8VOR Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_8VOR_007 | 1/D/12:22 | No text annotation | geometric HL_4LFB_001 HL_31940.1 | |
HL_8VOR_021 | 1/D/726:731 | GNRA | geometric HL_5J7L_016 NA | |
HL_8VOR_022 | 1/D/786:796 | No text annotation | geometric HL_5J7L_017 NA | |
HL_8VOR_024 | 1/D/862:867 | GNRA | geometric HL_5J7L_019 NA | |
HL_8VOR_025 | 1/D/897:902 | GNRA | geometric HL_4LFB_020 HL_34789.1 | |
HL_8VOR_027 | 1/D/1076:1081 | GNRA | geometric HL_5J7L_023 NA | |
HL_8VOR_040 | 1/a/194:201 | No text annotation | geometric HL_5J7L_139 NA | |
HL_8VOR_042 | 1/a/246:252 | No text annotation | geometric HL_5J7L_141 NA | |
HL_8VOR_048 | 1/a/462:467 | GNRA | geometric HL_5J7L_147 NA | |
HL_8VOR_051 | 1/a/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
HL_8VOR_056 | 1/a/779:785 | No text annotation | geometric HL_5J7L_156 NA | |
HL_8VOR_059 | 1/a/978:985 | No text annotation | geometric HL_5J7L_160 NA | |
HL_8VOR_065 | 1/a/1324:1330 | Pseudoknot geometry with 3' bulge | geometric HL_5J7L_166 NA | |
HL_8VOR_076 | 1/a/1777:1787 | No text annotation | geometric HL_5J7L_178 NA | |
HL_8VOR_082 | 1/a/2264:2276 | No text annotation | geometric HL_5J7L_187 NA | |
HL_8VOR_090 | 1/a/2594:2599 | GNRA | geometric HL_4V9F_065 HL_34789.1 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_8VOR_001 | No text annotation | ||
HL_8VOR_002 | No text annotation | ||
HL_8VOR_003 | T-loop with 2 stacked bulged bases | ||
HL_8VOR_004 | No text annotation | ||
HL_8VOR_005 | No text annotation | ||
HL_8VOR_006 | T-loop with 2 stacked bulged bases | ||
HL_8VOR_008 | No text annotation | ||
HL_8VOR_009 | GNRA | ||
HL_8VOR_010 | GNRA | ||
HL_8VOR_011 | No text annotation | ||
HL_8VOR_012 | GNRA related | ||
HL_8VOR_013 | GNRA | ||
HL_8VOR_014 | No text annotation | ||
HL_8VOR_015 | UNCG | ||
HL_8VOR_016 | GNRA | ||
HL_8VOR_017 | UNCG | ||
HL_8VOR_018 | GNRA wlth extra near cWW | ||
HL_8VOR_019 | GNRA-like with tWH | ||
HL_8VOR_020 | No text annotation | ||
HL_8VOR_023 | No text annotation | ||
HL_8VOR_026 | GNRA | ||
HL_8VOR_028 | T-loop related | ||
HL_8VOR_029 | No text annotation | ||
HL_8VOR_030 | GNRA | ||
HL_8VOR_031 | GNRA | ||
HL_8VOR_032 | T-loop with 3 stacked bulged bases | ||
HL_8VOR_033 | No text annotation | ||
HL_8VOR_034 | UNCG | ||
HL_8VOR_035 | No text annotation | ||
HL_8VOR_036 | No text annotation | ||
HL_8VOR_037 | No text annotation | ||
HL_8VOR_038 | UNCG | ||
HL_8VOR_039 | No text annotation | ||
HL_8VOR_041 | No text annotation | ||
HL_8VOR_043 | T-loop with 2 stacked bulged bases | ||
HL_8VOR_044 | No text annotation | ||
HL_8VOR_045 | T-loop with unstacked turn | ||
HL_8VOR_046 | No text annotation | ||
HL_8VOR_047 | Pseudoknot geometry | ||
HL_8VOR_049 | GNRA | ||
HL_8VOR_050 | No text annotation | ||
HL_8VOR_052 | No text annotation | ||
HL_8VOR_053 | GNRA | ||
HL_8VOR_054 | No text annotation | ||
HL_8VOR_055 | GNRA wlth tandem sheared | ||
HL_8VOR_057 | No text annotation | ||
HL_8VOR_058 | No text annotation | ||
HL_8VOR_060 | No text annotation | ||
HL_8VOR_061 | GNRA wlth tandem sheared | ||
HL_8VOR_062 | No text annotation | ||
HL_8VOR_063 | GNRA | ||
HL_8VOR_064 | T-loop with 2 stacked bulged bases | ||
HL_8VOR_066 | GNRA | ||
HL_8VOR_067 | No text annotation | ||
HL_8VOR_068 | Mini UNCG with extended bulge | ||
HL_8VOR_069 | Pseudoknot geometry with 3' bulge | ||
HL_8VOR_070 | UNCG | ||
HL_8VOR_071 | Mini UNCG | ||
HL_8VOR_072 | GNRA | ||
HL_8VOR_073 | UNCG | ||
HL_8VOR_074 | No text annotation | ||
HL_8VOR_075 | No text annotation | ||
HL_8VOR_077 | GNRA related | ||
HL_8VOR_078 | GNRA variation | ||
HL_8VOR_079 | No text annotation | ||
HL_8VOR_080 | UNCG | ||
HL_8VOR_081 | No text annotation | ||
HL_8VOR_083 | No text annotation | ||
HL_8VOR_084 | Pseudoknot geometry | ||
HL_8VOR_085 | GNRA | ||
HL_8VOR_086 | GNRA | ||
HL_8VOR_087 | No text annotation | ||
HL_8VOR_088 | No text annotation | ||
HL_8VOR_089 | GNRA variation | ||
HL_8VOR_091 | GNRA | ||
HL_8VOR_092 | Ribsomal LSU H95 | ||
HL_8VOR_093 | No text annotation | ||
HL_8VOR_094 | No text annotation | ||
HL_8VOR_095 | No text annotation | ||
HL_8VOR_096 | GNRA | ||
HL_8VOR_097 | No text annotation | ||
HL_8VOR_098 | No text annotation | ||
HL_8VOR_099 | Mini UNCG |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_8VOR_001 | 1/D/30:32, 1/D/552:553 | Single bulged G | geometric IL_4LFB_001 IL_28408.1 | |
IL_8VOR_003 | 1/D/47:52, 1/D/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
IL_8VOR_012 | 1/D/242:247, 1/D/277:284 | Kink-turn with non-sequential stacking | geometric IL_5J7L_014 NA | |
IL_8VOR_014 | 1/D/292:293, 1/D/304:308 | C-loop | geometric IL_4LFB_013 IL_06671.1 | |
IL_8VOR_022 | 1/D/504:511, 1/D/540:541 | SSU/LSU pseudoknot | geometric IL_5J7L_024 NA | |
IL_8VOR_023 | 1/D/569:575, 1/D/880:881 | No text annotation | geometric IL_5J7L_026 NA | |
IL_8VOR_024 | 1/D/580:584, 1/D/757:761 | tSH-tHW-tHS | geometric IL_5J7L_027 NA | |
IL_8VOR_033 | 1/D/774:778, 1/D/804:805 | Left turn | geometric IL_4LFB_032 IL_29346.3 | |
IL_8VOR_034 | 1/D/779:783, 1/D/799:803 | tSH-tHW-tHS | geometric IL_5J7L_037 NA | |
IL_8VOR_035 | 1/D/887:894, 1/D/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_5J7L_038 NA | |
IL_8VOR_036 | 1/D/922:923, 1/D/1393:1395 | Single bulged A | geometric IL_5J7L_039 NA | |
IL_8VOR_037 | 1/D/925:927, 1/D/1390:1391 | Single bulged G | geometric IL_5J7L_040 NA | |
IL_8VOR_038 | 1/D/933:935, 1/D/1380:1384 | Minor groove platform | geometric IL_5J7L_041 NA | |
IL_8VOR_045 | 1/D/1060:1061, 1/D/1195:1197 | Single bulged A | geometric IL_5J7L_049 NA | |
IL_8VOR_046 | 1/D/1061:1063, 1/D/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
IL_8VOR_053 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | geometric IL_5J7L_058 NA | |
IL_8VOR_054 | 1/D/1412:1414, 1/D/1486:1488 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
IL_8VOR_055 | 1/D/1416:1419, 1/D/1481:1484 | Double sheared | geometric IL_5J7L_062 NA | |
IL_8VOR_069 | 1/a/481:484, 1/a/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
IL_8VOR_071 | 1/a/564:566, 1/a/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
IL_8VOR_073 | 1/a/672:674, 1/a/806:808 | Isolated non-canonical cWW pair | geometric IL_5J7L_259 NA | |
IL_8VOR_074 | 1/a/674:678, 1/a/799:806 | tHW-tHW cross-strand stack | geometric IL_5J7L_260 NA | |
IL_8VOR_078 | 1/a/738:740, 1/a/757:758 | Major groove platform | geometric IL_5J7L_264 NA | |
IL_8VOR_079 | 1/a/741:742, 1/a/754:756 | Single stack bend | geometric IL_8P9A_328 IL_15011.1 | |
IL_8VOR_080 | 1/a/742:744, 1/a/753:754 | Single stack bend | geometric IL_4V84_420 NA | |
IL_8VOR_081 | 1/a/775:777, 1/a/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
IL_8VOR_106 | 1/a/1262:1269, 1/a/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_289 NA | |
IL_8VOR_123 | 1/a/1651:1656, 1/a/2004:2006 | No text annotation | geometric IL_5J7L_304 NA | |
IL_8VOR_124 | 1/a/1663:1665, 1/a/1995:1997 | Isolated tWW turn | geometric IL_5J7L_305 NA | |
IL_8VOR_126 | 1/a/1666:1674, 1/a/1990:1994 | No text annotation | geometric IL_5J7L_386 NA | |
IL_8VOR_127 | 1/a/1669:1674, 1/a/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
IL_8VOR_139 | 1/a/2050:2052, 1/a/2617:2618 | Major groove platform | geometric IL_5J7L_320 NA | |
IL_8VOR_140 | 1/a/2054:2056, 1/a/2612:2615 | No text annotation | geometric IL_5J7L_321 NA | |
IL_8VOR_141 | 1/a/2070:2071, 1/a/2438:2441 | Minor groove platform | geometric IL_9DFE_081 IL_34520.1 | |
IL_8VOR_154 | 1/a/2510:2512, 1/a/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 NA | |
IL_8VOR_155 | 1/a/2512:2513, 1/a/2571:2574 | No text annotation | geometric IL_5J7L_341 NA | |
IL_8VOR_157 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | geometric IL_1U9S_001 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_8VOR_002 | Single bulged A | ||
IL_8VOR_004 | Minor groove platform | ||
IL_8VOR_005 | Multiple bulged bases | ||
IL_8VOR_006 | Minor groove platform with extra cWW | ||
IL_8VOR_007 | Minor groove platform | ||
IL_8VOR_008 | Single bulged G | ||
IL_8VOR_009 | Isolated non-canonical cWW pair | ||
IL_8VOR_010 | Minor groove platform related | ||
IL_8VOR_011 | No text annotation | ||
IL_8VOR_013 | No text annotation | ||
IL_8VOR_015 | Single bulged U | ||
IL_8VOR_016 | C-loop | ||
IL_8VOR_017 | Single bulged G | ||
IL_8VOR_018 | No text annotation | ||
IL_8VOR_019 | No text annotation | ||
IL_8VOR_020 | tSH-tHW-tWW | ||
IL_8VOR_021 | No text annotation | ||
IL_8VOR_025 | Major groove platform | ||
IL_8VOR_026 | Major groove minor groove platform; mini C-loop | ||
IL_8VOR_027 | No text annotation | ||
IL_8VOR_028 | Major groove platform; stack outside cWW | ||
IL_8VOR_029 | Single stack bend | ||
IL_8VOR_030 | Tandem non-canonical cWW pairs | ||
IL_8VOR_031 | No text annotation | ||
IL_8VOR_032 | Kink-turn | ||
IL_8VOR_039 | Minor groove platform | ||
IL_8VOR_040 | Minor groove platform | ||
IL_8VOR_041 | No text annotation | ||
IL_8VOR_042 | Single bulged U | ||
IL_8VOR_043 | Isolated cWS basepair | ||
IL_8VOR_044 | Minor groove platform | ||
IL_8VOR_047 | No text annotation | ||
IL_8VOR_048 | Minor groove platform | ||
IL_8VOR_049 | No text annotation | ||
IL_8VOR_050 | No text annotation | ||
IL_8VOR_051 | No text annotation | ||
IL_8VOR_052 | No text annotation | ||
IL_8VOR_056 | Triple sheared related | ||
IL_8VOR_057 | Single bulged A | ||
IL_8VOR_058 | No text annotation | ||
IL_8VOR_059 | Triple sheared with non-canonical cWW | ||
IL_8VOR_060 | Single bulged A | ||
IL_8VOR_061 | Minor groove platform | ||
IL_8VOR_062 | No text annotation | ||
IL_8VOR_063 | Single stack bend | ||
IL_8VOR_064 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_8VOR_065 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_8VOR_066 | No text annotation | ||
IL_8VOR_067 | No text annotation | ||
IL_8VOR_068 | No text annotation | ||
IL_8VOR_070 | Double sheared | ||
IL_8VOR_072 | AAA cross-strand stack | ||
IL_8VOR_075 | Single bulged A | ||
IL_8VOR_076 | Single bulged G | ||
IL_8VOR_077 | Triple sheared | ||
IL_8VOR_082 | 90 degree turn | ||
IL_8VOR_083 | No text annotation | ||
IL_8VOR_084 | Stack outside cWW | ||
IL_8VOR_085 | Single stack bend | ||
IL_8VOR_086 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_8VOR_087 | Single bulged G | ||
IL_8VOR_088 | C-loop with bulged stacked A's | ||
IL_8VOR_089 | Isolated non-canonical cWW pair | ||
IL_8VOR_090 | Double sheared with non-canonical cWW | ||
IL_8VOR_091 | No text annotation | ||
IL_8VOR_092 | Single bulged C | ||
IL_8VOR_093 | UAA/GAN | ||
IL_8VOR_094 | SSU/LSU pseudoknot | ||
IL_8VOR_095 | Single bulged U | ||
IL_8VOR_096 | Kink-turn related | ||
IL_8VOR_097 | No text annotation | ||
IL_8VOR_098 | Isolated non-canonical cWW pair | ||
IL_8VOR_099 | Tandem non-canonical cWW pairs | ||
IL_8VOR_100 | Kink-turn | ||
IL_8VOR_101 | No text annotation | ||
IL_8VOR_102 | Major groove platform | ||
IL_8VOR_103 | Isolated cWS basepair | ||
IL_8VOR_104 | No text annotation | ||
IL_8VOR_105 | Kink-turn | ||
IL_8VOR_107 | Major groove platform; stack outside cWW | ||
IL_8VOR_108 | C-loop | ||
IL_8VOR_109 | UAA/GAN | ||
IL_8VOR_110 | tSH-tHW-tHS | ||
IL_8VOR_111 | Single stack bend | ||
IL_8VOR_112 | Single stack bend | ||
IL_8VOR_113 | No text annotation | ||
IL_8VOR_114 | UAA/GAN | ||
IL_8VOR_115 | Tandem non-canonical cWW pairs | ||
IL_8VOR_116 | tSH-tHW | ||
IL_8VOR_117 | Single bulged U | ||
IL_8VOR_118 | No text annotation | ||
IL_8VOR_119 | tSH-tHW-tHS | ||
IL_8VOR_120 | 180 degree turn | ||
IL_8VOR_121 | Single bulged A | ||
IL_8VOR_122 | UAA/GAN variation | ||
IL_8VOR_125 | Major groove platform; stack outside cWW | ||
IL_8VOR_128 | tSH-tSH-tHH-tHS | ||
IL_8VOR_129 | 6x5 Sarcin-Ricin; G-bulge | ||
IL_8VOR_130 | Triple sheared | ||
IL_8VOR_131 | Single bulged A | ||
IL_8VOR_132 | Kink-turn related | ||
IL_8VOR_133 | Minor groove platform, major groove intercalation | ||
IL_8VOR_134 | Major groove intercalation | ||
IL_8VOR_135 | Major groove minor groove platform; mini C-loop | ||
IL_8VOR_136 | No text annotation | ||
IL_8VOR_137 | UAA/GAN related | ||
IL_8VOR_138 | Bulged stacked bases | ||
IL_8VOR_142 | Isolated tHS basepair with bulges | ||
IL_8VOR_143 | Isolated non-canonical cWW pair | ||
IL_8VOR_144 | Isolated non-canonical cWW pair | ||
IL_8VOR_145 | Isolated non-canonical cWW pair | ||
IL_8VOR_146 | No text annotation | ||
IL_8VOR_147 | No text annotation | ||
IL_8VOR_148 | Kink-turn | ||
IL_8VOR_149 | Single bulged U | ||
IL_8VOR_150 | Double sheared | ||
IL_8VOR_151 | No text annotation | ||
IL_8VOR_152 | Major groove minor groove platform with extra cWW | ||
IL_8VOR_153 | Double sheared with non-canonical cWW | ||
IL_8VOR_156 | Major groove platform with intercalation | ||
IL_8VOR_158 | tSH-tHS-tHW | ||
IL_8VOR_159 | Sarcin-Ricin target in LSU H95; G-bulge | ||
IL_8VOR_160 | C-loop | ||
IL_8VOR_161 | UAA/GAN related, with intercalation | ||
IL_8VOR_162 | Multiple bulged bases | ||
IL_8VOR_163 | UAA/GAN with extra cWW | ||
IL_8VOR_164 | No text annotation | ||
IL_8VOR_165 | Major groove intercalation | ||
IL_8VOR_166 | Multiple bulged bases with non-canonical cWW | ||
IL_8VOR_167 | tHS double platform | ||
IL_8VOR_168 | Major groove intercalation | ||
IL_8VOR_169 | No text annotation | ||
IL_8VOR_170 | Major groove minor groove platform; mini C-loop | ||
IL_8VOR_171 | Symmetric double minor groove platform | ||
IL_8VOR_172 | Bacterial 5S Loop E |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_8VOR_002 | 1/D/46:52, 1/D/359:367, 1/D/393:395 | No text annotation | geometric J3_5J7L_050 NA | |
J3_8VOR_006 | 1/D/826:829, 1/D/857:861, 1/D/868:874 | No text annotation | geometric J3_5J7L_004 NA | |
J3_8VOR_012 | 1/D/1063:1068, 1/D/1107:1113, 1/D/1187:1193 | No text annotation | geometric J3_5J7L_008 NA | |
J3_8VOR_013 | 1/D/1073:1074, 1/D/1083:1087, 1/D/1098:1102 | No text annotation | ||
J3_8VOR_017 | 1/a/30:31, 1/a/474:481, 1/a/509:510 | No text annotation | geometric J3_5J7L_036 NA | |
J3_8VOR_018 | 1/a/30:31, 1/a/474:484, 1/a/496:510 | No text annotation | geometric J3_5J7L_066 NA | |
J3_8VOR_019 | 1/a/32:35, 1/a/445:461, 1/a/468:473 | No text annotation | geometric J3_5J7L_067 NA | |
J3_8VOR_022 | 1/a/683:689, 1/a/773:775, 1/a/791:794 | No text annotation | geometric J3_5J7L_038 NA | |
J3_8VOR_026 | 1/a/1306:1309, 1/a/1605:1611, 1/a/1620:1622 | No text annotation | geometric J3_7A0S_007 J3_47341.1 | |
J4_8VOR_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | ||
J4_8VOR_009 | 1/a/1270:1276, 1/a/1294:1295, 1/a/1645:1648, 1/a/2009:2010 | No text annotation | ||
J5_8VOR_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_8VOR_006 | 1/a/584:589, 1/a/668:671, 1/a/809:812, 1/a/1195:1196, 1/a/1250:1256 | No text annotation | ||
J7_8VOR_001 | 1/a/8:15, 1/a/525:531, 1/a/2018:2023, 1/a/2040:2043, 1/a/2625:2630, 1/a/2788:2789, 1/a/2894:2895 | No text annotation | ||
J7_8VOR_002 | 1/a/817:822, 1/a/835:838, 1/a/940:946, 1/a/971:976, 1/a/987:991, 1/a/1163:1164, 1/a/1185:1190 | No text annotation |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_8VOR_001 | No text annotation | ||
J3_8VOR_003 | No text annotation | ||
J3_8VOR_004 | No text annotation | ||
J3_8VOR_005 | No text annotation | ||
J3_8VOR_007 | No text annotation | ||
J3_8VOR_008 | No text annotation | ||
J3_8VOR_009 | No text annotation | ||
J3_8VOR_010 | No text annotation | ||
J3_8VOR_011 | No text annotation | ||
J3_8VOR_014 | No text annotation | ||
J3_8VOR_015 | No text annotation | ||
J3_8VOR_016 | No text annotation | ||
J3_8VOR_020 | No text annotation | ||
J3_8VOR_021 | No text annotation | ||
J3_8VOR_023 | No text annotation | ||
J3_8VOR_024 | No text annotation | ||
J3_8VOR_025 | No text annotation | ||
J3_8VOR_027 | No text annotation | ||
J3_8VOR_028 | No text annotation | ||
J3_8VOR_029 | Kink-turn 3-way junction | ||
J3_8VOR_030 | No text annotation | ||
J3_8VOR_031 | No text annotation | ||
J3_8VOR_032 | No text annotation | ||
J3_8VOR_033 | No text annotation | ||
J3_8VOR_034 | No text annotation | ||
J3_8VOR_035 | No text annotation | ||
J4_8VOR_001 | No text annotation | ||
J4_8VOR_002 | No text annotation | ||
J4_8VOR_003 | No text annotation | ||
J4_8VOR_004 | No text annotation | ||
J4_8VOR_006 | No text annotation | ||
J4_8VOR_007 | No text annotation | ||
J4_8VOR_008 | No text annotation | ||
J4_8VOR_010 | No text annotation | ||
J4_8VOR_011 | No text annotation | ||
J4_8VOR_012 | No text annotation | ||
J4_8VOR_013 | No text annotation | ||
J4_8VOR_014 | No text annotation | ||
J4_8VOR_015 | No text annotation | ||
J5_8VOR_001 | No text annotation | ||
J5_8VOR_002 | No text annotation | ||
J5_8VOR_003 | No text annotation | ||
J5_8VOR_004 | No text annotation | ||
J5_8VOR_007 | No text annotation | ||
J6_8VOR_001 | No text annotation |
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