6GXP Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6GXP_003 | 1/A/123:128 | No text annotation | homologous HL_4WF9_003 HL_75660.7 | |
| HL_6GXP_031 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_6GXP_039 | 1/A/1612:1619 | No text annotation | homologous HL_7RQB_040 NA | |
| HL_6GXP_044 | 1/A/1777:1787 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_6GXP_108 | 1/A/1950:1956 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6GXP_001 | No text annotation | ||
| HL_6GXP_002 | No text annotation | ||
| HL_6GXP_004 | No text annotation | ||
| HL_6GXP_005 | No text annotation | ||
| HL_6GXP_103 | No text annotation | ||
| HL_6GXP_006 | No text annotation | ||
| HL_6GXP_007 | No text annotation | ||
| HL_6GXP_008 | No text annotation | ||
| HL_6GXP_009 | T-loop with 2 stacked bulged bases | ||
| HL_6GXP_010 | No text annotation | ||
| HL_6GXP_011 | T-loop with unstacked turn | ||
| HL_6GXP_012 | No text annotation | ||
| HL_6GXP_112 | No text annotation | ||
| HL_6GXP_013 | Pseudoknot geometry | ||
| HL_6GXP_014 | GNRA | ||
| HL_6GXP_015 | GNRA | ||
| HL_6GXP_104 | No text annotation | ||
| HL_6GXP_016 | No text annotation | ||
| HL_6GXP_017 | T-loop with 2 stacked bulged bases | ||
| HL_6GXP_018 | No text annotation | ||
| HL_6GXP_019 | GNRA | ||
| HL_6GXP_020 | No text annotation | ||
| HL_6GXP_105 | No text annotation | ||
| HL_6GXP_021 | GNRA wlth tandem sheared | ||
| HL_6GXP_022 | No text annotation | ||
| HL_6GXP_023 | UNCG variation | ||
| HL_6GXP_024 | No text annotation | ||
| HL_6GXP_025 | No text annotation | ||
| HL_6GXP_026 | Anticodon loop related | ||
| HL_6GXP_027 | No text annotation | ||
| HL_6GXP_028 | No text annotation | ||
| HL_6GXP_029 | No text annotation | ||
| HL_6GXP_113 | No text annotation | ||
| HL_6GXP_030 | GNRA | ||
| HL_6GXP_032 | Pseudoknot geometry with 3' bulge | ||
| HL_6GXP_033 | GNRA | ||
| HL_6GXP_034 | No text annotation | ||
| HL_6GXP_035 | No text annotation | ||
| HL_6GXP_036 | Pseudoknot geometry with 3' bulge | ||
| HL_6GXP_106 | No text annotation | ||
| HL_6GXP_037 | No text annotation | ||
| HL_6GXP_038 | Mini UNCG | ||
| HL_6GXP_040 | GNRA with extra cWW | ||
| HL_6GXP_107 | GNRA | ||
| HL_6GXP_041 | UNCG | ||
| HL_6GXP_042 | No text annotation | ||
| HL_6GXP_043 | No text annotation | ||
| HL_6GXP_045 | GNRA related | ||
| HL_6GXP_046 | GNRA variation | ||
| HL_6GXP_047 | No text annotation | ||
| HL_6GXP_048 | No text annotation | ||
| HL_6GXP_049 | No text annotation | ||
| HL_6GXP_050 | No text annotation | ||
| HL_6GXP_051 | No text annotation | ||
| HL_6GXP_052 | No text annotation | ||
| HL_6GXP_053 | No text annotation | ||
| HL_6GXP_054 | No text annotation | ||
| HL_6GXP_109 | No text annotation | ||
| HL_6GXP_055 | Pseudoknot geometry | ||
| HL_6GXP_056 | GNRA | ||
| HL_6GXP_057 | GNRA | ||
| HL_6GXP_058 | No text annotation | ||
| HL_6GXP_059 | No text annotation | ||
| HL_6GXP_060 | GNRA variation | ||
| HL_6GXP_061 | No text annotation | ||
| HL_6GXP_062 | GNRA | ||
| HL_6GXP_063 | GNRA | ||
| HL_6GXP_064 | Ribsomal LSU H95 | ||
| HL_6GXP_065 | No text annotation | ||
| HL_6GXP_066 | UNCG variation | ||
| HL_6GXP_067 | No text annotation | ||
| HL_6GXP_068 | GNRA | ||
| HL_6GXP_069 | No text annotation | ||
| HL_6GXP_070 | Mini UNCG | ||
| HL_6GXP_071 | No text annotation | ||
| HL_6GXP_072 | No text annotation | ||
| HL_6GXP_073 | GNRA with extra near cWW | ||
| HL_6GXP_110 | GNRA | ||
| HL_6GXP_074 | GNRA | ||
| HL_6GXP_075 | No text annotation | ||
| HL_6GXP_076 | GNRA related | ||
| HL_6GXP_077 | GNRA | ||
| HL_6GXP_078 | No text annotation | ||
| HL_6GXP_079 | UNCG | ||
| HL_6GXP_111 | tRNA anticodon loop | ||
| HL_6GXP_080 | GNRA | ||
| HL_6GXP_081 | UNCG | ||
| HL_6GXP_082 | GNRA wlth extra near cWW | ||
| HL_6GXP_083 | No text annotation | ||
| HL_6GXP_084 | GNRA-like with tWH | ||
| HL_6GXP_085 | No text annotation | ||
| HL_6GXP_086 | GNRA | ||
| HL_6GXP_087 | No text annotation | ||
| HL_6GXP_088 | No text annotation | ||
| HL_6GXP_089 | GNRA | ||
| HL_6GXP_090 | GNRA | ||
| HL_6GXP_091 | No text annotation | ||
| HL_6GXP_092 | GNRA | ||
| HL_6GXP_093 | No text annotation | ||
| HL_6GXP_094 | GNRA | ||
| HL_6GXP_095 | T-loop related | ||
| HL_6GXP_096 | No text annotation | ||
| HL_6GXP_097 | GNRA | ||
| HL_6GXP_098 | GNRA | ||
| HL_6GXP_099 | T-loop with 3 stacked bulged bases | ||
| HL_6GXP_100 | No text annotation | ||
| HL_6GXP_101 | UNCG | ||
| HL_6GXP_102 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6GXP_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_250 NA | |
| IL_6GXP_067 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_4WF9_069 IL_17069.6 | |
| IL_6GXP_075 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6GXP_097 | 1/A/2591:2592, 1/A/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_6GXP_098 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7RQB_102 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6GXP_001 | Triple sheared with non-canonical cWW | ||
| IL_6GXP_002 | Single bulged A | ||
| IL_6GXP_178 | Minor groove platform with extra cWW | ||
| IL_6GXP_003 | Minor groove platform | ||
| IL_6GXP_004 | Kink-turn | ||
| IL_6GXP_005 | Single stack bend | ||
| IL_6GXP_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6GXP_008 | No text annotation | ||
| IL_6GXP_179 | No text annotation | ||
| IL_6GXP_009 | No text annotation | ||
| IL_6GXP_180 | No text annotation | ||
| IL_6GXP_010 | No text annotation | ||
| IL_6GXP_011 | No text annotation | ||
| IL_6GXP_012 | Double sheared | ||
| IL_6GXP_013 | Isolated non-canonical cWW pair | ||
| IL_6GXP_014 | AAA cross-strand stack | ||
| IL_6GXP_015 | Isolated non-canonical cWW pair | ||
| IL_6GXP_016 | tHW-tHW cross-strand stack | ||
| IL_6GXP_017 | Single bulged A | ||
| IL_6GXP_018 | Single bulged G | ||
| IL_6GXP_181 | Triple sheared | ||
| IL_6GXP_019 | Triple sheared with non-canonical cWW | ||
| IL_6GXP_020 | Major groove platform | ||
| IL_6GXP_021 | Multiple bulged bases | ||
| IL_6GXP_022 | 90 degree turn | ||
| IL_6GXP_182 | No text annotation | ||
| IL_6GXP_023 | Stack outside cWW | ||
| IL_6GXP_024 | Single stack bend | ||
| IL_6GXP_025 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_6GXP_026 | Single bulged G | ||
| IL_6GXP_027 | C-loop | ||
| IL_6GXP_028 | Isolated non-canonical cWW pair | ||
| IL_6GXP_029 | Double sheared with non-canonical cWW | ||
| IL_6GXP_201 | No text annotation | ||
| IL_6GXP_030 | Tandem non-canonical cWW pairs | ||
| IL_6GXP_031 | Single bulged C | ||
| IL_6GXP_032 | UAA/GAN | ||
| IL_6GXP_033 | SSU/LSU pseudoknot | ||
| IL_6GXP_034 | Single bulged U | ||
| IL_6GXP_035 | Kink-turn related | ||
| IL_6GXP_036 | No text annotation | ||
| IL_6GXP_037 | Isolated non-canonical cWW pair | ||
| IL_6GXP_038 | Tandem non-canonical cWW pairs | ||
| IL_6GXP_183 | Partly complementary | ||
| IL_6GXP_039 | Kink-turn | ||
| IL_6GXP_040 | No text annotation | ||
| IL_6GXP_184 | No text annotation | ||
| IL_6GXP_041 | Major groove platform | ||
| IL_6GXP_042 | Isolated cWS basepair | ||
| IL_6GXP_043 | No text annotation | ||
| IL_6GXP_044 | Kink-turn | ||
| IL_6GXP_045 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6GXP_046 | Major groove platform; stack outside cWW | ||
| IL_6GXP_047 | C-loop | ||
| IL_6GXP_048 | UAA/GAN | ||
| IL_6GXP_049 | tSH-tHW-tHS | ||
| IL_6GXP_050 | No text annotation | ||
| IL_6GXP_185 | No text annotation | ||
| IL_6GXP_051 | UAA/GAN | ||
| IL_6GXP_052 | Tandem non-canonical cWW pairs | ||
| IL_6GXP_053 | tSH-tHW | ||
| IL_6GXP_054 | No text annotation | ||
| IL_6GXP_186 | tSH-tHW-tHS | ||
| IL_6GXP_055 | No text annotation | ||
| IL_6GXP_056 | 180 degree turn | ||
| IL_6GXP_057 | Single bulged A | ||
| IL_6GXP_058 | UAA/GAN variation | ||
| IL_6GXP_059 | No text annotation | ||
| IL_6GXP_060 | Isolated tWW turn | ||
| IL_6GXP_061 | Major groove platform; stack outside cWW | ||
| IL_6GXP_187 | No text annotation | ||
| IL_6GXP_062 | Intercalated tWH | ||
| IL_6GXP_063 | tSH-tSH-tHH-tHS | ||
| IL_6GXP_064 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6GXP_065 | Triple sheared | ||
| IL_6GXP_066 | Single bulged A | ||
| IL_6GXP_068 | Minor groove platform, major groove intercalation | ||
| IL_6GXP_069 | Major groove intercalation | ||
| IL_6GXP_070 | Major groove minor groove platform; mini C-loop | ||
| IL_6GXP_188 | No text annotation | ||
| IL_6GXP_071 | UAA/GAN related | ||
| IL_6GXP_072 | Bulged stacked bases | ||
| IL_6GXP_073 | No text annotation | ||
| IL_6GXP_074 | Major groove platform | ||
| IL_6GXP_076 | Single bulged U | ||
| IL_6GXP_077 | Minor groove platform | ||
| IL_6GXP_078 | Isolated tHS basepair with bulges | ||
| IL_6GXP_079 | Isolated non-canonical cWW pair | ||
| IL_6GXP_189 | Triple non-canonical cWW pairs | ||
| IL_6GXP_202 | Isolated non-canonical cWW pair | ||
| IL_6GXP_080 | Other IL | ||
| IL_6GXP_081 | No text annotation | ||
| IL_6GXP_190 | No text annotation | ||
| IL_6GXP_082 | Kink-turn related | ||
| IL_6GXP_083 | No text annotation | ||
| IL_6GXP_191 | No text annotation | ||
| IL_6GXP_084 | Tandem non-canonical cWW pairs | ||
| IL_6GXP_085 | Single bulged U | ||
| IL_6GXP_086 | Double sheared | ||
| IL_6GXP_087 | No text annotation | ||
| IL_6GXP_088 | Single stack bend | ||
| IL_6GXP_089 | Major groove platform | ||
| IL_6GXP_090 | Major groove platform with extra pair | ||
| IL_6GXP_091 | Major groove minor groove platform with extra cWW | ||
| IL_6GXP_092 | Double sheared with non-canonical cWW | ||
| IL_6GXP_093 | No text annotation | ||
| IL_6GXP_094 | Isolated non-canonical cWW with bulges | ||
| IL_6GXP_095 | No text annotation | ||
| IL_6GXP_096 | Major groove platform with intercalation | ||
| IL_6GXP_192 | No text annotation | ||
| IL_6GXP_099 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6GXP_100 | C-loop | ||
| IL_6GXP_101 | UAA/GAN related, with intercalation | ||
| IL_6GXP_102 | Multiple bulged bases | ||
| IL_6GXP_103 | UAA/GAN with extra cWW | ||
| IL_6GXP_104 | No text annotation | ||
| IL_6GXP_105 | Major groove intercalation | ||
| IL_6GXP_106 | Multiple bulged bases with non-canonical cWW | ||
| IL_6GXP_107 | tHS double platform | ||
| IL_6GXP_108 | Major groove intercalation | ||
| IL_6GXP_109 | No text annotation | ||
| IL_6GXP_110 | Major groove minor groove platform; mini C-loop | ||
| IL_6GXP_111 | No text annotation | ||
| IL_6GXP_193 | No text annotation | ||
| IL_6GXP_112 | Bacterial 5S Loop E | ||
| IL_6GXP_113 | Single bulged G | ||
| IL_6GXP_114 | Single bulged A | ||
| IL_6GXP_115 | No text annotation | ||
| IL_6GXP_116 | Minor groove platform | ||
| IL_6GXP_117 | Multiple bulged bases | ||
| IL_6GXP_118 | Minor groove platform with extra cWW | ||
| IL_6GXP_119 | Minor groove platform | ||
| IL_6GXP_194 | Single bulged G | ||
| IL_6GXP_120 | Single bulged G, near cWW | ||
| IL_6GXP_121 | Isolated non-canonical cWW pair | ||
| IL_6GXP_122 | Minor groove platform related | ||
| IL_6GXP_123 | Isolated cWH basepair | ||
| IL_6GXP_124 | tWH-tWH-tHW-tHW | ||
| IL_6GXP_125 | Minor groove platform | ||
| IL_6GXP_126 | Kink-turn with non-sequential stacking | ||
| IL_6GXP_127 | No text annotation | ||
| IL_6GXP_128 | C-loop | ||
| IL_6GXP_129 | Single bulged U | ||
| IL_6GXP_130 | C-loop | ||
| IL_6GXP_131 | Single bulged G | ||
| IL_6GXP_132 | No text annotation | ||
| IL_6GXP_133 | No text annotation | ||
| IL_6GXP_134 | tSH-tHW-tWW | ||
| IL_6GXP_135 | No text annotation | ||
| IL_6GXP_136 | SSU/LSU pseudoknot | ||
| IL_6GXP_137 | Kink-turn related | ||
| IL_6GXP_138 | No text annotation | ||
| IL_6GXP_139 | tSH-tHW-tHS | ||
| IL_6GXP_140 | Major groove platform | ||
| IL_6GXP_141 | Major groove minor groove platform; mini C-loop | ||
| IL_6GXP_142 | No text annotation | ||
| IL_6GXP_143 | Major groove platform; stack outside cWW | ||
| IL_6GXP_144 | No text annotation | ||
| IL_6GXP_195 | Single stack bend | ||
| IL_6GXP_145 | Tandem non-canonical cWW pairs | ||
| IL_6GXP_146 | No text annotation | ||
| IL_6GXP_147 | No text annotation | ||
| IL_6GXP_148 | Left turn | ||
| IL_6GXP_149 | tSH-tHW-tHS | ||
| IL_6GXP_150 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6GXP_196 | 9x7 Sarcin-Ricin with inserted C; G-bulge | ||
| IL_6GXP_151 | Single bulged A | ||
| IL_6GXP_152 | Single bulged G | ||
| IL_6GXP_153 | Minor groove platform | ||
| IL_6GXP_154 | No text annotation | ||
| IL_6GXP_155 | Minor groove platform | ||
| IL_6GXP_156 | Single stack bend | ||
| IL_6GXP_197 | No text annotation | ||
| IL_6GXP_157 | Single bulged U | ||
| IL_6GXP_198 | Multiple bulged bases | ||
| IL_6GXP_158 | Isolated cWS basepair | ||
| IL_6GXP_159 | Minor groove platform | ||
| IL_6GXP_160 | Single bulged U | ||
| IL_6GXP_161 | Isolated non-canonical cWW pair | ||
| IL_6GXP_199 | No text annotation | ||
| IL_6GXP_162 | No text annotation | ||
| IL_6GXP_163 | Minor groove platform | ||
| IL_6GXP_164 | No text annotation | ||
| IL_6GXP_165 | No text annotation | ||
| IL_6GXP_166 | 180 degree turn | ||
| IL_6GXP_167 | Double sheared with non-canonical cWW | ||
| IL_6GXP_168 | No text annotation | ||
| IL_6GXP_200 | No text annotation | ||
| IL_6GXP_169 | No text annotation | ||
| IL_6GXP_170 | No text annotation | ||
| IL_6GXP_171 | Isolated non-canonical cWW pair | ||
| IL_6GXP_172 | No text annotation | ||
| IL_6GXP_173 | Isolated non-canonical cWW pair | ||
| IL_6GXP_174 | Double sheared | ||
| IL_6GXP_175 | Triple sheared related | ||
| IL_6GXP_176 | Single bulged A | ||
| IL_6GXP_177 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6GXP_026 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_6GXP_009 | 1/A/2295:2299, 1/A/2317:2323, 1/A/2332:2337 | No text annotation | homologous J3_5J7L_071 NA | |
| J4_6GXP_005 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_6GXP_006 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_6GXP_009 | 1/A/1833:1835, 1/A/1905:1906, 1/A/1924:1933, 1/A/1967:1972 | No text annotation | homologous J4_5J7L_026 NA | |
| J5_6GXP_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_6GXP_003 | 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 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6GXP_001 | No text annotation | ||
| J3_6GXP_002 | No text annotation | ||
| J3_6GXP_027 | No text annotation | ||
| J3_6GXP_003 | No text annotation | ||
| J3_6GXP_004 | No text annotation | ||
| J3_6GXP_005 | No text annotation | ||
| J3_6GXP_006 | No text annotation | ||
| J3_6GXP_028 | No text annotation | ||
| J3_6GXP_007 | No text annotation | ||
| J3_6GXP_029 | No text annotation | ||
| J3_6GXP_008 | Kink-turn 3-way junction | ||
| J3_6GXP_010 | No text annotation | ||
| J3_6GXP_011 | No text annotation | ||
| J3_6GXP_012 | No text annotation | ||
| J3_6GXP_013 | No text annotation | ||
| J3_6GXP_014 | No text annotation | ||
| J3_6GXP_030 | No text annotation | ||
| J3_6GXP_015 | No text annotation | ||
| J3_6GXP_031 | No text annotation | ||
| J3_6GXP_016 | No text annotation | ||
| J3_6GXP_017 | No text annotation | ||
| J3_6GXP_032 | No text annotation | ||
| J3_6GXP_018 | No text annotation | ||
| J3_6GXP_019 | No text annotation | ||
| J3_6GXP_020 | No text annotation | ||
| J3_6GXP_033 | No text annotation | ||
| J3_6GXP_021 | No text annotation | ||
| J3_6GXP_022 | No text annotation | ||
| J3_6GXP_034 | No text annotation | ||
| J3_6GXP_023 | No text annotation | ||
| J3_6GXP_024 | No text annotation | ||
| J3_6GXP_035 | No text annotation | ||
| J3_6GXP_025 | No text annotation | ||
| J4_6GXP_001 | No text annotation | ||
| J4_6GXP_002 | No text annotation | ||
| J4_6GXP_003 | No text annotation | ||
| J4_6GXP_004 | No text annotation | ||
| J4_6GXP_007 | No text annotation | ||
| J4_6GXP_008 | No text annotation | ||
| J4_6GXP_010 | No text annotation | ||
| J4_6GXP_011 | No text annotation | ||
| J4_6GXP_012 | No text annotation | ||
| J4_6GXP_013 | No text annotation | ||
| J5_6GXP_002 | No text annotation | ||
| J5_6GXP_004 | No text annotation | ||
| J5_6GXP_005 | No text annotation | ||
| J5_6GXP_006 | No text annotation | ||
| J5_6GXP_007 | No text annotation | ||
| J5_6GXP_008 | No text annotation | ||
| J6_6GXP_001 | No text annotation | ||
| J7_6GXP_001 | No text annotation | ||
| J7_6GXP_002 | No text annotation | ||
| J8_6GXP_002 | No text annotation | ||
| J8_6GXP_001 | No text annotation |
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