3J9Z Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_3J9Z_048 | 1/LA/1910:1920 | No text annotation | homologous HL_9DFE_046 HL_82185.1 | |
HL_3J9Z_054 | 1/LA/2264:2276 | No text annotation | homologous HL_7RQB_054 NA | |
HL_3J9Z_107 | 1/SA/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_3J9Z_001 | No text annotation | ||
HL_3J9Z_002 | No text annotation | ||
HL_3J9Z_003 | No text annotation | ||
HL_3J9Z_004 | UNCG | ||
HL_3J9Z_005 | No text annotation | ||
HL_3J9Z_006 | No text annotation | ||
HL_3J9Z_007 | No text annotation | ||
HL_3J9Z_008 | No text annotation | ||
HL_3J9Z_009 | T-loop with 2 stacked bulged bases | ||
HL_3J9Z_010 | No text annotation | ||
HL_3J9Z_011 | T-loop with unstacked turn | ||
HL_3J9Z_012 | No text annotation | ||
HL_3J9Z_112 | No text annotation | ||
HL_3J9Z_013 | Pseudoknot geometry | ||
HL_3J9Z_014 | GNRA | ||
HL_3J9Z_015 | GNRA | ||
HL_3J9Z_016 | No text annotation | ||
HL_3J9Z_017 | T-loop with 2 stacked bulged bases | ||
HL_3J9Z_018 | No text annotation | ||
HL_3J9Z_019 | GNRA | ||
HL_3J9Z_020 | No text annotation | ||
HL_3J9Z_021 | GNRA wlth tandem sheared | ||
HL_3J9Z_022 | No text annotation | ||
HL_3J9Z_023 | No text annotation | ||
HL_3J9Z_024 | No text annotation | ||
HL_3J9Z_025 | No text annotation | ||
HL_3J9Z_026 | GNRA with extra cWW | ||
HL_3J9Z_113 | GNRA | ||
HL_3J9Z_027 | No text annotation | ||
HL_3J9Z_028 | No text annotation | ||
HL_3J9Z_029 | No text annotation | ||
HL_3J9Z_030 | No text annotation | ||
HL_3J9Z_031 | GNRA | ||
HL_3J9Z_032 | T-loop with 2 stacked bulged bases | ||
HL_3J9Z_033 | Pseudoknot geometry with 3' bulge | ||
HL_3J9Z_034 | GNRA | ||
HL_3J9Z_035 | No text annotation | ||
HL_3J9Z_036 | UNCG variation | ||
HL_3J9Z_037 | No text annotation | ||
HL_3J9Z_038 | UNCG | ||
HL_3J9Z_039 | Mini UNCG | ||
HL_3J9Z_040 | No text annotation | ||
HL_3J9Z_041 | GNRA | ||
HL_3J9Z_042 | UNCG | ||
HL_3J9Z_043 | Mini UNCG | ||
HL_3J9Z_044 | No text annotation | ||
HL_3J9Z_045 | No text annotation | ||
HL_3J9Z_046 | GNRA related | ||
HL_3J9Z_047 | GNRA | ||
HL_3J9Z_049 | No text annotation | ||
HL_3J9Z_050 | No text annotation | ||
HL_3J9Z_051 | No text annotation | ||
HL_3J9Z_052 | No text annotation | ||
HL_3J9Z_053 | No text annotation | ||
HL_3J9Z_055 | No text annotation | ||
HL_3J9Z_056 | Pseudoknot geometry | ||
HL_3J9Z_057 | GNRA | ||
HL_3J9Z_058 | GNRA | ||
HL_3J9Z_059 | No text annotation | ||
HL_3J9Z_060 | No text annotation | ||
HL_3J9Z_061 | GNRA variation | ||
HL_3J9Z_062 | No text annotation | ||
HL_3J9Z_063 | GNRA | ||
HL_3J9Z_064 | GNRA related | ||
HL_3J9Z_065 | Ribsomal LSU H95 | ||
HL_3J9Z_066 | No text annotation | ||
HL_3J9Z_067 | No text annotation | ||
HL_3J9Z_068 | No text annotation | ||
HL_3J9Z_069 | GNRA | ||
HL_3J9Z_070 | No text annotation | ||
HL_3J9Z_071 | UNCG variation | ||
HL_3J9Z_110 | Mini UNCG | ||
HL_3J9Z_072 | No text annotation | ||
HL_3J9Z_073 | tRNA anticodon loop | ||
HL_3J9Z_074 | T-loop with 2 stacked bulged bases | ||
HL_3J9Z_075 | No text annotation | ||
HL_3J9Z_076 | tRNA anticodon loop with synthetase | ||
HL_3J9Z_111 | No text annotation | ||
HL_3J9Z_077 | No text annotation | ||
HL_3J9Z_078 | No text annotation | ||
HL_3J9Z_079 | No text annotation | ||
HL_3J9Z_114 | No text annotation | ||
HL_3J9Z_080 | GNRA | ||
HL_3J9Z_081 | GNRA | ||
HL_3J9Z_082 | No text annotation | ||
HL_3J9Z_083 | GNRA related | ||
HL_3J9Z_084 | GNRA | ||
HL_3J9Z_085 | No text annotation | ||
HL_3J9Z_086 | UNCG | ||
HL_3J9Z_087 | GNRA | ||
HL_3J9Z_088 | UNCG | ||
HL_3J9Z_089 | GNRA-like with tWH | ||
HL_3J9Z_090 | No text annotation | ||
HL_3J9Z_091 | GNRA-like with tWH | ||
HL_3J9Z_092 | No text annotation | ||
HL_3J9Z_093 | GNRA | ||
HL_3J9Z_094 | No text annotation | ||
HL_3J9Z_095 | No text annotation | ||
HL_3J9Z_096 | GNRA | ||
HL_3J9Z_097 | GNRA | ||
HL_3J9Z_098 | tRNA D-loop | ||
HL_3J9Z_115 | No text annotation | ||
HL_3J9Z_099 | GNRA | ||
HL_3J9Z_100 | UNCG | ||
HL_3J9Z_101 | GNRA | ||
HL_3J9Z_102 | T-loop related | ||
HL_3J9Z_103 | No text annotation | ||
HL_3J9Z_104 | GNRA | ||
HL_3J9Z_105 | GNRA | ||
HL_3J9Z_106 | T-loop with 3 stacked bulged bases | ||
HL_3J9Z_108 | UNCG | ||
HL_3J9Z_109 | GNRA |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_3J9Z_034 | 1/LA/994:996, 1/LA/1159:1160 | Single bulged C | homologous IL_7A0S_032 IL_05642.2 | |
IL_3J9Z_039 | 1/LA/1024:1030, 1/LA/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
IL_3J9Z_101 | 1/LA/2591:2592, 1/LA/2601:2603 | Single bulged A | homologous IL_5J7L_344 NA | |
IL_3J9Z_115 | 1/LB/34:38, 1/LB/44:48 | Symmetric double minor groove platform | geometric IL_4V9F_104 IL_58103.12 | |
IL_3J9Z_160 | 1/SA/953:954, 1/SA/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_34520.2 | |
IL_3J9Z_162 | 1/SA/998:999, 1/SA/1041:1043 | Single stack bend | homologous IL_5J7L_044 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_3J9Z_182 | No text annotation | ||
IL_3J9Z_001 | Triple sheared with non-canonical cWW | ||
IL_3J9Z_002 | Single bulged A | ||
IL_3J9Z_003 | Minor groove platform | ||
IL_3J9Z_004 | No text annotation | ||
IL_3J9Z_183 | No text annotation | ||
IL_3J9Z_005 | Single stack bend | ||
IL_3J9Z_184 | No text annotation | ||
IL_3J9Z_006 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3J9Z_007 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_3J9Z_008 | No text annotation | ||
IL_3J9Z_009 | No text annotation | ||
IL_3J9Z_010 | No text annotation | ||
IL_3J9Z_185 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_011 | No text annotation | ||
IL_3J9Z_012 | No text annotation | ||
IL_3J9Z_013 | Double sheared | ||
IL_3J9Z_014 | Isolated non-canonical cWW pair | ||
IL_3J9Z_015 | AAA cross-strand stack | ||
IL_3J9Z_016 | Isolated non-canonical cWW pair | ||
IL_3J9Z_017 | tHW-tHW cross-strand stack | ||
IL_3J9Z_018 | Single bulged A | ||
IL_3J9Z_019 | Single bulged G | ||
IL_3J9Z_020 | Triple sheared | ||
IL_3J9Z_021 | Major groove platform | ||
IL_3J9Z_022 | Multiple bulged bases | ||
IL_3J9Z_023 | Single stack bend | ||
IL_3J9Z_024 | Single stack bend | ||
IL_3J9Z_025 | No text annotation | ||
IL_3J9Z_026 | No text annotation | ||
IL_3J9Z_206 | Single stack bend | ||
IL_3J9Z_027 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_3J9Z_028 | Minor groove platform | ||
IL_3J9Z_029 | C-loop with bulged stacked A's | ||
IL_3J9Z_030 | Isolated non-canonical cWW pair | ||
IL_3J9Z_031 | No text annotation | ||
IL_3J9Z_207 | No text annotation | ||
IL_3J9Z_032 | Minor groove platform related | ||
IL_3J9Z_033 | No text annotation | ||
IL_3J9Z_035 | UAA/GAN | ||
IL_3J9Z_036 | SSU/LSU pseudoknot | ||
IL_3J9Z_037 | Single bulged U | ||
IL_3J9Z_038 | Kink-turn related | ||
IL_3J9Z_040 | Isolated non-canonical cWW pair | ||
IL_3J9Z_041 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_042 | Kink-turn | ||
IL_3J9Z_043 | No text annotation | ||
IL_3J9Z_044 | Major groove platform | ||
IL_3J9Z_186 | Partly complementary | ||
IL_3J9Z_208 | No text annotation | ||
IL_3J9Z_209 | Isolated cWS basepair | ||
IL_3J9Z_187 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_045 | No text annotation | ||
IL_3J9Z_188 | No text annotation | ||
IL_3J9Z_046 | No text annotation | ||
IL_3J9Z_047 | Kink-turn | ||
IL_3J9Z_210 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3J9Z_048 | 9x8 Sarcin-Ricin; G-bulge | ||
IL_3J9Z_049 | Major groove platform; stack outside cWW | ||
IL_3J9Z_050 | C-loop | ||
IL_3J9Z_051 | UAA/GAN | ||
IL_3J9Z_052 | tSH-tHW-tHS | ||
IL_3J9Z_053 | No text annotation | ||
IL_3J9Z_054 | UAA/GAN | ||
IL_3J9Z_055 | No text annotation | ||
IL_3J9Z_189 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_056 | tSH-tHW | ||
IL_3J9Z_057 | No text annotation | ||
IL_3J9Z_190 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_3J9Z_211 | tSH-tHW-tHS | ||
IL_3J9Z_058 | No text annotation | ||
IL_3J9Z_059 | No text annotation | ||
IL_3J9Z_212 | No text annotation | ||
IL_3J9Z_060 | Single bulged A | ||
IL_3J9Z_061 | UAA/GAN variation | ||
IL_3J9Z_062 | No text annotation | ||
IL_3J9Z_063 | Isolated tWW turn | ||
IL_3J9Z_064 | Major groove platform; stack outside cWW | ||
IL_3J9Z_191 | No text annotation | ||
IL_3J9Z_065 | Intercalated tWH | ||
IL_3J9Z_066 | tSH-tSH-tHH-tHS | ||
IL_3J9Z_067 | 6x5 Sarcin-Ricin; G-bulge | ||
IL_3J9Z_068 | Triple sheared with non-canonical cWW | ||
IL_3J9Z_069 | Single bulged C | ||
IL_3J9Z_070 | Single bulged A | ||
IL_3J9Z_071 | Kink-turn related | ||
IL_3J9Z_072 | Minor groove platform, major groove intercalation | ||
IL_3J9Z_073 | Major groove intercalation | ||
IL_3J9Z_074 | Minor groove platform | ||
IL_3J9Z_192 | No text annotation | ||
IL_3J9Z_075 | UAA/GAN related | ||
IL_3J9Z_076 | Bulged stacked bases | ||
IL_3J9Z_077 | No text annotation | ||
IL_3J9Z_078 | Major groove platform | ||
IL_3J9Z_079 | No text annotation | ||
IL_3J9Z_080 | Single bulged U | ||
IL_3J9Z_081 | No text annotation | ||
IL_3J9Z_082 | Isolated tHS basepair with bulges | ||
IL_3J9Z_083 | Isolated non-canonical cWW pair | ||
IL_3J9Z_084 | Isolated non-canonical cWW pair | ||
IL_3J9Z_085 | Partly complementary | ||
IL_3J9Z_213 | No text annotation | ||
IL_3J9Z_086 | No text annotation | ||
IL_3J9Z_087 | No text annotation | ||
IL_3J9Z_193 | No text annotation | ||
IL_3J9Z_088 | No text annotation | ||
IL_3J9Z_214 | No text annotation | ||
IL_3J9Z_089 | Single bulged U | ||
IL_3J9Z_090 | Double sheared | ||
IL_3J9Z_091 | No text annotation | ||
IL_3J9Z_092 | Single stack bend | ||
IL_3J9Z_194 | No text annotation | ||
IL_3J9Z_093 | Major groove platform | ||
IL_3J9Z_094 | Major groove platform | ||
IL_3J9Z_095 | No text annotation | ||
IL_3J9Z_096 | Double sheared with non-canonical cWW | ||
IL_3J9Z_097 | Major groove platform | ||
IL_3J9Z_098 | Isolated non-canonical cWW with bulges | ||
IL_3J9Z_099 | No text annotation | ||
IL_3J9Z_100 | No text annotation | ||
IL_3J9Z_215 | Major groove platform with intercalation | ||
IL_3J9Z_195 | Isolated non-canonical cWW pair | ||
IL_3J9Z_102 | tSH-tHS-tHW | ||
IL_3J9Z_103 | Sarcin-Ricin target in LSU H95; G-bulge | ||
IL_3J9Z_104 | No text annotation | ||
IL_3J9Z_196 | C-loop | ||
IL_3J9Z_105 | UAA/GAN related, with intercalation | ||
IL_3J9Z_106 | Multiple bulged bases | ||
IL_3J9Z_107 | UAA/GAN with extra cWW | ||
IL_3J9Z_108 | No text annotation | ||
IL_3J9Z_197 | Isolated non-canonical cWW pair | ||
IL_3J9Z_109 | Single bulged C | ||
IL_3J9Z_110 | Multiple bulged bases with non-canonical cWW | ||
IL_3J9Z_111 | No text annotation | ||
IL_3J9Z_112 | Major groove intercalation | ||
IL_3J9Z_113 | No text annotation | ||
IL_3J9Z_114 | No text annotation | ||
IL_3J9Z_116 | Bacterial 5S Loop E | ||
IL_3J9Z_216 | Single bulged G | ||
IL_3J9Z_117 | No text annotation | ||
IL_3J9Z_118 | Single bulged A | ||
IL_3J9Z_119 | No text annotation | ||
IL_3J9Z_120 | Minor groove platform | ||
IL_3J9Z_121 | Multiple bulged bases | ||
IL_3J9Z_122 | Minor groove platform with extra cWW | ||
IL_3J9Z_123 | Minor groove platform | ||
IL_3J9Z_198 | Single bulged G | ||
IL_3J9Z_124 | Single bulged G, near cWW | ||
IL_3J9Z_125 | Isolated non-canonical cWW pair | ||
IL_3J9Z_126 | No text annotation | ||
IL_3J9Z_127 | Isolated cWH basepair | ||
IL_3J9Z_128 | tWH-tWH-tHW-tHW | ||
IL_3J9Z_129 | Minor groove platform | ||
IL_3J9Z_130 | Kink-turn with non-sequential stacking | ||
IL_3J9Z_217 | No text annotation | ||
IL_3J9Z_199 | No text annotation | ||
IL_3J9Z_131 | No text annotation | ||
IL_3J9Z_132 | C-loop | ||
IL_3J9Z_133 | Single bulged U | ||
IL_3J9Z_218 | C-loop | ||
IL_3J9Z_134 | C-loop with extra cWW pair | ||
IL_3J9Z_219 | Single bulged G | ||
IL_3J9Z_135 | No text annotation | ||
IL_3J9Z_136 | No text annotation | ||
IL_3J9Z_137 | tSH-tHW-tWW | ||
IL_3J9Z_138 | No text annotation | ||
IL_3J9Z_139 | Partly complementary | ||
IL_3J9Z_220 | No text annotation | ||
IL_3J9Z_140 | Single stack bend | ||
IL_3J9Z_141 | SSU/LSU pseudoknot | ||
IL_3J9Z_142 | Kink-turn related | ||
IL_3J9Z_143 | No text annotation | ||
IL_3J9Z_144 | tSH-tHW-tHS | ||
IL_3J9Z_145 | Major groove platform | ||
IL_3J9Z_200 | Major groove minor groove platform; mini C-loop | ||
IL_3J9Z_146 | 8-nt loop receptor | ||
IL_3J9Z_147 | No text annotation | ||
IL_3J9Z_148 | Major groove platform; stack outside cWW | ||
IL_3J9Z_149 | Single stack bend | ||
IL_3J9Z_150 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_151 | No text annotation | ||
IL_3J9Z_152 | Kink-turn | ||
IL_3J9Z_201 | Kink-turn | ||
IL_3J9Z_153 | Left turn | ||
IL_3J9Z_154 | tSH-tHW-tHS | ||
IL_3J9Z_155 | Isolated cWS basepair | ||
IL_3J9Z_156 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
IL_3J9Z_157 | Single bulged A | ||
IL_3J9Z_158 | Single bulged G | ||
IL_3J9Z_159 | Minor groove platform | ||
IL_3J9Z_161 | Minor groove platform | ||
IL_3J9Z_163 | No text annotation | ||
IL_3J9Z_164 | Minor groove platform | ||
IL_3J9Z_165 | Single bulged A | ||
IL_3J9Z_166 | Isolated non-canonical cWW pair | ||
IL_3J9Z_167 | No text annotation | ||
IL_3J9Z_168 | Minor groove platform | ||
IL_3J9Z_169 | No text annotation | ||
IL_3J9Z_170 | No text annotation | ||
IL_3J9Z_171 | 180 degree turn | ||
IL_3J9Z_172 | Double sheared with non-canonical cWW | ||
IL_3J9Z_173 | No text annotation | ||
IL_3J9Z_174 | No text annotation | ||
IL_3J9Z_175 | No text annotation | ||
IL_3J9Z_176 | No text annotation | ||
IL_3J9Z_202 | Isolated non-canonical cWW pair | ||
IL_3J9Z_177 | Tandem non-canonical cWW pairs | ||
IL_3J9Z_178 | Double sheared | ||
IL_3J9Z_203 | No text annotation | ||
IL_3J9Z_179 | Triple sheared related | ||
IL_3J9Z_180 | Single bulged A | ||
IL_3J9Z_204 | No text annotation | ||
IL_3J9Z_205 | No text annotation | ||
IL_3J9Z_181 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_3J9Z_010 | 1/LA/2295:2299, 1/LA/2317:2323, 1/LA/2332:2337 | No text annotation | homologous J3_5J7L_071 NA | |
J3_3J9Z_034 | 1/LA/2517:2520, 1/LA/2545:2547, 1/LA/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
J4_3J9Z_017 | 1/S7/7:10, 1/S7/25:27, 1/S7/43:49, 1/S7/65:66 | tRNA junction | homologous J4_3TUP_001 J4_95067.1 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_3J9Z_001 | No text annotation | ||
J3_3J9Z_028 | No text annotation | ||
J3_3J9Z_029 | No text annotation | ||
J3_3J9Z_002 | No text annotation | ||
J3_3J9Z_030 | No text annotation | ||
J3_3J9Z_003 | No text annotation | ||
J3_3J9Z_004 | No text annotation | ||
J3_3J9Z_005 | No text annotation | ||
J3_3J9Z_006 | No text annotation | ||
J3_3J9Z_031 | No text annotation | ||
J3_3J9Z_007 | No text annotation | ||
J3_3J9Z_008 | No text annotation | ||
J3_3J9Z_032 | No text annotation | ||
J3_3J9Z_009 | Kink-turn 3-way junction | ||
J3_3J9Z_033 | No text annotation | ||
J3_3J9Z_011 | No text annotation | ||
J3_3J9Z_012 | No text annotation | ||
J3_3J9Z_013 | No text annotation | ||
J3_3J9Z_014 | No text annotation | ||
J3_3J9Z_015 | No text annotation | ||
J3_3J9Z_035 | No text annotation | ||
J3_3J9Z_016 | No text annotation | ||
J3_3J9Z_036 | No text annotation | ||
J3_3J9Z_017 | No text annotation | ||
J3_3J9Z_018 | No text annotation | ||
J3_3J9Z_019 | No text annotation | ||
J3_3J9Z_020 | No text annotation | ||
J3_3J9Z_021 | No text annotation | ||
J3_3J9Z_022 | No text annotation | ||
J3_3J9Z_037 | No text annotation | ||
J3_3J9Z_023 | No text annotation | ||
J3_3J9Z_024 | No text annotation | ||
J3_3J9Z_025 | No text annotation | ||
J3_3J9Z_026 | No text annotation | ||
J3_3J9Z_038 | No text annotation | ||
J3_3J9Z_027 | No text annotation | ||
J4_3J9Z_001 | No text annotation | ||
J4_3J9Z_002 | No text annotation | ||
J4_3J9Z_003 | No text annotation | ||
J4_3J9Z_004 | No text annotation | ||
J4_3J9Z_005 | No text annotation | ||
J4_3J9Z_006 | No text annotation | ||
J4_3J9Z_007 | No text annotation | ||
J4_3J9Z_008 | No text annotation | ||
J4_3J9Z_009 | No text annotation | ||
J4_3J9Z_010 | No text annotation | ||
J4_3J9Z_011 | No text annotation | ||
J4_3J9Z_012 | tRNA junction | ||
J4_3J9Z_013 | No text annotation | ||
J4_3J9Z_014 | No text annotation | ||
J4_3J9Z_015 | No text annotation | ||
J4_3J9Z_016 | No text annotation | ||
J5_3J9Z_001 | No text annotation | ||
J5_3J9Z_010 | No text annotation | ||
J5_3J9Z_002 | No text annotation | ||
J5_3J9Z_003 | No text annotation | ||
J5_3J9Z_004 | No text annotation | ||
J5_3J9Z_011 | No text annotation | ||
J5_3J9Z_005 | No text annotation | ||
J5_3J9Z_006 | No text annotation | ||
J5_3J9Z_007 | No text annotation | ||
J5_3J9Z_008 | No text annotation | ||
J5_3J9Z_009 | No text annotation | ||
J6_3J9Z_001 | No text annotation | ||
J7_3J9Z_001 | No text annotation | ||
J7_3J9Z_002 | No text annotation |
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