3J8G Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_3J8G_035 | 1/B/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
HL_3J8G_076 | 1/B/1777:1787 | No text annotation | homologous HL_5J7L_178 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_3J8G_073 | No text annotation | ||
HL_3J8G_001 | No text annotation | ||
HL_3J8G_002 | Mini UNCG | ||
HL_3J8G_003 | No text annotation | ||
HL_3J8G_004 | No text annotation | ||
HL_3J8G_005 | No text annotation | ||
HL_3J8G_006 | UNCG | ||
HL_3J8G_007 | No text annotation | ||
HL_3J8G_008 | No text annotation | ||
HL_3J8G_009 | No text annotation | ||
HL_3J8G_010 | No text annotation | ||
HL_3J8G_011 | T-loop with 2 stacked bulged bases | ||
HL_3J8G_012 | No text annotation | ||
HL_3J8G_013 | T-loop with unstacked turn | ||
HL_3J8G_014 | No text annotation | ||
HL_3J8G_015 | No text annotation | ||
HL_3J8G_016 | GNRA | ||
HL_3J8G_017 | GNRA | ||
HL_3J8G_018 | No text annotation | ||
HL_3J8G_019 | T-loop with 2 stacked bulged bases | ||
HL_3J8G_020 | No text annotation | ||
HL_3J8G_021 | GNRA | ||
HL_3J8G_022 | No text annotation | ||
HL_3J8G_023 | No text annotation | ||
HL_3J8G_024 | No text annotation | ||
HL_3J8G_079 | No text annotation | ||
HL_3J8G_025 | UNCG variation | ||
HL_3J8G_072 | No text annotation | ||
HL_3J8G_026 | No text annotation | ||
HL_3J8G_027 | No text annotation | ||
HL_3J8G_074 | No text annotation | ||
HL_3J8G_028 | GNRA | ||
HL_3J8G_029 | No text annotation | ||
HL_3J8G_030 | No text annotation | ||
HL_3J8G_031 | GNRA wlth tandem sheared | ||
HL_3J8G_032 | Mini UNCG | ||
HL_3J8G_033 | GNRA | ||
HL_3J8G_034 | T-loop with 2 stacked bulged bases | ||
HL_3J8G_036 | GNRA | ||
HL_3J8G_037 | No text annotation | ||
HL_3J8G_038 | No text annotation | ||
HL_3J8G_039 | Pseudoknot geometry with 3' bulge | ||
HL_3J8G_040 | No text annotation | ||
HL_3J8G_041 | Mini UNCG | ||
HL_3J8G_042 | No text annotation | ||
HL_3J8G_043 | GNRA with extra cWW | ||
HL_3J8G_075 | GNRA | ||
HL_3J8G_044 | UNCG | ||
HL_3J8G_045 | Mini UNCG | ||
HL_3J8G_046 | No text annotation | ||
HL_3J8G_047 | No text annotation | ||
HL_3J8G_048 | No text annotation | ||
HL_3J8G_049 | No text annotation | ||
HL_3J8G_050 | No text annotation | ||
HL_3J8G_051 | No text annotation | ||
HL_3J8G_052 | No text annotation | ||
HL_3J8G_053 | No text annotation | ||
HL_3J8G_077 | No text annotation | ||
HL_3J8G_054 | No text annotation | ||
HL_3J8G_055 | No text annotation | ||
HL_3J8G_078 | No text annotation | ||
HL_3J8G_056 | No text annotation | ||
HL_3J8G_057 | No text annotation | ||
HL_3J8G_058 | No text annotation | ||
HL_3J8G_080 | Pseudoknot geometry | ||
HL_3J8G_059 | GNRA | ||
HL_3J8G_060 | GNRA | ||
HL_3J8G_061 | No text annotation | ||
HL_3J8G_062 | No text annotation | ||
HL_3J8G_063 | GNRA variation | ||
HL_3J8G_064 | No text annotation | ||
HL_3J8G_065 | GNRA | ||
HL_3J8G_066 | GNRA | ||
HL_3J8G_067 | Ribsomal LSU H95 | ||
HL_3J8G_068 | No text annotation | ||
HL_3J8G_069 | Mini UNCG | ||
HL_3J8G_070 | No text annotation | ||
HL_3J8G_071 | GNRA |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_3J8G_038 | 1/B/870:872, 1/B/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
IL_3J8G_044 | 1/B/1018:1024, 1/B/1140:1144 | Kink-turn related | geometric IL_4WF9_039 IL_57188.6 | |
IL_3J8G_098 | 1/B/2510:2512, 1/B/2574:2578 | Isolated non-canonical cWW with bulges | homologous IL_5J7L_340 NA | |
IL_3J8G_105 | 1/B/2680:2684, 1/B/2725:2727 | C-loop | homologous IL_5J7L_347 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_3J8G_001 | Other IL | ||
IL_3J8G_002 | Isolated near basepair | ||
IL_3J8G_003 | Major groove intercalation | ||
IL_3J8G_004 | No text annotation | ||
IL_3J8G_005 | No text annotation | ||
IL_3J8G_127 | No text annotation | ||
IL_3J8G_113 | No text annotation | ||
IL_3J8G_006 | Symmetric double minor groove platform | ||
IL_3J8G_007 | Bacterial 5S Loop E | ||
IL_3J8G_008 | Triple sheared with non-canonical cWW | ||
IL_3J8G_009 | Single bulged A | ||
IL_3J8G_010 | Minor groove platform | ||
IL_3J8G_011 | No text annotation | ||
IL_3J8G_114 | No text annotation | ||
IL_3J8G_012 | Single stack bend | ||
IL_3J8G_013 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3J8G_014 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_3J8G_015 | No text annotation | ||
IL_3J8G_016 | No text annotation | ||
IL_3J8G_017 | No text annotation | ||
IL_3J8G_018 | No text annotation | ||
IL_3J8G_019 | Double sheared | ||
IL_3J8G_020 | Isolated non-canonical cWW pair | ||
IL_3J8G_021 | No text annotation | ||
IL_3J8G_022 | AAA cross-strand stack | ||
IL_3J8G_023 | Isolated non-canonical cWW pair | ||
IL_3J8G_024 | tHW-tHW cross-strand stack | ||
IL_3J8G_025 | Tandem non-canonical cWW pairs | ||
IL_3J8G_026 | Single bulged A | ||
IL_3J8G_115 | Isolated non-canonical cWW pair | ||
IL_3J8G_027 | Single bulged G | ||
IL_3J8G_028 | Triple sheared | ||
IL_3J8G_029 | Major groove platform | ||
IL_3J8G_030 | Multiple bulged bases | ||
IL_3J8G_032 | Single stack bend | ||
IL_3J8G_033 | No text annotation | ||
IL_3J8G_034 | Single stack bend | ||
IL_3J8G_035 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_3J8G_036 | Single bulged G | ||
IL_3J8G_037 | C-loop with bulged stacked A's | ||
IL_3J8G_039 | No text annotation | ||
IL_3J8G_128 | No text annotation | ||
IL_3J8G_129 | No text annotation | ||
IL_3J8G_116 | No text annotation | ||
IL_3J8G_040 | Single bulged C | ||
IL_3J8G_041 | UAA/GAN | ||
IL_3J8G_117 | No text annotation | ||
IL_3J8G_042 | SSU/LSU pseudoknot | ||
IL_3J8G_043 | Single bulged U | ||
IL_3J8G_045 | No text annotation | ||
IL_3J8G_046 | Isolated non-canonical cWW pair | ||
IL_3J8G_047 | Tandem non-canonical cWW pairs | ||
IL_3J8G_048 | Kink-turn | ||
IL_3J8G_049 | Isolated non-canonical cWW pair | ||
IL_3J8G_050 | No text annotation | ||
IL_3J8G_051 | Major groove platform | ||
IL_3J8G_052 | Tandem non-canonical cWW pairs | ||
IL_3J8G_130 | No text annotation | ||
IL_3J8G_118 | Isolated cWS basepair | ||
IL_3J8G_131 | No text annotation | ||
IL_3J8G_053 | No text annotation | ||
IL_3J8G_054 | Kink-turn | ||
IL_3J8G_055 | 8x7 Sarcin-Ricin; G-bulge | ||
IL_3J8G_056 | Major groove platform; stack outside cWW | ||
IL_3J8G_057 | C-loop | ||
IL_3J8G_058 | UAA/GAN | ||
IL_3J8G_119 | No text annotation | ||
IL_3J8G_059 | tSH-tHW-tHS | ||
IL_3J8G_060 | No text annotation | ||
IL_3J8G_061 | UAA/GAN | ||
IL_3J8G_062 | Tandem non-canonical cWW pairs | ||
IL_3J8G_063 | Other IL | ||
IL_3J8G_064 | No text annotation | ||
IL_3J8G_065 | tSH-tHW-tHS | ||
IL_3J8G_066 | No text annotation | ||
IL_3J8G_067 | No text annotation | ||
IL_3J8G_068 | UAA/GAN variation | ||
IL_3J8G_069 | No text annotation | ||
IL_3J8G_070 | Isolated tWW turn | ||
IL_3J8G_132 | Major groove platform; stack outside cWW | ||
IL_3J8G_071 | No text annotation | ||
IL_3J8G_133 | Intercalated tWH | ||
IL_3J8G_072 | tSH-tSH-tHH-tHS | ||
IL_3J8G_073 | 6x5 Sarcin-Ricin; G-bulge | ||
IL_3J8G_074 | Triple sheared | ||
IL_3J8G_075 | No text annotation | ||
IL_3J8G_076 | Single bulged C | ||
IL_3J8G_077 | Single bulged A | ||
IL_3J8G_078 | Kink-turn related | ||
IL_3J8G_079 | Major groove intercalation | ||
IL_3J8G_080 | No text annotation | ||
IL_3J8G_120 | No text annotation | ||
IL_3J8G_134 | Major groove minor groove platform; mini C-loop | ||
IL_3J8G_081 | No text annotation | ||
IL_3J8G_082 | Major groove platform | ||
IL_3J8G_083 | No text annotation | ||
IL_3J8G_121 | No text annotation | ||
IL_3J8G_084 | Single bulged U | ||
IL_3J8G_085 | No text annotation | ||
IL_3J8G_135 | Minor groove platform | ||
IL_3J8G_086 | Isolated tHS basepair with bulges | ||
IL_3J8G_087 | No text annotation | ||
IL_3J8G_122 | No text annotation | ||
IL_3J8G_088 | Single bulged U | ||
IL_3J8G_089 | No text annotation | ||
IL_3J8G_090 | Double sheared | ||
IL_3J8G_091 | Stack outside cWW | ||
IL_3J8G_092 | Single stack bend | ||
IL_3J8G_093 | Major groove platform | ||
IL_3J8G_123 | Decoding loop related | ||
IL_3J8G_094 | Major groove platform | ||
IL_3J8G_124 | No text annotation | ||
IL_3J8G_095 | No text annotation | ||
IL_3J8G_096 | Double sheared with non-canonical cWW | ||
IL_3J8G_097 | No text annotation | ||
IL_3J8G_136 | No text annotation | ||
IL_3J8G_099 | No text annotation | ||
IL_3J8G_100 | Major groove platform with intercalation | ||
IL_3J8G_101 | Single bulged A | ||
IL_3J8G_125 | Other IL | ||
IL_3J8G_102 | No text annotation | ||
IL_3J8G_137 | tSH-tHS-tHW | ||
IL_3J8G_103 | Sarcin-Ricin target in LSU H95; G-bulge | ||
IL_3J8G_104 | Isolated non-canonical cWW pair | ||
IL_3J8G_106 | UAA/GAN related, with intercalation | ||
IL_3J8G_107 | Multiple bulged bases | ||
IL_3J8G_108 | UAA/GAN with extra cWW | ||
IL_3J8G_126 | No text annotation | ||
IL_3J8G_109 | No text annotation | ||
IL_3J8G_110 | Major groove intercalation | ||
IL_3J8G_111 | Multiple bulged bases with non-canonical cWW | ||
IL_3J8G_112 | tHS double platform |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_3J8G_024 | 1/B/683:689, 1/B/773:775, 1/B/791:794 | No text annotation | homologous J3_4WF9_002 J3_46658.1 | |
J3_3J8G_009 | 1/B/2517:2520, 1/B/2545:2547, 1/B/2561:2567 | No text annotation | homologous J3_5J7L_046 NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_3J8G_001 | No text annotation | ||
J3_3J8G_014 | No text annotation | ||
J3_3J8G_015 | No text annotation | ||
J3_3J8G_011 | No text annotation | ||
J3_3J8G_016 | No text annotation | ||
J3_3J8G_012 | No text annotation | ||
J3_3J8G_002 | No text annotation | ||
J3_3J8G_017 | No text annotation | ||
J3_3J8G_018 | No text annotation | ||
J3_3J8G_003 | No text annotation | ||
J3_3J8G_019 | No text annotation | ||
J3_3J8G_004 | No text annotation | ||
J3_3J8G_005 | No text annotation | ||
J3_3J8G_006 | No text annotation | ||
J3_3J8G_020 | No text annotation | ||
J3_3J8G_021 | No text annotation | ||
J3_3J8G_007 | Kink-turn 3-way junction | ||
J3_3J8G_022 | No text annotation | ||
J3_3J8G_008 | No text annotation | ||
J3_3J8G_023 | No text annotation | ||
J3_3J8G_013 | No text annotation | ||
J3_3J8G_010 | No text annotation | ||
J4_3J8G_001 | No text annotation | ||
J4_3J8G_002 | No text annotation | ||
J4_3J8G_003 | No text annotation | ||
J4_3J8G_013 | No text annotation | ||
J4_3J8G_004 | No text annotation | ||
J4_3J8G_005 | No text annotation | ||
J4_3J8G_006 | No text annotation | ||
J4_3J8G_007 | No text annotation | ||
J4_3J8G_008 | No text annotation | ||
J4_3J8G_014 | No text annotation | ||
J4_3J8G_009 | No text annotation | ||
J4_3J8G_010 | No text annotation | ||
J4_3J8G_011 | No text annotation | ||
J4_3J8G_012 | No text annotation | ||
J5_3J8G_001 | No text annotation | ||
J5_3J8G_002 | No text annotation | ||
J5_3J8G_003 | No text annotation | ||
J5_3J8G_004 | No text annotation | ||
J5_3J8G_005 | No text annotation | ||
J5_3J8G_006 | No text annotation | ||
J6_3J8G_001 | No text annotation | ||
J7_3J8G_001 | No text annotation | ||
J7_3J8G_003 | No text annotation | ||
J7_3J8G_002 | No text annotation |
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