8VOO Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8VOO_025 | 1/D/897:902 | GNRA | geometric HL_8CRE_215 HL_34789.2 | |
| HL_8VOO_051 | 1/a/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_8VOO_056 | 1/a/779:785 | No text annotation | geometric HL_5J7L_156 NA | |
| HL_8VOO_076 | 1/a/1777:1787 | No text annotation | geometric HL_5J7L_178 NA | |
| HL_8VOO_090 | 1/a/2594:2599 | GNRA | geometric HL_4V9F_065 HL_34789.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8VOO_001 | No text annotation | ||
| HL_8VOO_002 | No text annotation | ||
| HL_8VOO_003 | T-loop with 2 stacked bulged bases | ||
| HL_8VOO_004 | No text annotation | ||
| HL_8VOO_005 | No text annotation | ||
| HL_8VOO_006 | T-loop with 2 stacked bulged bases | ||
| HL_8VOO_007 | No text annotation | ||
| HL_8VOO_008 | No text annotation | ||
| HL_8VOO_009 | GNRA | ||
| HL_8VOO_010 | GNRA | ||
| HL_8VOO_011 | No text annotation | ||
| HL_8VOO_012 | GNRA related | ||
| HL_8VOO_013 | GNRA | ||
| HL_8VOO_014 | No text annotation | ||
| HL_8VOO_015 | UNCG | ||
| HL_8VOO_016 | GNRA | ||
| HL_8VOO_017 | UNCG | ||
| HL_8VOO_018 | GNRA wlth extra near cWW | ||
| HL_8VOO_019 | GNRA-like with tWH | ||
| HL_8VOO_020 | No text annotation | ||
| HL_8VOO_021 | GNRA | ||
| HL_8VOO_022 | No text annotation | ||
| HL_8VOO_023 | No text annotation | ||
| HL_8VOO_024 | GNRA | ||
| HL_8VOO_026 | GNRA | ||
| HL_8VOO_027 | GNRA | ||
| HL_8VOO_028 | T-loop related | ||
| HL_8VOO_029 | No text annotation | ||
| HL_8VOO_030 | GNRA | ||
| HL_8VOO_031 | GNRA | ||
| HL_8VOO_032 | T-loop with 3 stacked bulged bases | ||
| HL_8VOO_033 | No text annotation | ||
| HL_8VOO_034 | UNCG | ||
| HL_8VOO_035 | No text annotation | ||
| HL_8VOO_036 | No text annotation | ||
| HL_8VOO_037 | No text annotation | ||
| HL_8VOO_038 | UNCG | ||
| HL_8VOO_039 | No text annotation | ||
| HL_8VOO_040 | No text annotation | ||
| HL_8VOO_041 | No text annotation | ||
| HL_8VOO_042 | No text annotation | ||
| HL_8VOO_043 | T-loop with 2 stacked bulged bases | ||
| HL_8VOO_044 | No text annotation | ||
| HL_8VOO_045 | T-loop with unstacked turn | ||
| HL_8VOO_046 | No text annotation | ||
| HL_8VOO_047 | Pseudoknot geometry | ||
| HL_8VOO_048 | GNRA | ||
| HL_8VOO_049 | GNRA | ||
| HL_8VOO_050 | No text annotation | ||
| HL_8VOO_052 | No text annotation | ||
| HL_8VOO_053 | GNRA | ||
| HL_8VOO_054 | No text annotation | ||
| HL_8VOO_055 | GNRA wlth tandem sheared | ||
| HL_8VOO_057 | No text annotation | ||
| HL_8VOO_058 | No text annotation | ||
| HL_8VOO_059 | No text annotation | ||
| HL_8VOO_060 | No text annotation | ||
| HL_8VOO_061 | GNRA wlth tandem sheared | ||
| HL_8VOO_062 | No text annotation | ||
| HL_8VOO_063 | GNRA | ||
| HL_8VOO_064 | T-loop with 2 stacked bulged bases | ||
| HL_8VOO_065 | Pseudoknot geometry with 3' bulge | ||
| HL_8VOO_066 | GNRA | ||
| HL_8VOO_067 | No text annotation | ||
| HL_8VOO_068 | Mini UNCG with extended bulge | ||
| HL_8VOO_069 | Pseudoknot geometry with 3' bulge | ||
| HL_8VOO_070 | UNCG | ||
| HL_8VOO_071 | Mini UNCG | ||
| HL_8VOO_072 | GNRA | ||
| HL_8VOO_073 | UNCG | ||
| HL_8VOO_074 | No text annotation | ||
| HL_8VOO_075 | No text annotation | ||
| HL_8VOO_077 | GNRA related | ||
| HL_8VOO_078 | GNRA variation | ||
| HL_8VOO_079 | No text annotation | ||
| HL_8VOO_080 | UNCG | ||
| HL_8VOO_081 | No text annotation | ||
| HL_8VOO_082 | No text annotation | ||
| HL_8VOO_083 | No text annotation | ||
| HL_8VOO_084 | Pseudoknot geometry | ||
| HL_8VOO_085 | GNRA | ||
| HL_8VOO_086 | GNRA | ||
| HL_8VOO_087 | No text annotation | ||
| HL_8VOO_088 | No text annotation | ||
| HL_8VOO_089 | GNRA variation | ||
| HL_8VOO_091 | GNRA | ||
| HL_8VOO_092 | Ribsomal LSU H95 | ||
| HL_8VOO_093 | No text annotation | ||
| HL_8VOO_094 | UNCG variation | ||
| HL_8VOO_095 | No text annotation | ||
| HL_8VOO_096 | GNRA | ||
| HL_8VOO_097 | No text annotation | ||
| HL_8VOO_098 | No text annotation | ||
| HL_8VOO_099 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8VOO_024 | 1/D/569:575, 1/D/880:881 | No text annotation | geometric IL_5J7L_026 NA | |
| IL_8VOO_036 | 1/D/887:894, 1/D/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_5J7L_038 NA | |
| IL_8VOO_056 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | geometric IL_8CRE_466 IL_18228.1 | |
| IL_8VOO_057 | 1/D/1412:1414, 1/D/1486:1488 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
| IL_8VOO_074 | 1/a/564:566, 1/a/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_8VOO_081 | 1/a/738:740, 1/a/757:758 | Major groove platform | geometric IL_5J7L_264 NA | |
| IL_8VOO_082 | 1/a/775:777, 1/a/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_8VOO_107 | 1/a/1262:1269, 1/a/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_289 NA | |
| IL_8VOO_127 | 1/a/1666:1674, 1/a/1990:1994 | No text annotation | geometric IL_5J7L_386 NA | |
| IL_8VOO_128 | 1/a/1669:1674, 1/a/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_8VOO_141 | 1/a/2054:2056, 1/a/2612:2615 | No text annotation | geometric IL_5J7L_321 NA | |
| IL_8VOO_142 | 1/a/2070:2071, 1/a/2438:2441 | Minor groove platform | geometric IL_9DFE_081 IL_34520.2 | |
| IL_8VOO_158 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | geometric IL_1U9S_001 IL_14190.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8VOO_001 | Single bulged G | ||
| IL_8VOO_002 | Single bulged A | ||
| IL_8VOO_003 | No text annotation | ||
| IL_8VOO_004 | Minor groove platform | ||
| IL_8VOO_005 | Multiple bulged bases | ||
| IL_8VOO_006 | Minor groove platform with extra cWW | ||
| IL_8VOO_007 | Minor groove platform | ||
| IL_8VOO_008 | Single bulged G | ||
| IL_8VOO_009 | Isolated non-canonical cWW pair | ||
| IL_8VOO_010 | Minor groove platform related | ||
| IL_8VOO_011 | Isolated cWH basepair | ||
| IL_8VOO_012 | tWH-tWH-tHW-tHW | ||
| IL_8VOO_013 | Kink-turn with non-sequential stacking | ||
| IL_8VOO_014 | No text annotation | ||
| IL_8VOO_015 | C-loop | ||
| IL_8VOO_016 | Single bulged U | ||
| IL_8VOO_017 | C-loop | ||
| IL_8VOO_018 | Single bulged G | ||
| IL_8VOO_019 | No text annotation | ||
| IL_8VOO_020 | No text annotation | ||
| IL_8VOO_021 | tSH-tHW-tWW | ||
| IL_8VOO_022 | No text annotation | ||
| IL_8VOO_023 | SSU/LSU pseudoknot | ||
| IL_8VOO_025 | tSH-tHW-tHS | ||
| IL_8VOO_026 | Major groove platform | ||
| IL_8VOO_027 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOO_028 | No text annotation | ||
| IL_8VOO_029 | Major groove platform; stack outside cWW | ||
| IL_8VOO_030 | Single stack bend | ||
| IL_8VOO_031 | Tandem non-canonical cWW pairs | ||
| IL_8VOO_032 | Triple non-canonical cWW pairs | ||
| IL_8VOO_033 | Kink-turn | ||
| IL_8VOO_034 | Left turn | ||
| IL_8VOO_035 | tSH-tHW-tHS | ||
| IL_8VOO_037 | Single bulged A | ||
| IL_8VOO_038 | Single bulged G | ||
| IL_8VOO_039 | Minor groove platform | ||
| IL_8VOO_040 | Minor groove platform | ||
| IL_8VOO_041 | Minor groove platform | ||
| IL_8VOO_042 | Single stack bend | ||
| IL_8VOO_043 | No text annotation | ||
| IL_8VOO_044 | Single bulged U | ||
| IL_8VOO_045 | Isolated cWS basepair | ||
| IL_8VOO_046 | Minor groove platform | ||
| IL_8VOO_047 | Single bulged A | ||
| IL_8VOO_048 | Isolated non-canonical cWW pair | ||
| IL_8VOO_049 | No text annotation | ||
| IL_8VOO_050 | Minor groove platform | ||
| IL_8VOO_051 | No text annotation | ||
| IL_8VOO_052 | No text annotation | ||
| IL_8VOO_053 | 180 degree turn | ||
| IL_8VOO_054 | Double sheared with non-canonical cWW | ||
| IL_8VOO_055 | No text annotation | ||
| IL_8VOO_058 | Double sheared | ||
| IL_8VOO_059 | Triple sheared related | ||
| IL_8VOO_060 | Single bulged A | ||
| IL_8VOO_061 | No text annotation | ||
| IL_8VOO_062 | Triple sheared with non-canonical cWW | ||
| IL_8VOO_063 | Single bulged A | ||
| IL_8VOO_064 | Minor groove platform | ||
| IL_8VOO_065 | No text annotation | ||
| IL_8VOO_066 | Single stack bend | ||
| IL_8VOO_067 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_8VOO_068 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_8VOO_069 | No text annotation | ||
| IL_8VOO_070 | No text annotation | ||
| IL_8VOO_071 | No text annotation | ||
| IL_8VOO_072 | No text annotation | ||
| IL_8VOO_073 | Double sheared | ||
| IL_8VOO_075 | AAA cross-strand stack | ||
| IL_8VOO_076 | Isolated non-canonical cWW pair | ||
| IL_8VOO_077 | tHW-tHW cross-strand stack | ||
| IL_8VOO_078 | Single bulged A | ||
| IL_8VOO_079 | Single bulged G | ||
| IL_8VOO_080 | Triple sheared | ||
| IL_8VOO_083 | 90 degree turn | ||
| IL_8VOO_084 | No text annotation | ||
| IL_8VOO_085 | Stack outside cWW | ||
| IL_8VOO_086 | Single stack bend | ||
| IL_8VOO_087 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_8VOO_088 | Single bulged G | ||
| IL_8VOO_089 | C-loop with bulged stacked A's | ||
| IL_8VOO_090 | Isolated non-canonical cWW pair | ||
| IL_8VOO_091 | Double sheared with non-canonical cWW | ||
| IL_8VOO_092 | Single bulged A | ||
| IL_8VOO_093 | Single bulged C | ||
| IL_8VOO_094 | UAA/GAN | ||
| IL_8VOO_095 | SSU/LSU pseudoknot | ||
| IL_8VOO_096 | Single bulged U | ||
| IL_8VOO_097 | Kink-turn related | ||
| IL_8VOO_098 | No text annotation | ||
| IL_8VOO_099 | Isolated non-canonical cWW pair | ||
| IL_8VOO_100 | Tandem non-canonical cWW pairs | ||
| IL_8VOO_101 | No text annotation | ||
| IL_8VOO_102 | No text annotation | ||
| IL_8VOO_103 | Major groove platform | ||
| IL_8VOO_104 | Isolated cWS basepair | ||
| IL_8VOO_105 | No text annotation | ||
| IL_8VOO_106 | Kink-turn | ||
| IL_8VOO_108 | Major groove platform; stack outside cWW | ||
| IL_8VOO_109 | C-loop | ||
| IL_8VOO_110 | UAA/GAN | ||
| IL_8VOO_111 | tSH-tHW-tHS | ||
| IL_8VOO_112 | Single stack bend | ||
| IL_8VOO_113 | Single stack bend | ||
| IL_8VOO_114 | No text annotation | ||
| IL_8VOO_115 | UAA/GAN | ||
| IL_8VOO_116 | Tandem non-canonical cWW pairs | ||
| IL_8VOO_117 | tSH-tHW | ||
| IL_8VOO_118 | Single bulged U | ||
| IL_8VOO_119 | No text annotation | ||
| IL_8VOO_120 | tSH-tHW-tHS | ||
| IL_8VOO_121 | 180 degree turn | ||
| IL_8VOO_122 | Single bulged A | ||
| IL_8VOO_123 | UAA/GAN variation | ||
| IL_8VOO_124 | No text annotation | ||
| IL_8VOO_125 | Isolated tWW turn | ||
| IL_8VOO_126 | Major groove platform; stack outside cWW | ||
| IL_8VOO_129 | tSH-tSH-tHH-tHS | ||
| IL_8VOO_130 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_8VOO_131 | Triple sheared | ||
| IL_8VOO_132 | Single bulged A | ||
| IL_8VOO_133 | Kink-turn related | ||
| IL_8VOO_134 | Minor groove platform, major groove intercalation | ||
| IL_8VOO_135 | Major groove intercalation | ||
| IL_8VOO_136 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOO_137 | No text annotation | ||
| IL_8VOO_138 | UAA/GAN related | ||
| IL_8VOO_139 | Bulged stacked bases | ||
| IL_8VOO_140 | Major groove platform | ||
| IL_8VOO_143 | Isolated tHS basepair with bulges | ||
| IL_8VOO_144 | Isolated non-canonical cWW pair | ||
| IL_8VOO_145 | Isolated non-canonical cWW pair | ||
| IL_8VOO_146 | Isolated non-canonical cWW pair | ||
| IL_8VOO_147 | No text annotation | ||
| IL_8VOO_148 | No text annotation | ||
| IL_8VOO_149 | Kink-turn | ||
| IL_8VOO_150 | Single bulged U | ||
| IL_8VOO_151 | Double sheared | ||
| IL_8VOO_152 | No text annotation | ||
| IL_8VOO_153 | Major groove minor groove platform with extra cWW | ||
| IL_8VOO_154 | Double sheared with non-canonical cWW | ||
| IL_8VOO_155 | Isolated non-canonical cWW with bulges | ||
| IL_8VOO_156 | No text annotation | ||
| IL_8VOO_157 | Major groove platform with intercalation | ||
| IL_8VOO_159 | tSH-tHS-tHW | ||
| IL_8VOO_160 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_8VOO_161 | C-loop | ||
| IL_8VOO_162 | UAA/GAN related, with intercalation | ||
| IL_8VOO_163 | Multiple bulged bases | ||
| IL_8VOO_164 | UAA/GAN with extra cWW | ||
| IL_8VOO_165 | No text annotation | ||
| IL_8VOO_166 | Major groove intercalation | ||
| IL_8VOO_167 | Multiple bulged bases with non-canonical cWW | ||
| IL_8VOO_168 | tHS double platform | ||
| IL_8VOO_169 | Major groove intercalation | ||
| IL_8VOO_170 | No text annotation | ||
| IL_8VOO_171 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOO_172 | Symmetric double minor groove platform | ||
| IL_8VOO_173 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8VOO_022 | 1/a/683:689, 1/a/773:775, 1/a/791:794 | No text annotation | geometric J3_5J7L_038 NA | |
| J4_8VOO_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | ||
| J5_8VOO_005 | 1/a/531:533, 1/a/560:564, 1/a/577:579, 1/a/1261:1262, 1/a/2017:2018 | No text annotation | ||
| J5_8VOO_006 | 1/a/584:589, 1/a/668:671, 1/a/809:812, 1/a/1195:1196, 1/a/1250:1256 | No text annotation | ||
| J5_8VOO_007 | 1/a/1674:1682, 1/a/1706:1707, 1/a/1751:1752, 1/a/1756:1764, 1/a/1988:1990 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8VOO_001 | No text annotation | ||
| J3_8VOO_002 | No text annotation | ||
| J3_8VOO_003 | No text annotation | ||
| J3_8VOO_004 | No text annotation | ||
| J3_8VOO_005 | No text annotation | ||
| J3_8VOO_006 | No text annotation | ||
| J3_8VOO_007 | No text annotation | ||
| J3_8VOO_008 | No text annotation | ||
| J3_8VOO_009 | No text annotation | ||
| J3_8VOO_010 | No text annotation | ||
| J3_8VOO_011 | No text annotation | ||
| J3_8VOO_012 | No text annotation | ||
| J3_8VOO_013 | No text annotation | ||
| J3_8VOO_014 | No text annotation | ||
| J3_8VOO_015 | No text annotation | ||
| J3_8VOO_016 | No text annotation | ||
| J3_8VOO_017 | No text annotation | ||
| J3_8VOO_018 | No text annotation | ||
| J3_8VOO_019 | No text annotation | ||
| J3_8VOO_020 | No text annotation | ||
| J3_8VOO_021 | No text annotation | ||
| J3_8VOO_023 | No text annotation | ||
| J3_8VOO_024 | No text annotation | ||
| J3_8VOO_025 | No text annotation | ||
| J3_8VOO_026 | No text annotation | ||
| J3_8VOO_027 | No text annotation | ||
| J3_8VOO_028 | No text annotation | ||
| J3_8VOO_029 | Kink-turn 3-way junction | ||
| J3_8VOO_030 | No text annotation | ||
| J3_8VOO_031 | No text annotation | ||
| J3_8VOO_032 | No text annotation | ||
| J3_8VOO_033 | No text annotation | ||
| J3_8VOO_034 | No text annotation | ||
| J3_8VOO_035 | No text annotation | ||
| J4_8VOO_001 | No text annotation | ||
| J4_8VOO_002 | No text annotation | ||
| J4_8VOO_003 | No text annotation | ||
| J4_8VOO_004 | No text annotation | ||
| J4_8VOO_006 | No text annotation | ||
| J4_8VOO_007 | No text annotation | ||
| J4_8VOO_008 | No text annotation | ||
| J4_8VOO_009 | No text annotation | ||
| J4_8VOO_010 | No text annotation | ||
| J4_8VOO_011 | No text annotation | ||
| J4_8VOO_012 | No text annotation | ||
| J4_8VOO_013 | No text annotation | ||
| J4_8VOO_014 | No text annotation | ||
| J4_8VOO_015 | No text annotation | ||
| J5_8VOO_001 | No text annotation | ||
| J5_8VOO_002 | No text annotation | ||
| J5_8VOO_003 | No text annotation | ||
| J5_8VOO_004 | No text annotation | ||
| J6_8VOO_001 | No text annotation | ||
| J7_8VOO_001 | No text annotation | ||
| J7_8VOO_002 | No text annotation |
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