3J0L Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3J0L_007 | 1/1/1023:1029 | No text annotation | ||
| HL_3J0L_008 | 1/2/2220:2225 | GNRA | homologous HL_8C3A_048 NA | |
| HL_3J0L_009 | 1/2/2253:2263 | No text annotation | geometric HL_2Y9H_003 HL_75660.5 | |
| HL_3J0L_010 | 1/2/2292:2300 | No text annotation | homologous HL_5TBW_050 NA | |
| HL_3J0L_011 | 1/4/2616:2624 | No text annotation | geometric HL_5TBW_054 NA | |
| HL_3J0L_012 | 1/6/2693:2700 | Pseudoknot geometry | geometric HL_5TBW_057 NA | |
| HL_3J0L_013 | 1/7/2840:2848 | No text annotation | homologous HL_8C3A_062 NA | |
| HL_3J0L_014 | 1/8/2963:2968 | GNRA | geometric HL_3IGI_003 HL_37824.7 | |
| HL_3J0L_018 | 1/V/13:22 | tRNA D-loop | homologous HL_3TUP_001 HL_45175.1 | |
| HL_3J0L_019 | 1/V/31:39 | tRNA anticodon loop | homologous HL_6UFG_007 HL_06059.6 | |
| HL_3J0L_020 | 1/V/53:61 | T-loop with 2 stacked bulged bases | homologous HL_6UGG_006 HL_28252.8 | |
| HL_3J0L_021 | 1/W/13:22 | tRNA D-loop | homologous HL_6JXM_001 HL_20811.4 | |
| HL_3J0L_022 | 1/W/30:40 | No text annotation | homologous HL_4V7M_039 HL_36684.4 | |
| HL_3J0L_023 | 1/W/53:61 | T-loop with 2 stacked bulged bases | homologous HL_6PMO_005 NA | |
| HL_3J0L_015 | 1/Y/13:22 | No text annotation | ||
| HL_3J0L_016 | 1/Y/31:39 | tRNA anticodon loop | homologous HL_4V9I_039 HL_06059.6 | |
| HL_3J0L_017 | 1/Y/53:61 | T-loop with 2 stacked bulged bases | homologous HL_3TUP_003 HL_28252.8 | |
| HL_3J0L_001 | 1/a/563:568 | GNRA variation | geometric HL_4V88_200 NA | |
| HL_3J0L_002 | 1/b/878:887 | No text annotation | geometric HL_5J7L_015 HL_75293.5 | |
| HL_3J0L_003 | 1/c/975:985 | No text annotation | geometric HL_5J7L_017 HL_75293.5 | |
| HL_3J0L_005 | 1/g/1160:1169 | No text annotation | geometric HL_2ZNI_001 HL_75660.5 | |
| HL_3J0L_006 | 1/h/1660:1665 | GNRA | geometric HL_7QR8_001 HL_37824.7 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3J0L_024 | No text annotation | ||
| HL_3J0L_025 | No text annotation | ||
| HL_3J0L_026 | No text annotation | ||
| HL_3J0L_027 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3J0L_017 | 1/1/1006:1009, 1/1/1041:1044 | Tandem non-canonical cWW pairs | geometric IL_3R2D_002 IL_77658.1 | |
| IL_3J0L_018 | 1/1/1009:1012, 1/1/1038:1041 | Tandem non-canonical cWW pairs | geometric IL_6CZR_168 NA | |
| IL_3J0L_019 | 1/1/1013:1015, 1/1/1036:1037 | Single bulged U | geometric IL_4WF9_038 IL_89505.4 | |
| IL_3J0L_020 | 1/1/1015:1017, 1/1/1035:1036 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3J0L_023 | 1/2/2196:2199, 1/2/2245:2246 | Major groove intercalation | homologous IL_5TBW_084 NA | |
| IL_3J0L_024 | 1/2/2200:2201, 1/2/2241:2244 | Multiple bulged bases | homologous IL_8C3A_090 NA | |
| IL_3J0L_025 | 1/2/2204:2206, 1/2/2237:2238 | No text annotation | ||
| IL_3J0L_026 | 1/2/2206:2210, 1/2/2235:2237 | No text annotation | ||
| IL_3J0L_027 | 1/2/2211:2217, 1/2/2228:2234 | No text annotation | homologous IL_5TBW_088 NA | |
| IL_3J0L_028 | 1/2/2250:2251, 1/2/2265:2267 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_3J0L_029 | 1/4/2614:2615, 1/4/2625:2627 | Single bulged A | geometric IL_4V9F_079 IL_31462.6 | |
| IL_3J0L_030 | 1/7/2824:2826, 1/7/2863:2865 | Isolated non-canonical cWW pair | geometric IL_5TBW_021 NA | |
| IL_3J0L_031 | 1/7/2826:2828, 1/7/2862:2863 | Major groove platform | homologous IL_8C3A_112 NA | |
| IL_3J0L_038 | 1/7/2826:2830, 1/7/2858:2863 | No text annotation | ||
| IL_3J0L_032 | 1/7/2828:2830, 1/7/2858:2862 | Major groove minor groove platform with extra cWW | geometric IL_5TBW_105 NA | |
| IL_3J0L_034 | 1/7/2835:2839, 1/7/2849:2853 | Triple sheared | geometric IL_5TBW_106 NA | |
| IL_3J0L_035 | 1/8/2960:2961, 1/8/2970:2972 | Single bulged A | geometric IL_2VPL_002 IL_31462.6 | |
| IL_3J0L_039 | 1/G/1430:1432, 1/g/1150:1151 | Minor groove platform | geometric IL_4LFB_038 IL_51454.3 | |
| IL_3J0L_040 | 1/G/1435:1437, 1/g/1145:1147 | Isolated non-canonical cWW pair | geometric IL_4V88_444 NA | |
| IL_3J0L_001 | 1/a/543:550, 1/a/581:582 | SSU/LSU pseudoknot | geometric IL_4V88_413 NA | |
| IL_3J0L_002 | 1/a/550:552, 1/a/580:581 | Single bulged U | geometric IL_6MWN_006 IL_89505.4 | |
| IL_3J0L_003 | 1/a/552:554, 1/a/579:580 | Single bulged A | geometric IL_6D3P_004 IL_31462.6 | |
| IL_3J0L_004 | 1/a/556:562, 1/a/569:577 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_3J0L_008 | 1/h/1614:1616, 1/h/1710:1712 | Isolated non-canonical cWW pair | homologous IL_4V88_465 NA | |
| IL_3J0L_009 | 1/h/1616:1618, 1/h/1707:1710 | Isolated non-canonical cWW pair | geometric IL_3TD0_005 IL_57744.1 | |
| IL_3J0L_010 | 1/h/1622:1628, 1/h/1697:1703 | No text annotation | ||
| IL_3J0L_011 | 1/h/1635:1638, 1/h/1687:1690 | Tandem non-canonical cWW pairs | geometric IL_4EYA_003 IL_77658.1 | |
| IL_3J0L_012 | 1/h/1640:1643, 1/h/1682:1685 | Double sheared | homologous IL_4V88_471 NA | |
| IL_3J0L_013 | 1/h/1644:1646, 1/h/1679:1681 | Isolated non-canonical cWW pair | geometric IL_3RW6_004 IL_87907.2 | |
| IL_3J0L_014 | 1/h/1646:1649, 1/h/1676:1679 | Tandem non-canonical cWW pairs | geometric IL_1D4R_001 IL_85033.2 | |
| IL_3J0L_015 | 1/h/1649:1653, 1/h/1672:1676 | Triple sheared | geometric IL_7RQB_075 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3J0L_021 | No text annotation | ||
| IL_3J0L_022 | Isolated non-canonical cWW pair | ||
| IL_3J0L_033 | Tandem non-canonical cWW pairs | ||
| IL_3J0L_037 | Isolated non-canonical cWW pair | ||
| IL_3J0L_036 | Isolated non-canonical cWW pair | ||
| IL_3J0L_016 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3J0L_002 | 1/Y/7:28, 1/Y/42:49, 1/Y/65:66 | No text annotation | ||
| J3_3J0L_001 | 1/Y/7:29, 1/Y/41:50, 1/Y/64:66 | No text annotation | ||
| J4_3J0L_001 | 1/V/7:10, 1/V/25:27, 1/V/43:49, 1/V/65:66 | tRNA junction | homologous J4_3WQY_001 J4_70449.28 | |
| J4_3J0L_004 | 1/W/7:10, 1/W/25:27, 1/W/43:49, 1/W/65:66 | No text annotation | homologous J4_4WT8_031 NA | |
| J4_3J0L_005 | 1/Y/7:13, 1/Y/22:28, 1/Y/42:49, 1/Y/65:66 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J4_3J0L_002 | No text annotation | ||
| J4_3J0L_003 | No text annotation |
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