6SPD Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6SPD_017 | 1/A/556:565 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_6SPD_022 | 1/A/734:743 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_6SPD_024 | 1/A/816:821 | No text annotation | homologous HL_7RQB_025 NA | |
| HL_6SPD_026 | 1/A/945:952 | GNRA | homologous HL_7A0S_026 HL_34789.4 | |
| HL_6SPD_027 | 1/A/968:975 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_6SPD_032 | 1/A/1268:1276 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_6SPD_033 | 1/A/1311:1317 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_6SPD_036 | 1/A/1437:1448 | UNCG variation | geometric HL_5J7L_200 NA | |
| HL_6SPD_041 | 1/A/1620:1626 | GNRA | homologous HL_5J7L_174 NA | |
| HL_6SPD_042 | 1/A/1681:1686 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_6SPD_044 | 1/A/1739:1743 | No text annotation | homologous HL_7RQB_044 NA | |
| HL_6SPD_045 | 1/A/1764:1774 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_6SPD_049 | 1/A/1936:1944 | No text annotation | homologous HL_5J7L_182 NA | |
| HL_6SPD_050 | 1/A/2014:2023 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_6SPD_054 | 1/A/2235:2243 | No text annotation | homologous HL_7A0S_052 HL_11974.2 | |
| HL_6SPD_055 | 1/A/2251:2263 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_6SPD_076 | 1/A/2291:2299 | No text annotation | homologous HL_7A0S_076 HL_02452.1 | |
| HL_6SPD_057 | 1/A/2311:2318 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_6SPD_058 | 1/A/2342:2349 | GNRA with extra cWW | homologous HL_4WF9_053 HL_87268.2 | |
| HL_6SPD_059 | 1/A/2361:2366 | GNRA | homologous HL_4WF9_054 HL_34789.4 | |
| HL_6SPD_061 | 1/A/2458:2466 | No text annotation | homologous HL_7A0S_059 HL_52011.1 | |
| HL_6SPD_062 | 1/A/2515:2522 | GNRA variation | homologous HL_4WF9_057 HL_46665.2 | |
| HL_6SPD_063 | 1/A/2538:2544 | No text annotation | homologous HL_4WF9_058 HL_48677.1 | |
| HL_6SPD_064 | 1/A/2581:2586 | GNRA | homologous HL_7A0S_062 HL_34789.4 | |
| HL_6SPD_065 | 1/A/2645:2650 | GNRA | homologous HL_7A0S_063 HL_34789.4 | |
| HL_6SPD_066 | 1/A/2687:2692 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_6SPD_067 | 1/A/2731:2745 | No text annotation | homologous HL_5J7L_199 NA | |
| HL_6SPD_069 | 1/A/2805:2813 | No text annotation | homologous HL_7RQB_068 NA | |
| HL_6SPD_070 | 1/A/2842:2847 | GNRA | homologous HL_7A0S_068 HL_34789.4 | |
| HL_6SPD_072 | 1/B/85:89 | Mini UNCG | homologous HL_5J7L_204 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6SPD_001 | No text annotation | ||
| HL_6SPD_002 | No text annotation | ||
| HL_6SPD_003 | No text annotation | ||
| HL_6SPD_004 | No text annotation | ||
| HL_6SPD_005 | No text annotation | ||
| HL_6SPD_006 | No text annotation | ||
| HL_6SPD_007 | No text annotation | ||
| HL_6SPD_008 | No text annotation | ||
| HL_6SPD_009 | T-loop with 1 bulged base | ||
| HL_6SPD_010 | No text annotation | ||
| HL_6SPD_011 | T-loop with unstacked turn | ||
| HL_6SPD_012 | No text annotation | ||
| HL_6SPD_013 | Pseudoknot geometry | ||
| HL_6SPD_014 | GNRA | ||
| HL_6SPD_015 | GNRA | ||
| HL_6SPD_016 | No text annotation | ||
| HL_6SPD_075 | No text annotation | ||
| HL_6SPD_018 | No text annotation | ||
| HL_6SPD_019 | GNRA | ||
| HL_6SPD_020 | GNRA wlth extra near cWW | ||
| HL_6SPD_073 | GNRA | ||
| HL_6SPD_021 | GNRA wlth tandem sheared | ||
| HL_6SPD_023 | No text annotation | ||
| HL_6SPD_025 | Externally structured | ||
| HL_6SPD_028 | No text annotation | ||
| HL_6SPD_029 | No text annotation | ||
| HL_6SPD_030 | No text annotation | ||
| HL_6SPD_031 | GNRA | ||
| HL_6SPD_034 | GNRA | ||
| HL_6SPD_035 | No text annotation | ||
| HL_6SPD_037 | No text annotation | ||
| HL_6SPD_038 | No text annotation | ||
| HL_6SPD_039 | Mini UNCG | ||
| HL_6SPD_040 | No text annotation | ||
| HL_6SPD_043 | No text annotation | ||
| HL_6SPD_046 | GNRA related | ||
| HL_6SPD_047 | GNRA | ||
| HL_6SPD_048 | No text annotation | ||
| HL_6SPD_051 | No text annotation | ||
| HL_6SPD_052 | Mini UNCG | ||
| HL_6SPD_053 | No text annotation | ||
| HL_6SPD_056 | No text annotation | ||
| HL_6SPD_060 | No text annotation | ||
| HL_6SPD_068 | UNCG variation | ||
| HL_6SPD_074 | No text annotation | ||
| HL_6SPD_071 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6SPD_009 | 1/A/527:530, 1/A/544:547 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_6SPD_010 | 1/A/554:556, 1/A/565:567 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_6SPD_022 | 1/A/845:851, 1/A/904:910 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_6SPD_023 | 1/A/851:852, 1/A/902:904 | Minor groove platform | geometric IL_4V9F_034 IL_34520.3 | |
| IL_6SPD_024 | 1/A/853:858, 1/A/897:901 | No text annotation | geometric IL_4V9F_035 IL_38603.1 | |
| IL_6SPD_025 | 1/A/859:861, 1/A/894:896 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_6SPD_026 | 1/A/864:868, 1/A/887:891 | Double sheared with non-canonical cWW | homologous IL_5J7L_274 NA | |
| IL_6SPD_108 | 1/A/864:872, 1/A/882:891 | No text annotation | ||
| IL_6SPD_033 | 1/A/1014:1020, 1/A/1114:1130 | No text annotation | geometric IL_4WF9_040 IL_50715.4 | |
| IL_6SPD_034 | 1/A/1020:1024, 1/A/1111:1114 | No text annotation | ||
| IL_6SPD_035 | 1/A/1028:1031, 1/A/1104:1107 | Tandem non-canonical cWW pairs | homologous IL_5J7L_283 NA | |
| IL_6SPD_116 | 1/A/1033:1041, 1/A/1098:1102 | Kink-turn | homologous IL_5J7L_284 NA | |
| IL_6SPD_042 | 1/A/1249:1256, 1/A/1998:2004 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5TBW_116 NA | |
| IL_6SPD_049 | 1/A/1419:1422, 1/A/1547:1551 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_6SPD_050 | 1/A/1424:1427, 1/A/1541:1545 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_6SPD_056 | 1/A/1641:1646, 1/A/1991:1993 | No text annotation | homologous IL_4WF9_062 IL_12566.5 | |
| IL_6SPD_057 | 1/A/1653:1655, 1/A/1982:1984 | Isolated tWW turn | homologous IL_5J7L_305 NA | |
| IL_6SPD_058 | 1/A/1656:1659, 1/A/1980:1981 | Major groove platform; stack outside cWW | geometric IL_5J7L_306 NA | |
| IL_6SPD_109 | 1/A/1656:1664, 1/A/1977:1981 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_6SPD_059 | 1/A/1659:1664, 1/A/1977:1980 | Intercalated tWH | homologous IL_4WF9_065 IL_28217.1 | |
| IL_6SPD_060 | 1/A/1676:1681, 1/A/1686:1692 | tSH-tSH-tHH-tHS | geometric IL_5J7L_308 NA | |
| IL_6SPD_062 | 1/A/1757:1758, 1/A/1967:1969 | Single bulged A | homologous IL_7A0S_064 IL_14190.2 | |
| IL_6SPD_068 | 1/A/1920:1921, 1/A/1951:1954 | Bulged stacked bases | homologous IL_7RQB_076 NA | |
| IL_6SPD_069 | 1/A/1921:1932, 1/A/1948:1951 | No text annotation | geometric IL_4WF9_077 IL_84014.1 | |
| IL_6SPD_070 | 1/A/2037:2039, 1/A/2604:2605 | Major groove platform | homologous IL_7A0S_073 IL_48076.8 | |
| IL_6SPD_071 | 1/A/2041:2043, 1/A/2599:2602 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6SPD_083 | 1/A/2440:2441, 1/A/2485:2487 | Single stack bend | homologous IL_4WF9_089 IL_15011.2 | |
| IL_6SPD_084 | 1/A/2441:2442, 1/A/2483:2485 | Major groove platform | geometric IL_7RQB_092 NA | |
| IL_6SPD_085 | 1/A/2444:2446, 1/A/2480:2481 | Major groove platform | geometric IL_5TBW_104 NA | |
| IL_6SPD_086 | 1/A/2446:2448, 1/A/2476:2480 | Major groove minor groove platform with extra cWW | homologous IL_5J7L_337 NA | |
| IL_6SPD_087 | 1/A/2453:2457, 1/A/2467:2471 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_6SPD_088 | 1/A/2494:2495, 1/A/2567:2569 | Major groove platform | homologous IL_4WF9_094 IL_46637.2 | |
| IL_6SPD_089 | 1/A/2497:2499, 1/A/2561:2565 | Isolated non-canonical cWW with bulges | geometric IL_7RQB_097 NA | |
| IL_6SPD_090 | 1/A/2499:2500, 1/A/2558:2561 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_6SPD_091 | 1/A/2509:2510, 1/A/2527:2530 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_6SPD_092 | 1/A/2578:2579, 1/A/2588:2590 | Single bulged A | homologous IL_5J7L_344 NA | |
| IL_6SPD_093 | 1/A/2623:2627, 1/A/2760:2768 | tSH-tHS-tHW | homologous IL_4WF9_099 IL_04638.4 | |
| IL_6SPD_094 | 1/A/2639:2645, 1/A/2650:2655 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_5J7L_346 NA | |
| IL_6SPD_095 | 1/A/2667:2671, 1/A/2711:2713 | C-loop | homologous IL_4WF9_101 IL_63596.12 | |
| IL_6SPD_097 | 1/A/2681:2682, 1/A/2697:2700 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_6SPD_098 | 1/A/2723:2728, 1/A/2748:2753 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_6SPD_099 | 1/A/2792:2797, 1/A/2875:2878 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_6SPD_114 | 1/A/2824:2825, 1/A/2864:2866 | Major groove intercalation | homologous IL_5J7L_352 NA | |
| IL_6SPD_101 | 1/A/2829:2832, 1/A/2856:2860 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_6SPD_102 | 1/A/2833:2839, 1/A/2850:2855 | No text annotation | ||
| IL_6SPD_118 | 1/B/16:17, 1/B/64:66 | Major groove intercalation | homologous IL_4WF9_112 IL_14190.2 | |
| IL_6SPD_104 | 1/B/22:27, 1/B/55:59 | No text annotation | homologous IL_5J7L_356 NA | |
| IL_6SPD_105 | 1/B/29:30, 1/B/50:53 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_357 NA | |
| IL_6SPD_107 | 1/B/70:78, 1/B/96:104 | Bacterial 5S Loop E | homologous IL_7RQB_115 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6SPD_001 | Triple sheared with non-canonical cWW | ||
| IL_6SPD_002 | Single bulged A | ||
| IL_6SPD_003 | Minor groove platform | ||
| IL_6SPD_004 | Single stack bend | ||
| IL_6SPD_005 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_6SPD_006 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_6SPD_007 | Isolated non-canonical cWW pair | ||
| IL_6SPD_008 | No text annotation | ||
| IL_6SPD_011 | AAA cross-strand stack | ||
| IL_6SPD_012 | No text annotation | ||
| IL_6SPD_013 | tHW-tHW cross-strand stack | ||
| IL_6SPD_014 | Single bulged A | ||
| IL_6SPD_015 | Single bulged G | ||
| IL_6SPD_016 | Triple sheared | ||
| IL_6SPD_017 | Major groove platform | ||
| IL_6SPD_018 | Isolated non-canonical cWW pair | ||
| IL_6SPD_019 | Multiple bulged bases | ||
| IL_6SPD_020 | Single stack bend | ||
| IL_6SPD_021 | No text annotation | ||
| IL_6SPD_027 | No text annotation | ||
| IL_6SPD_028 | Single bulged C | ||
| IL_6SPD_029 | UAA/GAN | ||
| IL_6SPD_030 | SSU/LSU pseudoknot | ||
| IL_6SPD_031 | Single bulged U | ||
| IL_6SPD_032 | No text annotation | ||
| IL_6SPD_036 | No text annotation | ||
| IL_6SPD_037 | No text annotation | ||
| IL_6SPD_038 | Major groove platform | ||
| IL_6SPD_117 | Isolated cWS basepair | ||
| IL_6SPD_039 | Tandem non-canonical cWW pairs | ||
| IL_6SPD_040 | No text annotation | ||
| IL_6SPD_041 | Kink-turn | ||
| IL_6SPD_043 | Major groove platform; stack outside cWW | ||
| IL_6SPD_044 | C-loop | ||
| IL_6SPD_045 | UAA/GAN | ||
| IL_6SPD_046 | tSH-tHW-tHS | ||
| IL_6SPD_047 | No text annotation | ||
| IL_6SPD_048 | UAA/GAN | ||
| IL_6SPD_051 | No text annotation | ||
| IL_6SPD_052 | No text annotation | ||
| IL_6SPD_053 | No text annotation | ||
| IL_6SPD_054 | Single bulged A | ||
| IL_6SPD_055 | UAA/GAN variation | ||
| IL_6SPD_061 | No text annotation | ||
| IL_6SPD_063 | Kink-turn related | ||
| IL_6SPD_064 | Minor groove platform, major groove intercalation | ||
| IL_6SPD_065 | Major groove intercalation | ||
| IL_6SPD_066 | Major groove minor groove platform; mini C-loop | ||
| IL_6SPD_110 | No text annotation | ||
| IL_6SPD_067 | UAA/GAN related | ||
| IL_6SPD_072 | Single bulged U | ||
| IL_6SPD_073 | Minor groove platform | ||
| IL_6SPD_074 | Isolated tHS basepair with bulges | ||
| IL_6SPD_075 | Isolated non-canonical cWW pair | ||
| IL_6SPD_076 | Isolated non-canonical cWW pair | ||
| IL_6SPD_077 | No text annotation | ||
| IL_6SPD_078 | No text annotation | ||
| IL_6SPD_111 | No text annotation | ||
| IL_6SPD_079 | No text annotation | ||
| IL_6SPD_080 | Isolated non-canonical cWW pair | ||
| IL_6SPD_112 | Partly complementary | ||
| IL_6SPD_081 | Double sheared | ||
| IL_6SPD_082 | No text annotation | ||
| IL_6SPD_113 | Isolated non-canonical cWW contact | ||
| IL_6SPD_096 | No text annotation | ||
| IL_6SPD_100 | Isolated non-canonical cWW with bulges | ||
| IL_6SPD_103 | No text annotation | ||
| IL_6SPD_115 | No text annotation | ||
| IL_6SPD_106 | Symmetric double minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6SPD_019 | 1/A/1045:1048, 1/A/1070:1077, 1/A/1092:1094 | No text annotation | ||
| J3_6SPD_006 | 1/A/1285:1290, 1/A/1615:1617, 1/A/1629:1632 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_6SPD_018 | 1/A/2269:2271, 1/A/2371:2382, 1/A/2408:2414 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_6SPD_010 | 1/A/2282:2286, 1/A/2304:2310, 1/A/2319:2324 | No text annotation | homologous J3_5J7L_071 NA | |
| J3_6SPD_011 | 1/A/2504:2507, 1/A/2532:2534, 1/A/2548:2554 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_6SPD_014 | 1/B/9:15, 1/B/67:68, 1/B/106:109 | No text annotation | homologous J3_7A0S_021 J3_47324.1 | |
| J4_6SPD_010 | 1/A/1257:1263, 1/A/1281:1282, 1/A/1635:1638, 1/A/1996:1997 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_6SPD_006 | 1/A/1759:1763, 1/A/1775:1779, 1/A/1814:1817, 1/A/1962:1966 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_6SPD_007 | 1/A/1820:1822, 1/A/1892:1893, 1/A/1911:1920, 1/A/1954:1959 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_6SPD_008 | 1/A/2272:2276, 1/A/2330:2334, 1/A/2357:2359, 1/A/2368:2370 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_6SPD_009 | 1/A/2630:2633, 1/A/2661:2663, 1/A/2717:2721, 1/A/2755:2757 | No text annotation | homologous J4_4WF9_009 J4_77044.5 | |
| J5_6SPD_002 | 1/A/522:524, 1/A/550:554, 1/A/567:569, 1/A/1248:1249, 1/A/2004:2005 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_6SPD_003 | 1/A/574:579, 1/A/658:661, 1/A/799:802, 1/A/1182:1183, 1/A/1237:1243 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_6SPD_004 | 1/A/1664:1672, 1/A/1696:1697, 1/A/1738:1739, 1/A/1743:1751, 1/A/1975:1977 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_6SPD_005 | 1/A/2044:2051, 1/A/2433:2441, 1/A/2485:2494, 1/A/2569:2575, 1/A/2593:2598 | No text annotation | ||
| J5_6SPD_008 | 1/A/2061:2064, 1/A/2230:2233, 1/A/2245:2246, 1/A/2268:2269, 1/A/2414:2422 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J6_6SPD_003 | 1/A/2061:2064, 1/A/2230:2233, 1/A/2245:2246, 1/A/2268:2271, 1/A/2371:2382, 1/A/2408:2422 | No text annotation | ||
| J6_6SPD_002 | 1/A/2061:2064, 1/A/2230:2233, 1/A/2245:2247, 1/A/2267:2271, 1/A/2371:2382, 1/A/2408:2422 | No text annotation | ||
| J7_6SPD_001 | 1/A/8:15, 1/A/516:522, 1/A/2005:2010, 1/A/2027:2030, 1/A/2612:2617, 1/A/2774:2775, 1/A/2880:2881 | No text annotation | ||
| J7_6SPD_002 | 1/A/807:812, 1/A/825:828, 1/A/930:936, 1/A/961:966, 1/A/977:981, 1/A/1154:1155, 1/A/1172:1177 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6SPD_001 | No text annotation | ||
| J3_6SPD_015 | No text annotation | ||
| J3_6SPD_002 | No text annotation | ||
| J3_6SPD_003 | No text annotation | ||
| J3_6SPD_004 | No text annotation | ||
| J3_6SPD_005 | No text annotation | ||
| J3_6SPD_007 | No text annotation | ||
| J3_6SPD_016 | No text annotation | ||
| J3_6SPD_017 | No text annotation | ||
| J3_6SPD_008 | Kink-turn 3-way junction | ||
| J3_6SPD_009 | No text annotation | ||
| J3_6SPD_012 | No text annotation | ||
| J3_6SPD_013 | No text annotation | ||
| J4_6SPD_001 | No text annotation | ||
| J4_6SPD_002 | No text annotation | ||
| J4_6SPD_003 | No text annotation | ||
| J4_6SPD_004 | No text annotation | ||
| J4_6SPD_005 | No text annotation | ||
| J5_6SPD_007 | No text annotation | ||
| J5_6SPD_001 | No text annotation | ||
| J5_6SPD_006 | No text annotation | ||
| J6_6SPD_001 | No text annotation |
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