3JA1 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_3JA1_028 | 1/LA/1064:1074 | No text annotation | geometric HL_2Y9H_003 HL_75660.6 | |
HL_3JA1_110 | 1/SA/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
HL_3JA1_085 | 1/SA/419:424 | UNCG | homologous HL_5J7L_011 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_3JA1_001 | Pseudoknot with intercalation | ||
HL_3JA1_107 | tRNA anticodon loop | ||
HL_3JA1_002 | No text annotation | ||
HL_3JA1_003 | No text annotation | ||
HL_3JA1_004 | UNCG | ||
HL_3JA1_005 | No text annotation | ||
HL_3JA1_006 | No text annotation | ||
HL_3JA1_007 | No text annotation | ||
HL_3JA1_008 | No text annotation | ||
HL_3JA1_009 | T-loop with 2 stacked bulged bases | ||
HL_3JA1_010 | No text annotation | ||
HL_3JA1_011 | T-loop with unstacked turn | ||
HL_3JA1_012 | No text annotation | ||
HL_3JA1_111 | No text annotation | ||
HL_3JA1_013 | Pseudoknot geometry | ||
HL_3JA1_014 | GNRA | ||
HL_3JA1_015 | GNRA | ||
HL_3JA1_016 | No text annotation | ||
HL_3JA1_017 | No text annotation | ||
HL_3JA1_018 | No text annotation | ||
HL_3JA1_019 | GNRA | ||
HL_3JA1_020 | No text annotation | ||
HL_3JA1_112 | No text annotation | ||
HL_3JA1_021 | No text annotation | ||
HL_3JA1_022 | No text annotation | ||
HL_3JA1_023 | UNCG variation | ||
HL_3JA1_024 | No text annotation | ||
HL_3JA1_025 | No text annotation | ||
HL_3JA1_026 | tRNA anticodon loop | ||
HL_3JA1_027 | No text annotation | ||
HL_3JA1_029 | No text annotation | ||
HL_3JA1_030 | Mini UNCG | ||
HL_3JA1_031 | GNRA | ||
HL_3JA1_032 | T-loop with 2 stacked bulged bases | ||
HL_3JA1_033 | Pseudoknot geometry with 3' bulge | ||
HL_3JA1_034 | GNRA | ||
HL_3JA1_035 | No text annotation | ||
HL_3JA1_036 | Mini UNCG | ||
HL_3JA1_037 | No text annotation | ||
HL_3JA1_038 | UNCG | ||
HL_3JA1_039 | Mini UNCG | ||
HL_3JA1_040 | No text annotation | ||
HL_3JA1_041 | GNRA | ||
HL_3JA1_042 | No text annotation | ||
HL_3JA1_043 | No text annotation | ||
HL_3JA1_044 | No text annotation | ||
HL_3JA1_045 | No text annotation | ||
HL_3JA1_046 | GNRA related | ||
HL_3JA1_047 | GNRA | ||
HL_3JA1_048 | No text annotation | ||
HL_3JA1_049 | No text annotation | ||
HL_3JA1_050 | No text annotation | ||
HL_3JA1_051 | No text annotation | ||
HL_3JA1_052 | No text annotation | ||
HL_3JA1_053 | No text annotation | ||
HL_3JA1_108 | No text annotation | ||
HL_3JA1_113 | No text annotation | ||
HL_3JA1_054 | No text annotation | ||
HL_3JA1_055 | No text annotation | ||
HL_3JA1_056 | Pseudoknot geometry | ||
HL_3JA1_109 | No text annotation | ||
HL_3JA1_057 | GNRA | ||
HL_3JA1_058 | GNRA | ||
HL_3JA1_059 | No text annotation | ||
HL_3JA1_060 | No text annotation | ||
HL_3JA1_114 | No text annotation | ||
HL_3JA1_061 | GNRA variation | ||
HL_3JA1_062 | No text annotation | ||
HL_3JA1_063 | GNRA | ||
HL_3JA1_064 | GNRA | ||
HL_3JA1_065 | No text annotation | ||
HL_3JA1_115 | Ribsomal LSU H95 | ||
HL_3JA1_066 | No text annotation | ||
HL_3JA1_067 | Mini UNCG | ||
HL_3JA1_068 | No text annotation | ||
HL_3JA1_069 | GNRA | ||
HL_3JA1_070 | No text annotation | ||
HL_3JA1_071 | No text annotation | ||
HL_3JA1_116 | Mini UNCG | ||
HL_3JA1_072 | No text annotation | ||
HL_3JA1_073 | tRNA anticodon loop | ||
HL_3JA1_074 | T-loop with 2 stacked bulged bases | ||
HL_3JA1_075 | No text annotation | ||
HL_3JA1_076 | No text annotation | ||
HL_3JA1_117 | No text annotation | ||
HL_3JA1_077 | GNRA | ||
HL_3JA1_078 | GNRA | ||
HL_3JA1_079 | No text annotation | ||
HL_3JA1_080 | GNRA related | ||
HL_3JA1_081 | GNRA | ||
HL_3JA1_082 | No text annotation | ||
HL_3JA1_083 | UNCG | ||
HL_3JA1_084 | GNRA | ||
HL_3JA1_086 | No text annotation | ||
HL_3JA1_087 | No text annotation | ||
HL_3JA1_088 | GNRA-like with tWH | ||
HL_3JA1_089 | No text annotation | ||
HL_3JA1_090 | GNRA | ||
HL_3JA1_091 | T-loop | ||
HL_3JA1_092 | No text annotation | ||
HL_3JA1_093 | GNRA | ||
HL_3JA1_094 | GNRA | ||
HL_3JA1_095 | No text annotation | ||
HL_3JA1_096 | GNRA | ||
HL_3JA1_097 | No text annotation | ||
HL_3JA1_098 | GNRA | ||
HL_3JA1_099 | T-loop related | ||
HL_3JA1_100 | No text annotation | ||
HL_3JA1_101 | GNRA | ||
HL_3JA1_102 | GNRA | ||
HL_3JA1_103 | T-loop with 3 stacked bulged bases | ||
HL_3JA1_104 | No text annotation | ||
HL_3JA1_105 | No text annotation | ||
HL_3JA1_106 | GNRA |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_3JA1_086 | 1/LA/2110:2120, 1/LA/2177:2179 | Major groove platform | geometric IL_5J7L_264 NA | |
IL_3JA1_094 | 1/LA/2466:2470, 1/LA/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
IL_3JA1_102 | 1/LA/2680:2684, 1/LA/2725:2727 | C-loop | homologous IL_4WF9_101 IL_63596.12 | |
IL_3JA1_105 | 1/LA/2737:2742, 1/LA/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
IL_3JA1_218 | 1/SA/446:450, 1/SA/483:488 | tSH-tHW-tWW | homologous IL_5J7L_022 NA | |
IL_3JA1_165 | 1/SA/1124:1128, 1/SA/1144:1149 | No text annotation | homologous IL_5J7L_051 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_3JA1_181 | No text annotation | ||
IL_3JA1_001 | Triple sheared with non-canonical cWW | ||
IL_3JA1_002 | Single bulged A | ||
IL_3JA1_003 | Minor groove platform | ||
IL_3JA1_004 | Kink-turn | ||
IL_3JA1_005 | Single stack bend | ||
IL_3JA1_006 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3JA1_007 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_3JA1_008 | No text annotation | ||
IL_3JA1_009 | No text annotation | ||
IL_3JA1_010 | No text annotation | ||
IL_3JA1_011 | No text annotation | ||
IL_3JA1_012 | Double sheared | ||
IL_3JA1_013 | Isolated non-canonical cWW pair | ||
IL_3JA1_014 | AAA cross-strand stack | ||
IL_3JA1_015 | Isolated non-canonical cWW pair | ||
IL_3JA1_016 | tHW-tHW cross-strand stack | ||
IL_3JA1_017 | Single bulged A | ||
IL_3JA1_018 | Single bulged G | ||
IL_3JA1_019 | Triple sheared | ||
IL_3JA1_020 | Major groove platform | ||
IL_3JA1_021 | Multiple bulged bases | ||
IL_3JA1_022 | Single stack bend | ||
IL_3JA1_023 | No text annotation | ||
IL_3JA1_024 | No text annotation | ||
IL_3JA1_206 | Single stack bend | ||
IL_3JA1_025 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_3JA1_026 | Single bulged G | ||
IL_3JA1_027 | No text annotation | ||
IL_3JA1_207 | C-loop with bulged stacked A's | ||
IL_3JA1_028 | Isolated non-canonical cWW pair | ||
IL_3JA1_029 | Double sheared with non-canonical cWW | ||
IL_3JA1_030 | No text annotation | ||
IL_3JA1_182 | No text annotation | ||
IL_3JA1_031 | No text annotation | ||
IL_3JA1_032 | Minor groove platform | ||
IL_3JA1_033 | Single bulged C | ||
IL_3JA1_034 | UAA/GAN | ||
IL_3JA1_035 | Multiple bulged bases | ||
IL_3JA1_036 | Single bulged U | ||
IL_3JA1_037 | Kink-turn related | ||
IL_3JA1_038 | No text annotation | ||
IL_3JA1_039 | Isolated non-canonical cWW pair | ||
IL_3JA1_040 | Tandem non-canonical cWW pairs | ||
IL_3JA1_041 | Kink-turn | ||
IL_3JA1_042 | No text annotation | ||
IL_3JA1_043 | No text annotation | ||
IL_3JA1_208 | Isolated cWS basepair | ||
IL_3JA1_044 | Tandem non-canonical cWW pairs | ||
IL_3JA1_183 | No text annotation | ||
IL_3JA1_045 | No text annotation | ||
IL_3JA1_046 | Kink-turn | ||
IL_3JA1_047 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3JA1_048 | Major groove platform; stack outside cWW | ||
IL_3JA1_049 | C-loop | ||
IL_3JA1_050 | UAA/GAN | ||
IL_3JA1_051 | tSH-tHW-tHS | ||
IL_3JA1_052 | No text annotation | ||
IL_3JA1_053 | UAA/GAN | ||
IL_3JA1_054 | Tandem non-canonical cWW pairs | ||
IL_3JA1_055 | tSH-tHW | ||
IL_3JA1_056 | No text annotation | ||
IL_3JA1_184 | tSH-tHW-tHS | ||
IL_3JA1_057 | No text annotation | ||
IL_3JA1_058 | No text annotation | ||
IL_3JA1_059 | Single bulged A | ||
IL_3JA1_060 | UAA/GAN variation | ||
IL_3JA1_061 | No text annotation | ||
IL_3JA1_062 | Isolated tWW turn | ||
IL_3JA1_063 | Major groove platform; stack outside cWW | ||
IL_3JA1_185 | No text annotation | ||
IL_3JA1_064 | Intercalated tWH | ||
IL_3JA1_065 | tSH-tSH-tHH-tHS | ||
IL_3JA1_066 | 6x5 Sarcin-Ricin; G-bulge | ||
IL_3JA1_186 | Triple sheared | ||
IL_3JA1_067 | Triple sheared with non-canonical cWW | ||
IL_3JA1_068 | Single bulged C | ||
IL_3JA1_069 | Single bulged A | ||
IL_3JA1_070 | Kink-turn related | ||
IL_3JA1_071 | Minor groove platform, major groove intercalation | ||
IL_3JA1_072 | Major groove intercalation | ||
IL_3JA1_073 | No text annotation | ||
IL_3JA1_209 | No text annotation | ||
IL_3JA1_187 | No text annotation | ||
IL_3JA1_074 | No text annotation | ||
IL_3JA1_075 | UAA/GAN related | ||
IL_3JA1_076 | Major groove intercalation | ||
IL_3JA1_188 | No text annotation | ||
IL_3JA1_077 | No text annotation | ||
IL_3JA1_078 | Major groove platform | ||
IL_3JA1_079 | No text annotation | ||
IL_3JA1_080 | Single bulged U | ||
IL_3JA1_081 | No text annotation | ||
IL_3JA1_082 | Isolated tHS basepair with bulges | ||
IL_3JA1_083 | Isolated non-canonical cWW pair | ||
IL_3JA1_210 | Isolated non-canonical cWW pair | ||
IL_3JA1_084 | Other IL | ||
IL_3JA1_211 | Isolated non-canonical cWW pair | ||
IL_3JA1_085 | No text annotation | ||
IL_3JA1_212 | Isolated non-canonical cWW pair | ||
IL_3JA1_189 | Single stack bend | ||
IL_3JA1_087 | No text annotation | ||
IL_3JA1_190 | No text annotation | ||
IL_3JA1_191 | Tandem non-canonical cWW pairs | ||
IL_3JA1_213 | Isolated non-canonical cWW pair | ||
IL_3JA1_088 | Single bulged U | ||
IL_3JA1_089 | No text annotation | ||
IL_3JA1_090 | Double sheared | ||
IL_3JA1_091 | Single bulged U | ||
IL_3JA1_092 | Isolated non-canonical cWW pair | ||
IL_3JA1_192 | No text annotation | ||
IL_3JA1_093 | No text annotation | ||
IL_3JA1_095 | Major groove platform | ||
IL_3JA1_193 | No text annotation | ||
IL_3JA1_096 | No text annotation | ||
IL_3JA1_097 | No text annotation | ||
IL_3JA1_098 | Isolated non-canonical cWW pair | ||
IL_3JA1_099 | Single bulged A | ||
IL_3JA1_100 | tSH-tHS-tHW | ||
IL_3JA1_101 | Sarcin-Ricin target in LSU H95; G-bulge | ||
IL_3JA1_103 | UAA/GAN related, with intercalation | ||
IL_3JA1_104 | Isolated cWS basepair | ||
IL_3JA1_194 | Multiple bulged bases | ||
IL_3JA1_106 | No text annotation | ||
IL_3JA1_107 | Major groove intercalation | ||
IL_3JA1_108 | Multiple bulged bases with non-canonical cWW | ||
IL_3JA1_109 | tHS double platform | ||
IL_3JA1_110 | Major groove intercalation | ||
IL_3JA1_111 | No text annotation | ||
IL_3JA1_112 | No text annotation | ||
IL_3JA1_113 | Symmetric double minor groove platform | ||
IL_3JA1_114 | Bacterial 5S Loop E | ||
IL_3JA1_214 | Single bulged G | ||
IL_3JA1_195 | Isolated non-canonical cWW contact | ||
IL_3JA1_115 | Tandem non-canonical cWW pairs | ||
IL_3JA1_116 | Single bulged A | ||
IL_3JA1_117 | No text annotation | ||
IL_3JA1_118 | Minor groove platform | ||
IL_3JA1_119 | Multiple bulged bases | ||
IL_3JA1_120 | Minor groove platform with extra cWW | ||
IL_3JA1_121 | Minor groove platform | ||
IL_3JA1_196 | Single bulged G | ||
IL_3JA1_122 | Single bulged G, near cWW | ||
IL_3JA1_123 | Isolated non-canonical cWW pair | ||
IL_3JA1_215 | Minor groove platform related | ||
IL_3JA1_197 | No text annotation | ||
IL_3JA1_124 | No text annotation | ||
IL_3JA1_125 | Isolated cWH basepair | ||
IL_3JA1_126 | tWH-tWH-tHW-tHW | ||
IL_3JA1_127 | Minor groove platform | ||
IL_3JA1_198 | No text annotation | ||
IL_3JA1_128 | Kink-turn with non-sequential stacking | ||
IL_3JA1_129 | No text annotation | ||
IL_3JA1_130 | No text annotation | ||
IL_3JA1_131 | Single bulged U | ||
IL_3JA1_216 | C-loop | ||
IL_3JA1_132 | No text annotation | ||
IL_3JA1_217 | Isolated cWS basepair | ||
IL_3JA1_133 | No text annotation | ||
IL_3JA1_134 | No text annotation | ||
IL_3JA1_135 | No text annotation | ||
IL_3JA1_136 | No text annotation | ||
IL_3JA1_199 | No text annotation | ||
IL_3JA1_137 | No text annotation | ||
IL_3JA1_219 | No text annotation | ||
IL_3JA1_138 | Minor groove platform | ||
IL_3JA1_139 | SSU/LSU pseudoknot | ||
IL_3JA1_140 | Kink-turn related | ||
IL_3JA1_141 | No text annotation | ||
IL_3JA1_142 | tSH-tHW-tHS-cWW | ||
IL_3JA1_220 | tSH-tHW-tHS | ||
IL_3JA1_143 | Major groove platform | ||
IL_3JA1_221 | Major groove minor groove platform; mini C-loop | ||
IL_3JA1_144 | 8-nt loop receptor | ||
IL_3JA1_145 | No text annotation | ||
IL_3JA1_146 | Major groove platform; stack outside cWW | ||
IL_3JA1_147 | Single stack bend | ||
IL_3JA1_148 | Tandem non-canonical cWW pairs | ||
IL_3JA1_149 | No text annotation | ||
IL_3JA1_150 | Kink-turn | ||
IL_3JA1_151 | Left turn | ||
IL_3JA1_152 | tSH-tHW-tHS | ||
IL_3JA1_200 | Isolated non-canonical cWW pair | ||
IL_3JA1_153 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
IL_3JA1_222 | Single bulged A | ||
IL_3JA1_154 | Isolated non-canonical cWW with bulges | ||
IL_3JA1_155 | Single bulged G | ||
IL_3JA1_156 | Minor groove platform | ||
IL_3JA1_157 | Minor groove platform | ||
IL_3JA1_158 | Minor groove platform | ||
IL_3JA1_201 | No text annotation | ||
IL_3JA1_159 | Single stack bend | ||
IL_3JA1_160 | No text annotation | ||
IL_3JA1_161 | Tandem non-canonical cWW pairs | ||
IL_3JA1_162 | Minor groove platform | ||
IL_3JA1_163 | Single bulged U | ||
IL_3JA1_164 | Isolated non-canonical cWW pair | ||
IL_3JA1_166 | Minor groove platform | ||
IL_3JA1_223 | No text annotation | ||
IL_3JA1_167 | No text annotation | ||
IL_3JA1_168 | No text annotation | ||
IL_3JA1_169 | 180 degree turn | ||
IL_3JA1_170 | Double sheared with non-canonical cWW | ||
IL_3JA1_171 | No text annotation | ||
IL_3JA1_172 | No text annotation | ||
IL_3JA1_173 | No text annotation | ||
IL_3JA1_174 | Isolated non-canonical cWW pair | ||
IL_3JA1_175 | Stack and bulge | ||
IL_3JA1_202 | Isolated non-canonical cWW pair | ||
IL_3JA1_176 | Tandem non-canonical cWW pairs | ||
IL_3JA1_203 | Double sheared | ||
IL_3JA1_177 | No text annotation | ||
IL_3JA1_178 | Triple sheared related | ||
IL_3JA1_179 | No text annotation | ||
IL_3JA1_204 | No text annotation | ||
IL_3JA1_224 | No text annotation | ||
IL_3JA1_205 | No text annotation | ||
IL_3JA1_180 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_3JA1_041 | 1/LA/2282:2284, 1/LA/2384:2395, 1/LA/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
J3_3JA1_014 | 1/LB/10:16, 1/LB/68:70, 1/LB/106:110 | No text annotation | homologous J3_5J7L_049 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_3JA1_001 | No text annotation | ||
J3_3JA1_027 | No text annotation | ||
J3_3JA1_028 | No text annotation | ||
J3_3JA1_039 | No text annotation | ||
J3_3JA1_002 | No text annotation | ||
J3_3JA1_029 | No text annotation | ||
J3_3JA1_003 | No text annotation | ||
J3_3JA1_004 | No text annotation | ||
J3_3JA1_005 | No text annotation | ||
J3_3JA1_006 | No text annotation | ||
J3_3JA1_007 | No text annotation | ||
J3_3JA1_030 | No text annotation | ||
J3_3JA1_040 | No text annotation | ||
J3_3JA1_031 | No text annotation | ||
J3_3JA1_008 | Kink-turn 3-way junction | ||
J3_3JA1_009 | No text annotation | ||
J3_3JA1_010 | No text annotation | ||
J3_3JA1_032 | No text annotation | ||
J3_3JA1_011 | No text annotation | ||
J3_3JA1_012 | No text annotation | ||
J3_3JA1_013 | No text annotation | ||
J3_3JA1_015 | No text annotation | ||
J3_3JA1_033 | No text annotation | ||
J3_3JA1_016 | No text annotation | ||
J3_3JA1_034 | No text annotation | ||
J3_3JA1_017 | No text annotation | ||
J3_3JA1_018 | No text annotation | ||
J3_3JA1_035 | No text annotation | ||
J3_3JA1_019 | No text annotation | ||
J3_3JA1_020 | No text annotation | ||
J3_3JA1_021 | No text annotation | ||
J3_3JA1_022 | No text annotation | ||
J3_3JA1_036 | No text annotation | ||
J3_3JA1_023 | No text annotation | ||
J3_3JA1_037 | No text annotation | ||
J3_3JA1_024 | No text annotation | ||
J3_3JA1_025 | No text annotation | ||
J3_3JA1_042 | No text annotation | ||
J3_3JA1_038 | No text annotation | ||
J3_3JA1_026 | No text annotation | ||
J4_3JA1_001 | No text annotation | ||
J4_3JA1_002 | No text annotation | ||
J4_3JA1_003 | No text annotation | ||
J4_3JA1_004 | No text annotation | ||
J4_3JA1_005 | No text annotation | ||
J4_3JA1_006 | No text annotation | ||
J4_3JA1_007 | No text annotation | ||
J4_3JA1_008 | No text annotation | ||
J4_3JA1_009 | No text annotation | ||
J4_3JA1_010 | No text annotation | ||
J4_3JA1_011 | No text annotation | ||
J4_3JA1_012 | tRNA junction | ||
J4_3JA1_016 | No text annotation | ||
J4_3JA1_013 | No text annotation | ||
J4_3JA1_014 | No text annotation | ||
J4_3JA1_015 | No text annotation | ||
J5_3JA1_001 | No text annotation | ||
J5_3JA1_010 | No text annotation | ||
J5_3JA1_002 | No text annotation | ||
J5_3JA1_003 | No text annotation | ||
J5_3JA1_004 | No text annotation | ||
J5_3JA1_005 | No text annotation | ||
J5_3JA1_006 | No text annotation | ||
J5_3JA1_007 | No text annotation | ||
J5_3JA1_008 | No text annotation | ||
J5_3JA1_011 | No text annotation | ||
J5_3JA1_009 | No text annotation | ||
J6_3JA1_001 | No text annotation | ||
J7_3JA1_001 | No text annotation | ||
J7_3JA1_002 | No text annotation |
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