6GSM Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6GSM_002 | 1/1/31:39 | tRNA anticodon loop | homologous HL_4WT8_216 HL_81376.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6GSM_001 | No text annotation | ||
| HL_6GSM_003 | T-loop with 2 stacked bulged bases | ||
| HL_6GSM_004 | No text annotation | ||
| HL_6GSM_005 | No text annotation | ||
| HL_6GSM_006 | No text annotation | ||
| HL_6GSM_042 | GNRA related | ||
| HL_6GSM_007 | No text annotation | ||
| HL_6GSM_008 | No text annotation | ||
| HL_6GSM_009 | T-loop with 1 bulged base | ||
| HL_6GSM_010 | No text annotation | ||
| HL_6GSM_011 | GNRA related | ||
| HL_6GSM_012 | No text annotation | ||
| HL_6GSM_041 | No text annotation | ||
| HL_6GSM_013 | No text annotation | ||
| HL_6GSM_014 | No text annotation | ||
| HL_6GSM_015 | No text annotation | ||
| HL_6GSM_016 | No text annotation | ||
| HL_6GSM_017 | No text annotation | ||
| HL_6GSM_018 | No text annotation | ||
| HL_6GSM_043 | No text annotation | ||
| HL_6GSM_019 | No text annotation | ||
| HL_6GSM_044 | No text annotation | ||
| HL_6GSM_020 | No text annotation | ||
| HL_6GSM_021 | No text annotation | ||
| HL_6GSM_045 | No text annotation | ||
| HL_6GSM_022 | No text annotation | ||
| HL_6GSM_023 | Pseudoknot geometry | ||
| HL_6GSM_024 | No text annotation | ||
| HL_6GSM_046 | No text annotation | ||
| HL_6GSM_025 | GNRA | ||
| HL_6GSM_026 | No text annotation | ||
| HL_6GSM_027 | No text annotation | ||
| HL_6GSM_028 | GNRA | ||
| HL_6GSM_029 | GNRA | ||
| HL_6GSM_030 | No text annotation | ||
| HL_6GSM_031 | No text annotation | ||
| HL_6GSM_032 | GNRA | ||
| HL_6GSM_033 | No text annotation | ||
| HL_6GSM_034 | No text annotation | ||
| HL_6GSM_035 | No text annotation | ||
| HL_6GSM_036 | GNRA | ||
| HL_6GSM_037 | No text annotation | ||
| HL_6GSM_047 | No text annotation | ||
| HL_6GSM_038 | No text annotation | ||
| HL_6GSM_039 | No text annotation | ||
| HL_6GSM_040 | GNRA variation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6GSM_026 | 1/2/446:447, 1/2/457:459 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_6GSM_046 | 1/2/892:898, 1/2/909:918 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_6GSM_047 | 1/2/984:993, 1/2/1009:1015 | No text annotation | ||
| IL_6GSM_048 | 1/2/1033:1035, 1/2/1094:1100 | No text annotation | homologous IL_4V88_437 NA | |
| IL_6GSM_091 | 1/2/1145:1146, 1/2/1628:1630 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_6GSM_070 | 1/2/1486:1492, 1/2/1511:1516 | 180 degree turn | geometric IL_5J7L_055 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6GSM_001 | Isolated non-canonical cWW pair | ||
| IL_6GSM_002 | Isolated non-canonical cWW pair | ||
| IL_6GSM_003 | Triple sheared related | ||
| IL_6GSM_004 | No text annotation | ||
| IL_6GSM_005 | Minor groove platform | ||
| IL_6GSM_006 | No text annotation | ||
| IL_6GSM_085 | No text annotation | ||
| IL_6GSM_100 | No text annotation | ||
| IL_6GSM_007 | No text annotation | ||
| IL_6GSM_008 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_009 | Single stack bend | ||
| IL_6GSM_010 | Single stack bend | ||
| IL_6GSM_101 | No text annotation | ||
| IL_6GSM_011 | No text annotation | ||
| IL_6GSM_102 | Single stack bend | ||
| IL_6GSM_012 | tWH-tWH-tHW-tHW | ||
| IL_6GSM_013 | Isolated non-canonical cWW contact | ||
| IL_6GSM_014 | Double sheared | ||
| IL_6GSM_015 | Major groove platform with extra cWW | ||
| IL_6GSM_016 | Single stack bend | ||
| IL_6GSM_103 | Single stack bend | ||
| IL_6GSM_017 | No text annotation | ||
| IL_6GSM_018 | Single bulged A | ||
| IL_6GSM_104 | No text annotation | ||
| IL_6GSM_019 | No text annotation | ||
| IL_6GSM_020 | Kink-turn with non-sequential stacking | ||
| IL_6GSM_021 | No text annotation | ||
| IL_6GSM_022 | No text annotation | ||
| IL_6GSM_023 | Isolated cWH basepair | ||
| IL_6GSM_024 | Single bulged U | ||
| IL_6GSM_086 | No text annotation | ||
| IL_6GSM_025 | C-loop | ||
| IL_6GSM_027 | No text annotation | ||
| IL_6GSM_028 | No text annotation | ||
| IL_6GSM_105 | Minor groove platform | ||
| IL_6GSM_029 | Double sheared | ||
| IL_6GSM_106 | Minor groove platform | ||
| IL_6GSM_030 | No text annotation | ||
| IL_6GSM_087 | No text annotation | ||
| IL_6GSM_107 | No text annotation | ||
| IL_6GSM_031 | Single bulged U | ||
| IL_6GSM_032 | Kink-turn related | ||
| IL_6GSM_033 | No text annotation | ||
| IL_6GSM_034 | Isolated non-canonical cWW pair | ||
| IL_6GSM_035 | tSH-tWH-tHS | ||
| IL_6GSM_036 | No text annotation | ||
| IL_6GSM_037 | No text annotation | ||
| IL_6GSM_038 | Major groove minor groove platform; mini C-loop | ||
| IL_6GSM_088 | No text annotation | ||
| IL_6GSM_089 | No text annotation | ||
| IL_6GSM_039 | No text annotation | ||
| IL_6GSM_040 | Isolated non-canonical cWW pair | ||
| IL_6GSM_041 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_090 | Isolated non-canonical cWW pair | ||
| IL_6GSM_108 | Isolated non-canonical cWW pair | ||
| IL_6GSM_042 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_043 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_044 | No text annotation | ||
| IL_6GSM_045 | Single stack bend | ||
| IL_6GSM_049 | No text annotation | ||
| IL_6GSM_050 | Single bulged U | ||
| IL_6GSM_051 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6GSM_052 | Isolated non-canonical cWW with bulges | ||
| IL_6GSM_053 | Single bulged G | ||
| IL_6GSM_092 | C-loop | ||
| IL_6GSM_054 | No text annotation | ||
| IL_6GSM_055 | Isolated non-canonical cWW pair | ||
| IL_6GSM_056 | Minor groove platform | ||
| IL_6GSM_057 | Isolated non-canonical cWW pair | ||
| IL_6GSM_093 | No text annotation | ||
| IL_6GSM_109 | No text annotation | ||
| IL_6GSM_058 | Single stack bend | ||
| IL_6GSM_059 | Single bulged U | ||
| IL_6GSM_060 | Isolated cWS basepair | ||
| IL_6GSM_094 | No text annotation | ||
| IL_6GSM_061 | Minor groove platform with extra cWW | ||
| IL_6GSM_095 | Isolated non-canonical cWW pair | ||
| IL_6GSM_062 | Single bulged A | ||
| IL_6GSM_063 | Minor groove platform | ||
| IL_6GSM_064 | Isolated non-canonical cWW pair | ||
| IL_6GSM_065 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_096 | Isolated non-canonical cWW pair | ||
| IL_6GSM_110 | No text annotation | ||
| IL_6GSM_066 | No text annotation | ||
| IL_6GSM_067 | No text annotation | ||
| IL_6GSM_097 | No text annotation | ||
| IL_6GSM_068 | No text annotation | ||
| IL_6GSM_069 | No text annotation | ||
| IL_6GSM_098 | No text annotation | ||
| IL_6GSM_111 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_071 | No text annotation | ||
| IL_6GSM_072 | No text annotation | ||
| IL_6GSM_073 | No text annotation | ||
| IL_6GSM_074 | No text annotation | ||
| IL_6GSM_075 | Isolated non-canonical cWW pair | ||
| IL_6GSM_076 | No text annotation | ||
| IL_6GSM_077 | Isolated non-canonical cWW pair | ||
| IL_6GSM_078 | Double sheared | ||
| IL_6GSM_099 | No text annotation | ||
| IL_6GSM_079 | Single bulged U | ||
| IL_6GSM_080 | Isolated non-canonical cWW pair | ||
| IL_6GSM_081 | Double sheared | ||
| IL_6GSM_082 | Tandem non-canonical cWW pairs | ||
| IL_6GSM_083 | Triple sheared | ||
| IL_6GSM_084 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6GSM_003 | 1/2/879:883, 1/2/927:935, 1/2/942:947 | No text annotation | ||
| J3_6GSM_017 | 1/2/1160:1163, 1/2/1579:1585, 1/2/1607:1614 | No text annotation | ||
| J4_6GSM_002 | 1/2/99:107, 1/2/306:308, 1/2/356:360, 1/2/382:383 | No text annotation | homologous J4_8C3A_021 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6GSM_001 | No text annotation | ||
| J3_6GSM_013 | No text annotation | ||
| J3_6GSM_002 | No text annotation | ||
| J3_6GSM_014 | No text annotation | ||
| J3_6GSM_004 | No text annotation | ||
| J3_6GSM_005 | No text annotation | ||
| J3_6GSM_006 | No text annotation | ||
| J3_6GSM_015 | No text annotation | ||
| J3_6GSM_007 | No text annotation | ||
| J3_6GSM_018 | No text annotation | ||
| J3_6GSM_008 | No text annotation | ||
| J3_6GSM_009 | No text annotation | ||
| J3_6GSM_010 | No text annotation | ||
| J3_6GSM_011 | No text annotation | ||
| J3_6GSM_016 | No text annotation | ||
| J3_6GSM_012 | No text annotation | ||
| J4_6GSM_001 | tRNA junction | ||
| J4_6GSM_003 | No text annotation | ||
| J5_6GSM_006 | No text annotation | ||
| J5_6GSM_001 | No text annotation | ||
| J5_6GSM_007 | No text annotation | ||
| J5_6GSM_002 | No text annotation | ||
| J5_6GSM_003 | No text annotation | ||
| J5_6GSM_004 | No text annotation | ||
| J5_6GSM_008 | No text annotation | ||
| J5_6GSM_009 | No text annotation | ||
| J5_6GSM_005 | No text annotation |
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