_6X9Q_037 | GNRA | ||
| HL_6X9Q_038 | No text annotation | ||
| HL_6X9Q_039 | No text annotation | ||
| HL_6X9Q_040 | No text annotation | ||
| HL_6X9Q_041 | UNCG | ||
| HL_6X9Q_042 | No text annotation | ||
| HL_6X9Q_043 | No text annotation | ||
| HL_6X9Q_044 | No text annotation | ||
| HL_6X9Q_045 | No text annotation | ||
| HL_6X9Q_046 | T-loop with 2 stacked bulged bases | ||
| HL_6X9Q_047 | No text annotation | ||
| HL_6X9Q_048 | T-loop with unstacked turn | ||
| HL_6X9Q_049 | No text annotation | ||
| HL_6X9Q_050 | Pseudoknot geometry | ||
| HL_6X9Q_051 | GNRA | ||
| HL_6X9Q_052 | GNRA | ||
| HL_6X9Q_053 | No text annotation | ||
| HL_6X9Q_055 | No text annotation | ||
| HL_6X9Q_056 | GNRA | ||
| HL_6X9Q_057 | No text annotation | ||
| HL_6X9Q_058 | GNRA wlth tandem sheared | ||
| HL_6X9Q_059 | No text annotation | ||
| HL_6X9Q_061 | No text annotation | ||
| HL_6X9Q_111 | No text annotation | ||
| HL_6X9Q_062 | No text annotation | ||
| HL_6X9Q_063 | No text annotation | ||
| HL_6X9Q_064 | No text annotation | ||
| HL_6X9Q_065 | No text annotation | ||
| HL_6X9Q_066 | GNRA wlth tandem sheared | ||
| HL_6X9Q_067 | No text annotation | ||
| HL_6X9Q_068 | GNRA | ||
| HL_6X9Q_069 | T-loop with 2 stacked bulged bases | ||
| HL_6X9Q_070 | Pseudoknot geometry with 3' bulge | ||
| HL_6X9Q_071 | GNRA | ||
| HL_6X9Q_072 | No text annotation | ||
| HL_6X9Q_073 | Mini UNCG with extended bulge | ||
| HL_6X9Q_074 | Pseudoknot geometry with 3' bulge | ||
| HL_6X9Q_075 | UNCG | ||
| HL_6X9Q_076 | Mini UNCG | ||
| HL_6X9Q_077 | No text annotation | ||
| HL_6X9Q_078 | GNRA | ||
| HL_6X9Q_079 | UNCG | ||
| HL_6X9Q_112 | No text annotation | ||
| HL_6X9Q_080 | No text annotation | ||
| HL_6X9Q_081 | No text annotation | ||
| HL_6X9Q_083 | GNRA related | ||
| HL_6X9Q_084 | GNRA variation | ||
| HL_6X9Q_085 | No text annotation | ||
| HL_6X9Q_086 | No text annotation | ||
| HL_6X9Q_087 | No text annotation | ||
| HL_6X9Q_088 | No text annotation | ||
| HL_6X9Q_089 | No text annotation | ||
| HL_6X9Q_090 | No text annotation | ||
| HL_6X9Q_091 | No text annotation | ||
| HL_6X9Q_092 | No text annotation | ||
| HL_6X9Q_114 | No text annotation | ||
| HL_6X9Q_093 | Pseudoknot geometry | ||
| HL_6X9Q_094 | GNRA | ||
| HL_6X9Q_095 | GNRA | ||
| HL_6X9Q_096 | No text annotation | ||
| HL_6X9Q_097 | No text annotation | ||
| HL_6X9Q_098 | GNRA variation | ||
| HL_6X9Q_099 | No text annotation | ||
| HL_6X9Q_100 | GNRA | ||
| HL_6X9Q_101 | GNRA | ||
| HL_6X9Q_102 | Ribsomal LSU H95 | ||
| HL_6X9Q_103 | No text annotation | ||
| HL_6X9Q_104 | No text annotation | ||
| HL_6X9Q_115 | UNCG variation | ||
| HL_6X9Q_105 | No text annotation | ||
| HL_6X9Q_106 | GNRA | ||
| HL_6X9Q_113 | No text annotation | ||
| HL_6X9Q_107 | No text annotation | ||
| HL_6X9Q_108 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6X9Q_026 | 1/D/569:575, 1/D/880:881 | No text annotation | homologous IL_5J7L_026 IL_38186.6 | |
| IL_6X9Q_038 | 1/D/887:894, 1/D/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 IL_41756.4 | |
| IL_6X9Q_059 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | geometric IL_5J7L_058 IL_61438.4 | |
| IL_6X9Q_089 | 1/a/775:777, 1/a/787:791 | Multiple bulged bases | homologous IL_5J7L_265 IL_06549.2 | |
| IL_6X9Q_197 | 1/a/1666:1674, 1/a/1990:1994 | No text annotation | homologous IL_5J7L_386 IL_22854.4 | |
| IL_6X9Q_133 | 1/a/1669:1674, 1/a/1990:1993 | Intercalated tWH | homologous IL_5J7L_307 IL_76758.2 | |
| IL_6X9Q_147 | 1/a/2054:2056, 1/a/2612:2615 | No text annotation | homologous IL_5J7L_321 IL_83389.2 | |
| IL_6X9Q_150 | 1/a/2070:2071, 1/a/2438:2441 | Minor groove platform | homologous IL_5J7L_324 IL_51454.3 | |
| IL_6X9Q_151 | 1/a/2081:2083, 1/a/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 IL_85599.2 | |
| IL_6X9Q_170 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6X9Q_186 | No text annotation | ||
| IL_6X9Q_187 | No text annotation | ||
| IL_6X9Q_188 | No text annotation | ||
| IL_6X9Q_001 | Single bulged G | ||
| IL_6X9Q_002 | Single bulged A | ||
| IL_6X9Q_003 | No text annotation | ||
| IL_6X9Q_004 | Minor groove platform | ||
| IL_6X9Q_005 | Multiple bulged bases | ||
| IL_6X9Q_006 | Minor groove platform with extra cWW | ||
| IL_6X9Q_007 | Minor groove platform | ||
| IL_6X9Q_189 | Single bulged G | ||
| IL_6X9Q_008 | Single bulged G, near cWW | ||
| IL_6X9Q_009 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_010 | Minor groove platform related | ||
| IL_6X9Q_011 | Isolated cWH basepair | ||
| IL_6X9Q_190 | No text annotation | ||
| IL_6X9Q_012 | tWH-tWH-tHW-tHW | ||
| IL_6X9Q_013 | No text annotation | ||
| IL_6X9Q_014 | Kink-turn with non-sequential stacking | ||
| IL_6X9Q_015 | No text annotation | ||
| IL_6X9Q_016 | C-loop | ||
| IL_6X9Q_017 | Single bulged U | ||
| IL_6X9Q_018 | C-loop | ||
| IL_6X9Q_019 | Single bulged G | ||
| IL_6X9Q_020 | No text annotation | ||
| IL_6X9Q_021 | No text annotation | ||
| IL_6X9Q_022 | tSH-tHW-tWW | ||
| IL_6X9Q_023 | No text annotation | ||
| IL_6X9Q_024 | SSU/LSU pseudoknot | ||
| IL_6X9Q_025 | Kink-turn related | ||
| IL_6X9Q_027 | tSH-tHW-tHS | ||
| IL_6X9Q_028 | Major groove platform | ||
| IL_6X9Q_029 | Major groove minor groove platform; mini C-loop | ||
| IL_6X9Q_030 | No text annotation | ||
| IL_6X9Q_031 | Major groove platform; stack outside cWW | ||
| IL_6X9Q_032 | Single stack bend | ||
| IL_6X9Q_033 | Tandem non-canonical cWW pairs | ||
| IL_6X9Q_034 | No text annotation | ||
| IL_6X9Q_035 | Kink-turn | ||
| IL_6X9Q_036 | Left turn | ||
| IL_6X9Q_037 | tSH-tHW-tHS | ||
| IL_6X9Q_039 | Single bulged A | ||
| IL_6X9Q_040 | Single bulged G | ||
| IL_6X9Q_041 | Minor groove platform | ||
| IL_6X9Q_042 | No text annotation | ||
| IL_6X9Q_043 | Minor groove platform | ||
| IL_6X9Q_201 | Single stack bend | ||
| IL_6X9Q_044 | No text annotation | ||
| IL_6X9Q_045 | No text annotation | ||
| IL_6X9Q_046 | Single bulged U | ||
| IL_6X9Q_047 | No text annotation | ||
| IL_6X9Q_048 | Isolated cWS basepair | ||
| IL_6X9Q_049 | Minor groove platform | ||
| IL_6X9Q_050 | Single bulged U | ||
| IL_6X9Q_051 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_052 | No text annotation | ||
| IL_6X9Q_053 | Minor groove platform | ||
| IL_6X9Q_054 | No text annotation | ||
| IL_6X9Q_055 | No text annotation | ||
| IL_6X9Q_056 | 180 degree turn | ||
| IL_6X9Q_191 | No text annotation | ||
| IL_6X9Q_057 | Double sheared with non-canonical cWW | ||
| IL_6X9Q_058 | No text annotation | ||
| IL_6X9Q_060 | No text annotation | ||
| IL_6X9Q_061 | Partly complementary | ||
| IL_6X9Q_062 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_063 | Double sheared | ||
| IL_6X9Q_064 | Triple sheared related | ||
| IL_6X9Q_065 | Single bulged A | ||
| IL_6X9Q_066 | No text annotation | ||
| IL_6X9Q_067 | Triple sheared with non-canonical cWW | ||
| IL_6X9Q_068 | Single bulged A | ||
| IL_6X9Q_069 | Minor groove platform | ||
| IL_6X9Q_070 | No text annotation | ||
| IL_6X9Q_071 | Single stack bend | ||
| IL_6X9Q_072 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6X9Q_073 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6X9Q_074 | No text annotation | ||
| IL_6X9Q_075 | No text annotation | ||
| IL_6X9Q_076 | No text annotation | ||
| IL_6X9Q_077 | No text annotation | ||
| IL_6X9Q_078 | Double sheared | ||
| IL_6X9Q_079 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_080 | AAA cross-strand stack | ||
| IL_6X9Q_081 | No text annotation | ||
| IL_6X9Q_082 | tHW-tHW cross-strand stack | ||
| IL_6X9Q_083 | Single bulged A | ||
| IL_6X9Q_084 | Single bulged G | ||
| IL_6X9Q_085 | Triple sheared | ||
| IL_6X9Q_086 | Major groove platform | ||
| IL_6X9Q_087 | Single stack bend | ||
| IL_6X9Q_088 | Single stack bend | ||
| IL_6X9Q_090 | 90 degree turn | ||
| IL_6X9Q_192 | No text annotation | ||
| IL_6X9Q_091 | Stack outside cWW | ||
| IL_6X9Q_092 | Single stack bend | ||
| IL_6X9Q_193 | No text annotation | ||
| IL_6X9Q_093 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_6X9Q_094 | Single bulged G | ||
| IL_6X9Q_095 | C-loop with bulged stacked A's | ||
| IL_6X9Q_096 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_097 | Double sheared with non-canonical cWW | ||
| IL_6X9Q_194 | No text annotation | ||
| IL_6X9Q_098 | No text annotation | ||
| IL_6X9Q_099 | Single bulged C | ||
| IL_6X9Q_100 | UAA/GAN | ||
| IL_6X9Q_101 | SSU/LSU pseudoknot | ||
| IL_6X9Q_102 | Single bulged U | ||
| IL_6X9Q_103 | Kink-turn related | ||
| IL_6X9Q_104 | No text annotation | ||
| IL_6X9Q_105 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_106 | Tandem non-canonical cWW pairs | ||
| IL_6X9Q_107 | Kink-turn | ||
| IL_6X9Q_195 | No text annotation | ||
| IL_6X9Q_108 | No text annotation | ||
| IL_6X9Q_109 | Major groove platform | ||
| IL_6X9Q_110 | Isolated cWS basepair | ||
| IL_6X9Q_111 | No text annotation | ||
| IL_6X9Q_112 | Kink-turn | ||
| IL_6X9Q_113 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6X9Q_114 | Major groove platform; stack outside cWW | ||
| IL_6X9Q_115 | C-loop | ||
| IL_6X9Q_116 | UAA/GAN | ||
| IL_6X9Q_117 | tSH-tHW-tHS | ||
| IL_6X9Q_118 | Single stack bend | ||
| IL_6X9Q_119 | Single stack bend | ||
| IL_6X9Q_196 | No text annotation | ||
| IL_6X9Q_120 | No text annotation | ||
| IL_6X9Q_121 | UAA/GAN | ||
| IL_6X9Q_122 | Tandem non-canonical cWW pairs | ||
| IL_6X9Q_123 | tSH-tHW | ||
| IL_6X9Q_124 | Single bulged U | ||
| IL_6X9Q_125 | No text annotation | ||
| IL_6X9Q_126 | tSH-tHW-tHS | ||
| IL_6X9Q_127 | No text annotation | ||
| IL_6X9Q_200 | 180 degree turn | ||
| IL_6X9Q_128 | Single bulged A | ||
| IL_6X9Q_129 | UAA/GAN variation | ||
| IL_6X9Q_130 | No text annotation | ||
| IL_6X9Q_131 | Isolated tWW turn | ||
| IL_6X9Q_132 | Major groove platform; stack outside cWW | ||
| IL_6X9Q_134 | tSH-tSH-tHH-tHS | ||
| IL_6X9Q_135 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6X9Q_136 | Triple sheared | ||
| IL_6X9Q_137 | Single bulged C | ||
| IL_6X9Q_138 | Single bulged A | ||
| IL_6X9Q_139 | Kink-turn related | ||
| IL_6X9Q_140 | Minor groove platform, major groove intercalation | ||
| IL_6X9Q_141 | Major groove intercalation | ||
| IL_6X9Q_142 | Major groove minor groove platform; mini C-loop | ||
| IL_6X9Q_198 | No text annotation | ||
| IL_6X9Q_143 | UAA/GAN related | ||
| IL_6X9Q_144 | Bulged stacked bases | ||
| IL_6X9Q_145 | No text annotation | ||
| IL_6X9Q_146 | Major groove platform | ||
| IL_6X9Q_148 | No text annotation | ||
| IL_6X9Q_149 | Not an internal loop | ||
| IL_6X9Q_152 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_153 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_154 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_155 | Isolated non-canonical cWW pair | ||
| IL_6X9Q_156 | No text annotation | ||
| IL_6X9Q_199 | No text annotation | ||
| IL_6X9Q_157 | Kink-turn | ||
| IL_6X9Q_158 | Single bulged U | ||
| IL_6X9Q_159 | Double sheared | ||
| IL_6X9Q_160 | No text annotation | ||
| IL_6X9Q_161 | No text annotation | ||
| IL_6X9Q_162 | No text annotation | ||
| IL_6X9Q_163 | Major groove minor groove platform with extra cWW | ||
| IL_6X9Q_164 | Double sheared with non-canonical cWW | ||
| IL_6X9Q_165 | No text annotation | ||
| IL_6X9Q_166 | Isolated non-canonical cWW with bulges | ||
| IL_6X9Q_167 | No text annotation | ||
| IL_6X9Q_168 | Major groove platform with intercalation | ||
| IL_6X9Q_169 | No text annotation | ||
| IL_6X9Q_171 | tSH-tHS-tHW | ||
| IL_6X9Q_172 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6X9Q_173 | C-loop | ||
| IL_6X9Q_174 | UAA/GAN related, with intercalation | ||
| IL_6X9Q_175 | Multiple bulged bases | ||
| IL_6X9Q_176 | UAA/GAN with extra cWW | ||
| IL_6X9Q_177 | No text annotation | ||
| IL_6X9Q_178 | Major groove intercalation | ||
| IL_6X9Q_179 | Multiple bulged bases with non-canonical cWW | ||
| IL_6X9Q_180 | tHS double platform | ||
| IL_6X9Q_181 | Major groove intercalation | ||
| IL_6X9Q_182 | No text annotation | ||
| IL_6X9Q_183 | Major groove minor groove platform; mini C-loop | ||
| IL_6X9Q_184 | Symmetric double minor groove platform | ||
| IL_6X9Q_185 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6X9Q_004 | 1/D/826:829, 1/D/857:861, 1/D/868:874 | No text annotation | homologous J3_5J7L_004 J3_85054.4 | |
| J3_6X9Q_015 | 1/a/683:689, 1/a/773:775, 1/a/791:794 | No text annotation | homologous J3_5J7L_038 J3_64189.2 | |
| J4_6X9Q_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | homologous J4_5J7L_003 J4_61885.6 | |
| J5_6X9Q_006 | 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 J5_74302.5 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6X9Q_001 | No text annotation | ||
| J3_6X9Q_027 | No text annotation | ||
| J3_6X9Q_002 | No text annotation | ||
| J3_6X9Q_028 | No text annotation | ||
| J3_6X9Q_003 | No text annotation | ||
| J3_6X9Q_005 | No text annotation | ||
| J3_6X9Q_006 | No text annotation | ||
| J3_6X9Q_029 | No text annotation | ||
| J3_6X9Q_007 | No text annotation | ||
| J3_6X9Q_008 | No text annotation | ||
| J3_6X9Q_030 | No text annotation | ||
| J3_6X9Q_009 | No text annotation | ||
| J3_6X9Q_010 | No text annotation | ||
| J3_6X9Q_011 | No text annotation | ||
| J3_6X9Q_031 | No text annotation | ||
| J3_6X9Q_012 | No text annotation | ||
| J3_6X9Q_013 | No text annotation | ||
| J3_6X9Q_032 | No text annotation | ||
| J3_6X9Q_033 | No text annotation | ||
| J3_6X9Q_014 | No text annotation | ||
| J3_6X9Q_034 | No text annotation | ||
| J3_6X9Q_016 | No text annotation | ||
| J3_6X9Q_017 | No text annotation | ||
| J3_6X9Q_018 | No text annotation | ||
| J3_6X9Q_019 | No text annotation | ||
| J3_6X9Q_020 | No text annotation | ||
| J3_6X9Q_035 | No text annotation | ||
| J3_6X9Q_021 | Kink-turn 3-way junction | ||
| J3_6X9Q_036 | No text annotation | ||
| J3_6X9Q_022 | No text annotation | ||
| J3_6X9Q_023 | No text annotation | ||
| J3_6X9Q_024 | No text annotation | ||
| J3_6X9Q_025 | No text annotation | ||
| J3_6X9Q_026 | No text annotation | ||
| J4_6X9Q_001 | tRNA junction | ||
| J4_6X9Q_002 | tRNA junction | ||
| J4_6X9Q_003 | No text annotation | ||
| J4_6X9Q_004 | No text annotation | ||
| J4_6X9Q_006 | No text annotation | ||
| J4_6X9Q_007 | No text annotation | ||
| J4_6X9Q_008 | No text annotation | ||
| J4_6X9Q_009 | No text annotation | ||
| J4_6X9Q_010 | No text annotation | ||
| J4_6X9Q_011 | No text annotation | ||
| J4_6X9Q_012 | No text annotation | ||
| J4_6X9Q_013 | No text annotation | ||
| J4_6X9Q_014 | No text annotation | ||
| J4_6X9Q_015 | No text annotation | ||
| J5_6X9Q_001 | No text annotation | ||
| J5_6X9Q_002 | No text annotation | ||
| J5_6X9Q_003 | No text annotation | ||
| J5_6X9Q_004 | No text annotation | ||
| J5_6X9Q_005 | No text annotation | ||
| J5_6X9Q_007 | No text annotation | ||
| J6_6X9Q_001 | No text annotation | ||
| J7_6X9Q_001 | No text annotation | ||
| J7_6X9Q_002 | No text annotation |
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