6GSN Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6GSN_003 | 1/1/53:61 | T-loop with 2 stacked bulged bases | homologous HL_3TUP_003 HL_33597.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6GSN_001 | tRNA D-loop | ||
| HL_6GSN_002 | tRNA anticodon loop | ||
| HL_6GSN_004 | No text annotation | ||
| HL_6GSN_005 | No text annotation | ||
| HL_6GSN_006 | No text annotation | ||
| HL_6GSN_007 | No text annotation | ||
| HL_6GSN_008 | No text annotation | ||
| HL_6GSN_009 | T-loop with 1 bulged base | ||
| HL_6GSN_010 | No text annotation | ||
| HL_6GSN_011 | GNRA related | ||
| HL_6GSN_012 | No text annotation | ||
| HL_6GSN_013 | No text annotation | ||
| HL_6GSN_014 | UNCG | ||
| HL_6GSN_015 | No text annotation | ||
| HL_6GSN_016 | No text annotation | ||
| HL_6GSN_017 | No text annotation | ||
| HL_6GSN_018 | GNRA variation | ||
| HL_6GSN_019 | No text annotation | ||
| HL_6GSN_042 | No text annotation | ||
| HL_6GSN_020 | No text annotation | ||
| HL_6GSN_043 | No text annotation | ||
| HL_6GSN_021 | No text annotation | ||
| HL_6GSN_022 | No text annotation | ||
| HL_6GSN_023 | Pseudoknot geometry | ||
| HL_6GSN_024 | No text annotation | ||
| HL_6GSN_044 | No text annotation | ||
| HL_6GSN_025 | GNRA | ||
| HL_6GSN_026 | No text annotation | ||
| HL_6GSN_041 | No text annotation | ||
| HL_6GSN_027 | No text annotation | ||
| HL_6GSN_028 | GNRA | ||
| HL_6GSN_029 | GNRA | ||
| HL_6GSN_030 | No text annotation | ||
| HL_6GSN_031 | No text annotation | ||
| HL_6GSN_032 | GNRA | ||
| HL_6GSN_033 | No text annotation | ||
| HL_6GSN_034 | No text annotation | ||
| HL_6GSN_035 | GNRA | ||
| HL_6GSN_036 | GNRA | ||
| HL_6GSN_037 | No text annotation | ||
| HL_6GSN_045 | No text annotation | ||
| HL_6GSN_038 | No text annotation | ||
| HL_6GSN_039 | No text annotation | ||
| HL_6GSN_040 | GNRA variation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6GSN_004 | 1/2/42:48, 1/2/430:432 | No text annotation | geometric IL_4V88_387 NA | |
| IL_6GSN_011 | 1/2/113:117, 1/2/298:299 | Multiple bulged bases | geometric IL_4YAZ_007 IL_71421.1 | |
| IL_6GSN_106 | 1/2/113:121, 1/2/294:300 | No text annotation | ||
| IL_6GSN_048 | 1/2/892:898, 1/2/909:918 | No text annotation | homologous IL_8P9A_422 IL_57741.1 | |
| IL_6GSN_091 | 1/2/1768:1770, 1/2/1787:1788 | Single stack bend | geometric IL_4V83_236 IL_15011.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6GSN_001 | Decoding loop related | ||
| IL_6GSN_092 | No text annotation | ||
| IL_6GSN_002 | Isolated non-canonical cWW pair | ||
| IL_6GSN_093 | No text annotation | ||
| IL_6GSN_003 | Triple sheared related | ||
| IL_6GSN_005 | Minor groove platform | ||
| IL_6GSN_094 | No text annotation | ||
| IL_6GSN_006 | No text annotation | ||
| IL_6GSN_007 | Single stack bend | ||
| IL_6GSN_095 | Double sheared | ||
| IL_6GSN_008 | Double sheared with non-canonical cWW | ||
| IL_6GSN_009 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_010 | Single stack bend | ||
| IL_6GSN_096 | No text annotation | ||
| IL_6GSN_012 | No text annotation | ||
| IL_6GSN_013 | Single stack bend | ||
| IL_6GSN_014 | Single stack bend | ||
| IL_6GSN_015 | tWH-tWH-tHW-tHW | ||
| IL_6GSN_016 | Isolated non-canonical cWW contact | ||
| IL_6GSN_017 | Double sheared | ||
| IL_6GSN_018 | Major groove platform with extra cWW | ||
| IL_6GSN_019 | Single stack bend | ||
| IL_6GSN_020 | Single stack bend | ||
| IL_6GSN_107 | Single bulged A | ||
| IL_6GSN_021 | Isolated non-canonical cWW pair | ||
| IL_6GSN_022 | No text annotation | ||
| IL_6GSN_023 | Kink-turn with non-sequential stacking | ||
| IL_6GSN_024 | No text annotation | ||
| IL_6GSN_025 | No text annotation | ||
| IL_6GSN_026 | Isolated cWH basepair | ||
| IL_6GSN_027 | Single bulged U | ||
| IL_6GSN_028 | C-loop | ||
| IL_6GSN_029 | Single bulged G | ||
| IL_6GSN_108 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_030 | No text annotation | ||
| IL_6GSN_031 | No text annotation | ||
| IL_6GSN_032 | No text annotation | ||
| IL_6GSN_033 | Single bulged U | ||
| IL_6GSN_034 | Kink-turn related | ||
| IL_6GSN_035 | No text annotation | ||
| IL_6GSN_036 | Isolated non-canonical cWW pair | ||
| IL_6GSN_037 | tSH-tHW-tHS | ||
| IL_6GSN_038 | No text annotation | ||
| IL_6GSN_039 | No text annotation | ||
| IL_6GSN_040 | No text annotation | ||
| IL_6GSN_041 | No text annotation | ||
| IL_6GSN_097 | No text annotation | ||
| IL_6GSN_098 | No text annotation | ||
| IL_6GSN_042 | Isolated non-canonical cWW pair | ||
| IL_6GSN_109 | No text annotation | ||
| IL_6GSN_043 | No text annotation | ||
| IL_6GSN_110 | No text annotation | ||
| IL_6GSN_099 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_044 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_100 | Isolated cWH basepair | ||
| IL_6GSN_045 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_046 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_047 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_101 | No text annotation | ||
| IL_6GSN_049 | No text annotation | ||
| IL_6GSN_050 | No text annotation | ||
| IL_6GSN_051 | Single bulged U | ||
| IL_6GSN_052 | Single stack bend | ||
| IL_6GSN_053 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6GSN_054 | Isolated non-canonical cWW pair | ||
| IL_6GSN_055 | Single stack bend | ||
| IL_6GSN_102 | Single bulged A | ||
| IL_6GSN_056 | Isolated non-canonical cWW with bulges | ||
| IL_6GSN_057 | Single bulged G | ||
| IL_6GSN_058 | C-loop | ||
| IL_6GSN_059 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_060 | Minor groove platform | ||
| IL_6GSN_061 | Multiple bulged bases | ||
| IL_6GSN_062 | Isolated non-canonical cWW pair | ||
| IL_6GSN_063 | No text annotation | ||
| IL_6GSN_111 | No text annotation | ||
| IL_6GSN_064 | No text annotation | ||
| IL_6GSN_065 | Single bulged U | ||
| IL_6GSN_066 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_103 | Isolated cWS basepair | ||
| IL_6GSN_104 | No text annotation | ||
| IL_6GSN_067 | Minor groove platform with extra cWW | ||
| IL_6GSN_068 | Single bulged A | ||
| IL_6GSN_069 | Isolated cWH basepair | ||
| IL_6GSN_070 | Minor groove platform | ||
| IL_6GSN_071 | Isolated non-canonical cWW pair | ||
| IL_6GSN_072 | Minor groove platform | ||
| IL_6GSN_105 | Single bulged U | ||
| IL_6GSN_073 | Isolated non-canonical cWW with bulges | ||
| IL_6GSN_074 | No text annotation | ||
| IL_6GSN_075 | No text annotation | ||
| IL_6GSN_076 | 180 degree turn | ||
| IL_6GSN_077 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_112 | Isolated non-canonical cWW pair | ||
| IL_6GSN_078 | No text annotation | ||
| IL_6GSN_079 | No text annotation | ||
| IL_6GSN_080 | No text annotation | ||
| IL_6GSN_081 | Isolated non-canonical cWW pair | ||
| IL_6GSN_082 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_083 | Isolated non-canonical cWW pair | ||
| IL_6GSN_084 | Double sheared | ||
| IL_6GSN_085 | Single bulged U | ||
| IL_6GSN_086 | Isolated non-canonical cWW pair | ||
| IL_6GSN_087 | Double sheared | ||
| IL_6GSN_088 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_089 | Triple sheared | ||
| IL_6GSN_090 | No text annotation | ||
| IL_6GSN_113 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6GSN_010 | 1/2/1291:1293, 1/2/1302:1305, 1/2/1317:1322 | No text annotation | ||
| J4_6GSN_003 | 1/2/621:623, 1/2/974:979, 1/2/1020:1031, 1/2/1102:1103 | No text annotation | homologous J4_8C3A_022 NA | |
| J5_6GSN_001 | 1/2/31:35, 1/2/472:479, 1/2/507:519, 1/2/531:545, 1/2/591:594 | No text annotation | ||
| J5_6GSN_003 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:264, 1/2/288:292 | No text annotation | ||
| J5_6GSN_006 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:266, 1/2/287:292 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6GSN_001 | No text annotation | ||
| J3_6GSN_013 | No text annotation | ||
| J3_6GSN_002 | No text annotation | ||
| J3_6GSN_016 | No text annotation | ||
| J3_6GSN_003 | No text annotation | ||
| J3_6GSN_004 | No text annotation | ||
| J3_6GSN_005 | No text annotation | ||
| J3_6GSN_006 | No text annotation | ||
| J3_6GSN_007 | No text annotation | ||
| J3_6GSN_014 | No text annotation | ||
| J3_6GSN_008 | No text annotation | ||
| J3_6GSN_009 | No text annotation | ||
| J3_6GSN_011 | No text annotation | ||
| J3_6GSN_015 | No text annotation | ||
| J3_6GSN_012 | No text annotation | ||
| J4_6GSN_001 | No text annotation | ||
| J4_6GSN_002 | No text annotation | ||
| J5_6GSN_002 | No text annotation | ||
| J5_6GSN_004 | No text annotation | ||
| J5_6GSN_007 | No text annotation | ||
| J5_6GSN_005 | No text annotation |
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