3J5L Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3J5L_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_3J5L_017 | 1/A/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_3J5L_022 | 1/A/744:753 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_3J5L_023 | 1/A/779:785 | UNCG variation | homologous HL_7A0S_023 HL_51020.1 | |
| HL_3J5L_026 | 1/A/955:962 | GNRA | homologous HL_4WF9_027 HL_34789.1 | |
| HL_3J5L_032 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_3J5L_035 | 1/A/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_3J5L_042 | 1/A/1691:1696 | UNCG | homologous HL_5J7L_175 NA | |
| HL_3J5L_045 | 1/A/1777:1787 | No text annotation | homologous HL_5J7L_178 NA | |
| HL_3J5L_046 | 1/A/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_3J5L_049 | 1/A/1949:1957 | No text annotation | homologous HL_5J7L_182 NA | |
| HL_3J5L_050 | 1/A/2027:2036 | No text annotation | homologous HL_7RQB_050 NA | |
| HL_3J5L_054 | 1/A/2264:2276 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_3J5L_062 | 1/A/2551:2557 | No text annotation | homologous HL_4WF9_058 HL_48677.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3J5L_001 | No text annotation | ||
| HL_3J5L_003 | No text annotation | ||
| HL_3J5L_004 | No text annotation | ||
| HL_3J5L_072 | No text annotation | ||
| HL_3J5L_005 | No text annotation | ||
| HL_3J5L_006 | No text annotation | ||
| HL_3J5L_007 | No text annotation | ||
| HL_3J5L_008 | No text annotation | ||
| HL_3J5L_009 | T-loop with 2 stacked bulged bases | ||
| HL_3J5L_010 | No text annotation | ||
| HL_3J5L_011 | T-loop with unstacked turn | ||
| HL_3J5L_012 | No text annotation | ||
| HL_3J5L_013 | Pseudoknot geometry | ||
| HL_3J5L_014 | GNRA | ||
| HL_3J5L_015 | GNRA | ||
| HL_3J5L_016 | No text annotation | ||
| HL_3J5L_018 | No text annotation | ||
| HL_3J5L_019 | GNRA | ||
| HL_3J5L_020 | No text annotation | ||
| HL_3J5L_021 | GNRA wlth tandem sheared | ||
| HL_3J5L_024 | No text annotation | ||
| HL_3J5L_025 | No text annotation | ||
| HL_3J5L_027 | No text annotation | ||
| HL_3J5L_028 | No text annotation | ||
| HL_3J5L_029 | GNRA wlth tandem sheared | ||
| HL_3J5L_073 | No text annotation | ||
| HL_3J5L_030 | No text annotation | ||
| HL_3J5L_031 | GNRA | ||
| HL_3J5L_033 | Pseudoknot geometry with 3' bulge | ||
| HL_3J5L_034 | GNRA | ||
| HL_3J5L_036 | Mini UNCG with extended bulge | ||
| HL_3J5L_037 | No text annotation | ||
| HL_3J5L_078 | Pseudoknot geometry with 3' bulge | ||
| HL_3J5L_038 | UNCG | ||
| HL_3J5L_039 | No text annotation | ||
| HL_3J5L_040 | No text annotation | ||
| HL_3J5L_041 | GNRA | ||
| HL_3J5L_043 | No text annotation | ||
| HL_3J5L_044 | No text annotation | ||
| HL_3J5L_074 | No text annotation | ||
| HL_3J5L_047 | GNRA variation | ||
| HL_3J5L_048 | No text annotation | ||
| HL_3J5L_075 | No text annotation | ||
| HL_3J5L_051 | No text annotation | ||
| HL_3J5L_052 | No text annotation | ||
| HL_3J5L_053 | No text annotation | ||
| HL_3J5L_055 | No text annotation | ||
| HL_3J5L_076 | No text annotation | ||
| HL_3J5L_056 | Pseudoknot geometry | ||
| HL_3J5L_057 | GNRA | ||
| HL_3J5L_058 | GNRA | ||
| HL_3J5L_059 | No text annotation | ||
| HL_3J5L_060 | No text annotation | ||
| HL_3J5L_061 | GNRA variation | ||
| HL_3J5L_063 | GNRA | ||
| HL_3J5L_064 | GNRA | ||
| HL_3J5L_065 | Ribsomal LSU H95 | ||
| HL_3J5L_066 | No text annotation | ||
| HL_3J5L_067 | No text annotation | ||
| HL_3J5L_068 | No text annotation | ||
| HL_3J5L_069 | GNRA | ||
| HL_3J5L_077 | No text annotation | ||
| HL_3J5L_070 | No text annotation | ||
| HL_3J5L_071 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3J5L_016 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_5J7L_259 NA | |
| IL_3J5L_017 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | geometric IL_5J7L_260 NA | |
| IL_3J5L_018 | 1/A/697:698, 1/A/763:765 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_3J5L_021 | 1/A/738:740, 1/A/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_3J5L_022 | 1/A/775:777, 1/A/787:791 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_3J5L_029 | 1/A/870:872, 1/A/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_3J5L_032 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_3J5L_036 | 1/A/1018:1024, 1/A/1140:1144 | Kink-turn related | homologous IL_5J7L_280 NA | |
| IL_3J5L_037 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_3J5L_122 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_3J5L_047 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_3J5L_050 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_3J5L_054 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_3J5L_065 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW | homologous IL_5J7L_306 NA | |
| IL_3J5L_123 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_3J5L_066 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_3J5L_071 | 1/A/1770:1771, 1/A/1980:1982 | Single bulged A | homologous IL_5J7L_312 NA | |
| IL_3J5L_072 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_3J5L_124 | 1/A/1851:1860, 1/A/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_3J5L_089 | 1/A/2350:2353, 1/A/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_3J5L_094 | 1/A/2459:2461, 1/A/2489:2493 | Major groove minor groove platform with extra cWW | homologous IL_7A0S_086 IL_36931.1 | |
| IL_3J5L_104 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_3J5L_105 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_3J5L_110 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3J5L_001 | Not an internal loop | ||
| IL_3J5L_002 | Triple sheared with non-canonical cWW | ||
| IL_3J5L_003 | Single bulged A | ||
| IL_3J5L_004 | Minor groove platform | ||
| IL_3J5L_005 | No text annotation | ||
| IL_3J5L_006 | Single stack bend | ||
| IL_3J5L_007 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_3J5L_008 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_3J5L_009 | No text annotation | ||
| IL_3J5L_010 | No text annotation | ||
| IL_3J5L_011 | No text annotation | ||
| IL_3J5L_012 | No text annotation | ||
| IL_3J5L_013 | Double sheared | ||
| IL_3J5L_014 | Isolated non-canonical cWW pair | ||
| IL_3J5L_015 | AAA cross-strand stack | ||
| IL_3J5L_019 | Single bulged G | ||
| IL_3J5L_020 | Triple sheared | ||
| IL_3J5L_023 | 90 degree turn | ||
| IL_3J5L_118 | No text annotation | ||
| IL_3J5L_024 | Stack outside cWW | ||
| IL_3J5L_025 | Single stack bend | ||
| IL_3J5L_026 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_3J5L_027 | Single bulged G | ||
| IL_3J5L_028 | C-loop with bulged stacked A's | ||
| IL_3J5L_030 | Double sheared with non-canonical cWW | ||
| IL_3J5L_031 | Single bulged A | ||
| IL_3J5L_119 | Isolated non-canonical cWW pair | ||
| IL_3J5L_033 | UAA/GAN | ||
| IL_3J5L_034 | SSU/LSU pseudoknot | ||
| IL_3J5L_035 | Single bulged U | ||
| IL_3J5L_038 | Isolated non-canonical cWW pair | ||
| IL_3J5L_039 | Tandem non-canonical cWW pairs | ||
| IL_3J5L_120 | Partly complementary | ||
| IL_3J5L_040 | Kink-turn | ||
| IL_3J5L_041 | No text annotation | ||
| IL_3J5L_121 | No text annotation | ||
| IL_3J5L_042 | No text annotation | ||
| IL_3J5L_043 | No text annotation | ||
| IL_3J5L_044 | Tandem non-canonical cWW pairs | ||
| IL_3J5L_045 | No text annotation | ||
| IL_3J5L_046 | Kink-turn | ||
| IL_3J5L_048 | Major groove platform; stack outside cWW | ||
| IL_3J5L_049 | C-loop | ||
| IL_3J5L_051 | tSH-tHW-tHS | ||
| IL_3J5L_052 | No text annotation | ||
| IL_3J5L_053 | UAA/GAN | ||
| IL_3J5L_055 | tSH-tHW | ||
| IL_3J5L_056 | Single bulged U | ||
| IL_3J5L_057 | No text annotation | ||
| IL_3J5L_058 | tSH-tHW-tHS | ||
| IL_3J5L_059 | 180 degree turn | ||
| IL_3J5L_060 | No text annotation | ||
| IL_3J5L_061 | Single bulged A | ||
| IL_3J5L_062 | UAA/GAN variation | ||
| IL_3J5L_063 | No text annotation | ||
| IL_3J5L_064 | Isolated tWW turn | ||
| IL_3J5L_067 | tSH-tSH-tHH-tHS | ||
| IL_3J5L_068 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_3J5L_069 | Triple sheared | ||
| IL_3J5L_070 | Single bulged C | ||
| IL_3J5L_073 | Minor groove platform, major groove intercalation | ||
| IL_3J5L_074 | Major groove intercalation | ||
| IL_3J5L_075 | Minor groove platform | ||
| IL_3J5L_076 | UAA/GAN related | ||
| IL_3J5L_077 | Bulged stacked bases | ||
| IL_3J5L_078 | No text annotation | ||
| IL_3J5L_079 | Major groove platform | ||
| IL_3J5L_080 | No text annotation | ||
| IL_3J5L_081 | Single bulged U | ||
| IL_3J5L_082 | Minor groove platform | ||
| IL_3J5L_083 | Isolated tHS basepair with bulges | ||
| IL_3J5L_084 | Isolated non-canonical cWW pair | ||
| IL_3J5L_085 | Isolated cWH basepair | ||
| IL_3J5L_086 | Isolated non-canonical cWW pair | ||
| IL_3J5L_087 | Isolated non-canonical cWW pair | ||
| IL_3J5L_088 | Single bulged U | ||
| IL_3J5L_090 | No text annotation | ||
| IL_3J5L_091 | Single stack bend | ||
| IL_3J5L_092 | Major groove platform | ||
| IL_3J5L_093 | Major groove platform | ||
| IL_3J5L_095 | Double sheared with non-canonical cWW | ||
| IL_3J5L_096 | Major groove platform | ||
| IL_3J5L_097 | Isolated non-canonical cWW with bulges | ||
| IL_3J5L_098 | No text annotation | ||
| IL_3J5L_099 | Major groove platform with intercalation | ||
| IL_3J5L_100 | Single bulged A | ||
| IL_3J5L_101 | tSH-tHS-tHW | ||
| IL_3J5L_102 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_3J5L_103 | C-loop | ||
| IL_3J5L_106 | UAA/GAN with extra cWW | ||
| IL_3J5L_107 | Single bulged A | ||
| IL_3J5L_108 | No text annotation | ||
| IL_3J5L_109 | Major groove intercalation | ||
| IL_3J5L_111 | tHS double platform | ||
| IL_3J5L_112 | Not an internal loop | ||
| IL_3J5L_113 | Major groove intercalation | ||
| IL_3J5L_114 | No text annotation | ||
| IL_3J5L_115 | Major groove minor groove platform; mini C-loop | ||
| IL_3J5L_116 | Symmetric double minor groove platform | ||
| IL_3J5L_117 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3J5L_001 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_3J5L_002 | 1/A/698:700, 1/A/732:736, 1/A/760:763 | No text annotation | homologous J3_5J7L_039 NA | |
| J3_3J5L_008 | 1/A/2517:2520, 1/A/2545:2547, 1/A/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_3J5L_009 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_3J5L_003 | 1/A/601:604, 1/A/624:628, 1/A/635:638, 1/A/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_3J5L_004 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_3J5L_005 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_3J5L_006 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_3J5L_009 | 1/A/1833:1835, 1/A/1905:1906, 1/A/1924:1933, 1/A/1967:1972 | No text annotation | homologous J4_5J7L_026 NA | |
| J4_3J5L_010 | 1/A/2285:2289, 1/A/2343:2347, 1/A/2370:2372, 1/A/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_3J5L_011 | 1/A/2643:2646, 1/A/2674:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J5_3J5L_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_3J5L_003 | 1/A/584:589, 1/A/668:671, 1/A/809:812, 1/A/1195:1196, 1/A/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_3J5L_004 | 1/A/1674:1682, 1/A/1706:1707, 1/A/1751:1752, 1/A/1756:1764, 1/A/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_3J5L_005 | 1/A/2057:2064, 1/A/2446:2453, 1/A/2500:2507, 1/A/2582:2588, 1/A/2606:2611 | No text annotation | ||
| J7_3J5L_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2630, 1/A/2788:2789, 1/A/2894:2895 | No text annotation | ||
| J7_3J5L_002 | 1/A/817:822, 1/A/835:838, 1/A/940:946, 1/A/971:976, 1/A/987:991, 1/A/1163:1164, 1/A/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3J5L_011 | No text annotation | ||
| J3_3J5L_015 | No text annotation | ||
| J3_3J5L_016 | No text annotation | ||
| J3_3J5L_012 | No text annotation | ||
| J3_3J5L_017 | No text annotation | ||
| J3_3J5L_003 | No text annotation | ||
| J3_3J5L_004 | No text annotation | ||
| J3_3J5L_005 | No text annotation | ||
| J3_3J5L_013 | No text annotation | ||
| J3_3J5L_018 | No text annotation | ||
| J3_3J5L_006 | Kink-turn 3-way junction | ||
| J3_3J5L_019 | No text annotation | ||
| J3_3J5L_007 | No text annotation | ||
| J3_3J5L_014 | No text annotation | ||
| J3_3J5L_010 | No text annotation | ||
| J4_3J5L_001 | No text annotation | ||
| J4_3J5L_002 | No text annotation | ||
| J4_3J5L_007 | No text annotation | ||
| J4_3J5L_008 | No text annotation | ||
| J5_3J5L_002 | No text annotation | ||
| J5_3J5L_006 | No text annotation | ||
| J6_3J5L_001 | No text annotation | ||
| J6_3J5L_002 | No text annotation |
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