8YDJ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8YDJ_001 | 1/1/59:68 | No text annotation | geometric HL_8B0X_033 HL_35677.5 | |
| HL_8YDJ_016 | 1/1/566:575 | No text annotation | geometric HL_8B0X_048 HL_33597.2 | |
| HL_8YDJ_021 | 1/1/744:753 | No text annotation | geometric HL_7A0S_022 HL_50204.1 | |
| HL_8YDJ_022 | 1/1/779:785 | UNCG variation | geometric HL_7A0S_023 HL_51020.2 | |
| HL_8YDJ_025 | 1/1/955:962 | No text annotation | geometric HL_9AXU_023 HL_34789.2 | |
| HL_8YDJ_038 | 1/1/1565:1568 | Mini UNCG | geometric HL_7A0S_039 HL_90436.2 | |
| HL_8YDJ_039 | 1/1/1612:1619 | No text annotation | geometric HL_9DFE_038 HL_28592.1 | |
| HL_8YDJ_044 | 1/1/1777:1787 | No text annotation | geometric HL_4WF9_043 HL_87681.1 | |
| HL_8YDJ_049 | 1/1/2027:2036 | No text annotation | geometric HL_8B0X_078 HL_78372.1 | |
| HL_8YDJ_062 | 1/1/2594:2599 | GNRA | geometric HL_2Z75_004 HL_34789.2 | |
| HL_8YDJ_064 | 1/1/2701:2706 | No text annotation | geometric HL_9E6Q_063 HL_12125.2 | |
| HL_8YDJ_083 | 1/3/522:527 | No text annotation | geometric HL_8B0X_099 HL_34789.2 | |
| HL_8YDJ_085 | 1/3/689:698 | No text annotation | geometric HL_4LFB_015 HL_38491.2 | |
| HL_8YDJ_090 | 1/3/897:902 | GNRA | geometric HL_4YAZ_003 HL_34789.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8YDJ_002 | No text annotation | ||
| HL_8YDJ_003 | No text annotation | ||
| HL_8YDJ_004 | No text annotation | ||
| HL_8YDJ_005 | No text annotation | ||
| HL_8YDJ_006 | No text annotation | ||
| HL_8YDJ_007 | UNCG | ||
| HL_8YDJ_008 | No text annotation | ||
| HL_8YDJ_009 | No text annotation | ||
| HL_8YDJ_010 | No text annotation | ||
| HL_8YDJ_011 | No text annotation | ||
| HL_8YDJ_012 | No text annotation | ||
| HL_8YDJ_013 | GNRA | ||
| HL_8YDJ_014 | No text annotation | ||
| HL_8YDJ_015 | No text annotation | ||
| HL_8YDJ_017 | No text annotation | ||
| HL_8YDJ_018 | GNRA | ||
| HL_8YDJ_019 | No text annotation | ||
| HL_8YDJ_020 | GNRA wlth tandem sheared | ||
| HL_8YDJ_023 | No text annotation | ||
| HL_8YDJ_024 | No text annotation | ||
| HL_8YDJ_026 | No text annotation | ||
| HL_8YDJ_027 | No text annotation | ||
| HL_8YDJ_028 | No text annotation | ||
| HL_8YDJ_029 | No text annotation | ||
| HL_8YDJ_030 | No text annotation | ||
| HL_8YDJ_031 | No text annotation | ||
| HL_8YDJ_032 | No text annotation | ||
| HL_8YDJ_033 | No text annotation | ||
| HL_8YDJ_034 | No text annotation | ||
| HL_8YDJ_035 | No text annotation | ||
| HL_8YDJ_036 | No text annotation | ||
| HL_8YDJ_037 | No text annotation | ||
| HL_8YDJ_040 | No text annotation | ||
| HL_8YDJ_041 | UNCG | ||
| HL_8YDJ_042 | No text annotation | ||
| HL_8YDJ_043 | No text annotation | ||
| HL_8YDJ_045 | No text annotation | ||
| HL_8YDJ_046 | GNRA related | ||
| HL_8YDJ_047 | No text annotation | ||
| HL_8YDJ_048 | No text annotation | ||
| HL_8YDJ_050 | No text annotation | ||
| HL_8YDJ_051 | No text annotation | ||
| HL_8YDJ_052 | No text annotation | ||
| HL_8YDJ_053 | No text annotation | ||
| HL_8YDJ_054 | No text annotation | ||
| HL_8YDJ_055 | No text annotation | ||
| HL_8YDJ_056 | No text annotation | ||
| HL_8YDJ_057 | GNRA | ||
| HL_8YDJ_058 | No text annotation | ||
| HL_8YDJ_059 | No text annotation | ||
| HL_8YDJ_060 | No text annotation | ||
| HL_8YDJ_061 | No text annotation | ||
| HL_8YDJ_063 | GNRA | ||
| HL_8YDJ_065 | No text annotation | ||
| HL_8YDJ_066 | No text annotation | ||
| HL_8YDJ_067 | No text annotation | ||
| HL_8YDJ_068 | No text annotation | ||
| HL_8YDJ_069 | No text annotation | ||
| HL_8YDJ_070 | Mini UNCG | ||
| HL_8YDJ_071 | No text annotation | ||
| HL_8YDJ_072 | No text annotation | ||
| HL_8YDJ_073 | tRNA anticodon loop | ||
| HL_8YDJ_074 | GNRA | ||
| HL_8YDJ_075 | No text annotation | ||
| HL_8YDJ_076 | No text annotation | ||
| HL_8YDJ_077 | No text annotation | ||
| HL_8YDJ_078 | No text annotation | ||
| HL_8YDJ_079 | UNCG | ||
| HL_8YDJ_080 | GNRA | ||
| HL_8YDJ_081 | No text annotation | ||
| HL_8YDJ_082 | GNRA related | ||
| HL_8YDJ_084 | No text annotation | ||
| HL_8YDJ_086 | GNRA | ||
| HL_8YDJ_087 | No text annotation | ||
| HL_8YDJ_088 | No text annotation | ||
| HL_8YDJ_089 | GNRA | ||
| HL_8YDJ_091 | No text annotation | ||
| HL_8YDJ_092 | GNRA | ||
| HL_8YDJ_093 | GNRA | ||
| HL_8YDJ_094 | T-loop related | ||
| HL_8YDJ_095 | No text annotation | ||
| HL_8YDJ_096 | No text annotation | ||
| HL_8YDJ_097 | GNRA | ||
| HL_8YDJ_098 | T-loop with 3 stacked bulged bases | ||
| HL_8YDJ_099 | No text annotation | ||
| HL_8YDJ_100 | No text annotation | ||
| HL_8YDJ_101 | GNRA | ||
| HL_8YDJ_102 | No text annotation | ||
| HL_8YDJ_103 | No text annotation | ||
| HL_8YDJ_104 | No text annotation | ||
| HL_8YDJ_105 | tRNA D-loop | ||
| HL_8YDJ_106 | No text annotation | ||
| HL_8YDJ_107 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8YDJ_011 | 1/1/564:566, 1/1/575:577 | Isolated non-canonical cWW pair | geometric IL_7A0S_011 IL_71625.2 | |
| IL_8YDJ_015 | 1/1/697:698, 1/1/763:765 | No text annotation | geometric IL_8B0X_081 IL_14190.2 | |
| IL_8YDJ_017 | 1/1/703:707, 1/1/724:728 | Triple sheared | geometric IL_4V9F_027 IL_15190.2 | |
| IL_8YDJ_018 | 1/1/738:740, 1/1/757:758 | Major groove platform | geometric IL_4WF9_026 IL_48076.8 | |
| IL_8YDJ_043 | 1/1/1262:1269, 1/1/2011:2017 | No text annotation | geometric IL_8B0X_108 IL_62167.2 | |
| IL_8YDJ_056 | 1/1/1526:1531, 1/1/1540:1546 | No text annotation | ||
| IL_8YDJ_057 | 1/1/1651:1656, 1/1/2004:2006 | No text annotation | geometric IL_7A0S_059 IL_12566.5 | |
| IL_8YDJ_058 | 1/1/1663:1665, 1/1/1995:1997 | No text annotation | geometric IL_8B0X_124 IL_10432.1 | |
| IL_8YDJ_067 | 1/1/1837:1840, 1/1/1902:1903 | No text annotation | geometric IL_8B0X_133 IL_55206.1 | |
| IL_8YDJ_073 | 1/1/1934:1945, 1/1/1961:1964 | No text annotation | ||
| IL_8YDJ_074 | 1/1/2050:2052, 1/1/2617:2618 | No text annotation | geometric IL_9FN2_003 IL_48076.8 | |
| IL_8YDJ_075 | 1/1/2054:2056, 1/1/2612:2615 | No text annotation | ||
| IL_8YDJ_086 | 1/1/2401:2403, 1/1/2414:2415 | No text annotation | ||
| IL_8YDJ_092 | 1/1/2509:2513, 1/1/2571:2579 | No text annotation | ||
| IL_8YDJ_097 | 1/1/2680:2684, 1/1/2725:2727 | C-loop | geometric IL_6XJQ_001 IL_63596.12 | |
| IL_8YDJ_098 | 1/1/2687:2691, 1/1/2718:2722 | UAA/GAN related, with intercalation | geometric IL_4WF9_102 IL_82016.1 | |
| IL_8YDJ_099 | 1/1/2695:2696, 1/1/2711:2714 | No text annotation | geometric IL_8B0X_164 IL_44609.2 | |
| IL_8YDJ_101 | 1/1/2838:2839, 1/1/2878:2880 | Major groove intercalation | geometric IL_4WF9_106 IL_77710.1 | |
| IL_8YDJ_102 | 1/1/2843:2846, 1/1/2870:2874 | No text annotation | geometric IL_8B0X_169 IL_60988.2 | |
| IL_8YDJ_139 | 1/3/673:677, 1/3/713:717 | No text annotation | geometric IL_8B0X_176 IL_71154.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8YDJ_001 | No text annotation | ||
| IL_8YDJ_002 | Single bulged A | ||
| IL_8YDJ_003 | Minor groove platform related | ||
| IL_8YDJ_004 | No text annotation | ||
| IL_8YDJ_005 | No text annotation | ||
| IL_8YDJ_006 | No text annotation | ||
| IL_8YDJ_007 | No text annotation | ||
| IL_8YDJ_008 | No text annotation | ||
| IL_8YDJ_009 | No text annotation | ||
| IL_8YDJ_010 | No text annotation | ||
| IL_8YDJ_012 | No text annotation | ||
| IL_8YDJ_013 | Isolated non-canonical cWW pair | ||
| IL_8YDJ_014 | No text annotation | ||
| IL_8YDJ_016 | Single bulged G | ||
| IL_8YDJ_019 | No text annotation | ||
| IL_8YDJ_020 | No text annotation | ||
| IL_8YDJ_021 | No text annotation | ||
| IL_8YDJ_022 | No text annotation | ||
| IL_8YDJ_023 | No text annotation | ||
| IL_8YDJ_024 | No text annotation | ||
| IL_8YDJ_025 | No text annotation | ||
| IL_8YDJ_026 | No text annotation | ||
| IL_8YDJ_027 | No text annotation | ||
| IL_8YDJ_028 | No text annotation | ||
| IL_8YDJ_029 | No text annotation | ||
| IL_8YDJ_030 | No text annotation | ||
| IL_8YDJ_031 | UAA/GAN with extra cWW | ||
| IL_8YDJ_032 | No text annotation | ||
| IL_8YDJ_033 | No text annotation | ||
| IL_8YDJ_034 | No text annotation | ||
| IL_8YDJ_035 | No text annotation | ||
| IL_8YDJ_036 | No text annotation | ||
| IL_8YDJ_037 | Tandem non-canonical cWW pairs | ||
| IL_8YDJ_038 | No text annotation | ||
| IL_8YDJ_039 | No text annotation | ||
| IL_8YDJ_040 | No text annotation | ||
| IL_8YDJ_041 | No text annotation | ||
| IL_8YDJ_042 | No text annotation | ||
| IL_8YDJ_044 | Major groove platform; stack outside cWW | ||
| IL_8YDJ_045 | No text annotation | ||
| IL_8YDJ_046 | No text annotation | ||
| IL_8YDJ_047 | No text annotation | ||
| IL_8YDJ_048 | No text annotation | ||
| IL_8YDJ_049 | UAA/GAN | ||
| IL_8YDJ_050 | No text annotation | ||
| IL_8YDJ_051 | No text annotation | ||
| IL_8YDJ_052 | No text annotation | ||
| IL_8YDJ_053 | No text annotation | ||
| IL_8YDJ_054 | No text annotation | ||
| IL_8YDJ_055 | Single bulged A | ||
| IL_8YDJ_059 | No text annotation | ||
| IL_8YDJ_060 | No text annotation | ||
| IL_8YDJ_061 | No text annotation | ||
| IL_8YDJ_062 | No text annotation | ||
| IL_8YDJ_063 | No text annotation | ||
| IL_8YDJ_064 | No text annotation | ||
| IL_8YDJ_065 | No text annotation | ||
| IL_8YDJ_066 | No text annotation | ||
| IL_8YDJ_068 | Major groove intercalation | ||
| IL_8YDJ_069 | No text annotation | ||
| IL_8YDJ_070 | No text annotation | ||
| IL_8YDJ_071 | No text annotation | ||
| IL_8YDJ_072 | Bulged stacked bases | ||
| IL_8YDJ_076 | No text annotation | ||
| IL_8YDJ_077 | Minor groove platform | ||
| IL_8YDJ_078 | Isolated tHS basepair with bulges | ||
| IL_8YDJ_079 | No text annotation | ||
| IL_8YDJ_080 | No text annotation | ||
| IL_8YDJ_081 | No text annotation | ||
| IL_8YDJ_082 | No text annotation | ||
| IL_8YDJ_083 | No text annotation | ||
| IL_8YDJ_084 | Double sheared | ||
| IL_8YDJ_085 | No text annotation | ||
| IL_8YDJ_087 | Single stack bend | ||
| IL_8YDJ_088 | Major groove platform | ||
| IL_8YDJ_089 | No text annotation | ||
| IL_8YDJ_090 | Double sheared with non-canonical cWW | ||
| IL_8YDJ_091 | Major groove platform | ||
| IL_8YDJ_093 | No text annotation | ||
| IL_8YDJ_094 | Single bulged A | ||
| IL_8YDJ_095 | No text annotation | ||
| IL_8YDJ_096 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_8YDJ_100 | No text annotation | ||
| IL_8YDJ_103 | No text annotation | ||
| IL_8YDJ_104 | Major groove intercalation | ||
| IL_8YDJ_105 | No text annotation | ||
| IL_8YDJ_106 | No text annotation | ||
| IL_8YDJ_107 | No text annotation | ||
| IL_8YDJ_108 | No text annotation | ||
| IL_8YDJ_109 | No text annotation | ||
| IL_8YDJ_110 | No text annotation | ||
| IL_8YDJ_111 | No text annotation | ||
| IL_8YDJ_112 | Major groove intercalation | ||
| IL_8YDJ_113 | No text annotation | ||
| IL_8YDJ_114 | Minor groove platform | ||
| IL_8YDJ_115 | No text annotation | ||
| IL_8YDJ_116 | No text annotation | ||
| IL_8YDJ_117 | No text annotation | ||
| IL_8YDJ_118 | No text annotation | ||
| IL_8YDJ_119 | No text annotation | ||
| IL_8YDJ_120 | No text annotation | ||
| IL_8YDJ_121 | No text annotation | ||
| IL_8YDJ_122 | No text annotation | ||
| IL_8YDJ_123 | No text annotation | ||
| IL_8YDJ_124 | No text annotation | ||
| IL_8YDJ_125 | Single bulged G | ||
| IL_8YDJ_126 | No text annotation | ||
| IL_8YDJ_127 | No text annotation | ||
| IL_8YDJ_128 | No text annotation | ||
| IL_8YDJ_129 | No text annotation | ||
| IL_8YDJ_130 | No text annotation | ||
| IL_8YDJ_131 | No text annotation | ||
| IL_8YDJ_132 | No text annotation | ||
| IL_8YDJ_133 | No text annotation | ||
| IL_8YDJ_134 | No text annotation | ||
| IL_8YDJ_135 | Major groove minor groove platform; mini C-loop | ||
| IL_8YDJ_136 | No text annotation | ||
| IL_8YDJ_137 | Single stack bend | ||
| IL_8YDJ_138 | No text annotation | ||
| IL_8YDJ_140 | No text annotation | ||
| IL_8YDJ_141 | No text annotation | ||
| IL_8YDJ_142 | tSH-tHW-tHS | ||
| IL_8YDJ_143 | No text annotation | ||
| IL_8YDJ_144 | No text annotation | ||
| IL_8YDJ_145 | Single bulged G | ||
| IL_8YDJ_146 | No text annotation | ||
| IL_8YDJ_147 | No text annotation | ||
| IL_8YDJ_148 | Single stack bend | ||
| IL_8YDJ_149 | No text annotation | ||
| IL_8YDJ_150 | No text annotation | ||
| IL_8YDJ_151 | Isolated cWS basepair | ||
| IL_8YDJ_152 | No text annotation | ||
| IL_8YDJ_153 | No text annotation | ||
| IL_8YDJ_154 | No text annotation | ||
| IL_8YDJ_155 | No text annotation | ||
| IL_8YDJ_156 | Minor groove platform | ||
| IL_8YDJ_157 | No text annotation | ||
| IL_8YDJ_158 | No text annotation | ||
| IL_8YDJ_159 | No text annotation | ||
| IL_8YDJ_160 | No text annotation | ||
| IL_8YDJ_161 | No text annotation | ||
| IL_8YDJ_162 | No text annotation | ||
| IL_8YDJ_163 | Isolated non-canonical cWW pair | ||
| IL_8YDJ_164 | No text annotation | ||
| IL_8YDJ_165 | No text annotation | ||
| IL_8YDJ_166 | Double sheared | ||
| IL_8YDJ_167 | No text annotation | ||
| IL_8YDJ_168 | No text annotation | ||
| IL_8YDJ_169 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8YDJ_006 | 1/1/683:689, 1/1/773:775, 1/1/791:794 | No text annotation | geometric J3_8B0X_016 J3_46658.1 | |
| J3_8YDJ_007 | 1/1/698:700, 1/1/732:736, 1/1/760:763 | No text annotation | geometric J3_8B0X_017 J3_69816.1 | |
| J3_8YDJ_009 | 1/1/1298:1303, 1/1/1625:1627, 1/1/1639:1642 | No text annotation | geometric J3_8B0X_018 J3_32852.7 | |
| J3_8YDJ_011 | 1/1/1344:1349, 1/1/1382:1385, 1/1/1402:1403 | No text annotation | ||
| J3_8YDJ_016 | 1/1/2517:2520, 1/1/2545:2547, 1/1/2561:2567 | No text annotation | geometric J3_4WF9_009 J3_32601.6 | |
| J3_8YDJ_018 | 1/1/2806:2815, 1/1/2831:2836, 1/1/2882:2892 | No text annotation | ||
| J4_8YDJ_003 | 1/1/1270:1276, 1/1/1294:1295, 1/1/1645:1648, 1/1/2009:2010 | No text annotation | ||
| J4_8YDJ_007 | 1/1/1772:1776, 1/1/1788:1792, 1/1/1827:1830, 1/1/1975:1979 | No text annotation | ||
| J4_8YDJ_008 | 1/1/1833:1835, 1/1/1905:1906, 1/1/1924:1933, 1/1/1967:1972 | No text annotation | ||
| J5_8YDJ_002 | 1/1/531:533, 1/1/560:564, 1/1/577:579, 1/1/1261:1262, 1/1/2017:2018 | No text annotation | ||
| J5_8YDJ_003 | 1/1/584:591, 1/1/666:671, 1/1/809:812, 1/1/1195:1196, 1/1/1250:1256 | No text annotation | ||
| J5_8YDJ_004 | 1/1/1674:1682, 1/1/1706:1707, 1/1/1751:1752, 1/1/1756:1764, 1/1/1988:1990 | No text annotation | ||
| J5_8YDJ_005 | 1/1/2057:2064, 1/1/2446:2453, 1/1/2500:2507, 1/1/2582:2588, 1/1/2606:2611 | No text annotation | ||
| J7_8YDJ_001 | 1/1/8:15, 1/1/525:531, 1/1/2018:2023, 1/1/2040:2043, 1/1/2625:2630, 1/1/2788:2789, 1/1/2894:2895 | No text annotation | ||
| J7_8YDJ_002 | 1/1/817:822, 1/1/835:838, 1/1/940:946, 1/1/971:976, 1/1/987:991, 1/1/1163:1164, 1/1/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8YDJ_001 | No text annotation | ||
| J3_8YDJ_002 | No text annotation | ||
| J3_8YDJ_003 | No text annotation | ||
| J3_8YDJ_004 | No text annotation | ||
| J3_8YDJ_005 | No text annotation | ||
| J3_8YDJ_008 | No text annotation | ||
| J3_8YDJ_010 | No text annotation | ||
| J3_8YDJ_012 | No text annotation | ||
| J3_8YDJ_013 | No text annotation | ||
| J3_8YDJ_014 | No text annotation | ||
| J3_8YDJ_015 | No text annotation | ||
| J3_8YDJ_017 | No text annotation | ||
| J3_8YDJ_019 | No text annotation | ||
| J3_8YDJ_020 | No text annotation | ||
| J3_8YDJ_021 | No text annotation | ||
| J3_8YDJ_022 | No text annotation | ||
| J3_8YDJ_023 | No text annotation | ||
| J3_8YDJ_024 | No text annotation | ||
| J3_8YDJ_025 | No text annotation | ||
| J3_8YDJ_026 | No text annotation | ||
| J3_8YDJ_027 | No text annotation | ||
| J3_8YDJ_028 | No text annotation | ||
| J3_8YDJ_029 | No text annotation | ||
| J3_8YDJ_030 | No text annotation | ||
| J3_8YDJ_031 | No text annotation | ||
| J3_8YDJ_032 | No text annotation | ||
| J4_8YDJ_001 | No text annotation | ||
| J4_8YDJ_002 | No text annotation | ||
| J4_8YDJ_004 | No text annotation | ||
| J4_8YDJ_005 | No text annotation | ||
| J4_8YDJ_006 | No text annotation | ||
| J4_8YDJ_009 | No text annotation | ||
| J4_8YDJ_010 | No text annotation | ||
| J4_8YDJ_011 | No text annotation | ||
| J4_8YDJ_012 | No text annotation | ||
| J4_8YDJ_013 | No text annotation | ||
| J4_8YDJ_014 | No text annotation | ||
| J4_8YDJ_015 | No text annotation | ||
| J4_8YDJ_016 | No text annotation | ||
| J5_8YDJ_001 | No text annotation | ||
| J5_8YDJ_006 | No text annotation | ||
| J5_8YDJ_007 | No text annotation | ||
| J5_8YDJ_008 | No text annotation | ||
| J5_8YDJ_009 | No text annotation | ||
| J6_8YDJ_001 | No text annotation | ||
| J6_8YDJ_002 | No text annotation |
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