1VW3 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_1VW3_003 | 1/A/153:158 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_1VW3_004 | 1/A/234:241 | No text annotation | geometric HL_4WF9_006 HL_30068.2 | |
| HL_1VW3_005 | 1/A/265:270 | No text annotation | geometric HL_5J7L_140 HL_62934.1 | |
| HL_1VW3_006 | 1/A/286:292 | No text annotation | geometric HL_7A0S_008 HL_37369.2 | |
| HL_1VW3_007 | 1/A/324:332 | No text annotation | geometric HL_5U3G_001 HL_75660.5 | |
| HL_1VW3_008 | 1/A/347:355 | Pseudoknot geometry | geometric HL_3IVK_004 HL_30680.3 | |
| HL_1VW3_009 | 1/A/393:398 | GNRA | geometric HL_4WF9_015 HL_37824.7 | |
| HL_1VW3_010 | 1/A/440:449 | Other HL | geometric HL_5J7L_200 HL_08100.1 | |
| HL_1VW3_011 | 1/A/465:474 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 HL_28252.6 | |
| HL_1VW3_012 | 1/A/505:511 | No text annotation | ||
| HL_1VW3_013 | 1/A/542:551 | No text annotation | geometric HL_4TUE_219 HL_75293.5 | |
| HL_1VW3_014 | 1/A/612:619 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_1VW3_015 | 1/A/635:644 | No text annotation | geometric HL_5TBW_020 NA | |
| HL_1VW3_016 | 1/A/670:676 | No text annotation | geometric HL_7RQB_024 NA | |
| HL_1VW3_017 | 1/A/717:722 | No text annotation | geometric HL_5J7L_157 HL_55195.3 | |
| HL_1VW3_018 | 1/A/881:888 | GNRA | geometric HL_7RQB_027 NA | |
| HL_1VW3_019 | 1/A/904:911 | No text annotation | geometric HL_1WZ2_007 HL_75660.5 | |
| HL_1VW3_021 | 1/A/1075:1078 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 | |
| HL_1VW3_024 | 1/A/1254:1258 | Mini UNCG | geometric HL_5J7L_204 HL_48778.2 | |
| HL_1VW3_025 | 1/A/1313:1320 | No text annotation | ||
| HL_1VW3_026 | 1/A/1343:1351 | No text annotation | ||
| HL_1VW3_027 | 1/A/1384:1389 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_1VW3_029 | 1/A/1564:1571 | No text annotation | geometric HL_7RQB_040 NA | |
| HL_1VW3_030 | 1/A/1581:1589 | GNRA with extra cWW | geometric HL_4WF9_039 HL_20167.2 | |
| HL_1VW3_031 | 1/A/1643:1649 | UNCG | geometric HL_6DLR_002 HL_34617.5 | |
| HL_1VW3_032 | 1/A/1684:1694 | No text annotation | geometric HL_4WF9_043 HL_01962.2 | |
| HL_1VW3_033 | 1/A/1713:1719 | GNRA related | geometric HL_5J7L_179 HL_04783.2 | |
| HL_1VW3_034 | 1/A/1773:1778 | GNRA | geometric HL_3RG5_007 HL_37824.7 | |
| HL_1VW3_035 | 1/A/1811:1820 | No text annotation | geometric HL_4V9F_003 HL_75660.5 | |
| HL_1VW3_036 | 1/A/1849:1857 | No text annotation | geometric HL_5J7L_182 HL_20167.2 | |
| HL_1VW3_037 | 1/A/1927:1936 | No text annotation | geometric HL_4WF9_047 HL_61996.2 | |
| HL_1VW3_039 | 1/A/2196:2201 | No text annotation | geometric HL_1KH6_003 HL_27483.1 | |
| HL_1VW3_041 | 1/A/2290:2302 | No text annotation | geometric HL_5J7L_187 HL_91939.2 | |
| HL_1VW3_042 | 1/A/2327:2332 | No text annotation | geometric HL_1WZ2_007 HL_75660.5 | |
| HL_1VW3_043 | 1/A/2357:2363 | tRNA D-loop | geometric HL_4V9K_033 HL_48417.5 | |
| HL_1VW3_045 | 1/A/2454:2462 | No text annotation | geometric HL_4V9F_057 HL_50860.2 | |
| HL_1VW3_048 | 1/A/2622:2629 | GNRA with extra cWW | geometric HL_4WF9_053 HL_04259.3 | |
| HL_1VW3_049 | 1/A/2641:2646 | GNRA | geometric HL_5TBW_186 NA | |
| HL_1VW3_050 | 1/A/2671:2680 | No text annotation | geometric HL_5J7L_192 HL_53454.2 | |
| HL_1VW3_051 | 1/A/2737:2745 | No text annotation | geometric HL_4WF9_056 HL_32735.2 | |
| HL_1VW3_052 | 1/A/2794:2802 | No text annotation | geometric HL_4V9F_063 HL_31585.3 | |
| HL_1VW3_053 | 1/A/2818:2824 | No text annotation | geometric HL_5TBW_063 NA | |
| HL_1VW3_054 | 1/A/2861:2866 | GNRA | geometric HL_4V9F_065 HL_37824.7 | |
| HL_1VW3_055 | 1/A/2925:2930 | GNRA | geometric HL_5B2P_001 HL_37824.7 | |
| HL_1VW3_058 | 1/A/3081:3096 | No text annotation | geometric HL_4V9F_068 HL_74055.2 | |
| HL_1VW3_059 | 1/A/3135:3143 | No text annotation | geometric HL_7RQB_068 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_1VW3_001 | No text annotation | ||
| HL_1VW3_002 | No text annotation | ||
| HL_1VW3_020 | No text annotation | ||
| HL_1VW3_022 | No text annotation | ||
| HL_1VW3_023 | Mini UNCG | ||
| HL_1VW3_028 | No text annotation | ||
| HL_1VW3_038 | No text annotation | ||
| HL_1VW3_040 | No text annotation | ||
| HL_1VW3_044 | No text annotation | ||
| HL_1VW3_046 | No text annotation | ||
| HL_1VW3_047 | No text annotation | ||
| HL_1VW3_056 | No text annotation | ||
| HL_1VW3_057 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_1VW3_001 | 1/A/22:24, 1/A/3275:3277 | Isolated non-canonical cWW pair | geometric IL_2OE5_001 IL_28037.2 | |
| IL_1VW3_002 | 1/A/25:32, 1/A/3273:3274 | No text annotation | ||
| IL_1VW3_003 | 1/A/58:63, 1/A/407:413 | Triple sheared with non-canonical cWW | geometric IL_7A0S_018 IL_06136.2 | |
| IL_1VW3_004 | 1/A/96:97, 1/A/378:380 | Single bulged A | geometric IL_7RQB_002 NA | |
| IL_1VW3_005 | 1/A/113:121, 1/A/140:145 | No text annotation | ||
| IL_1VW3_008 | 1/A/173:176, 1/A/202:205 | Tandem non-canonical cWW pairs | geometric IL_4WF9_109 NA | |
| IL_1VW3_009 | 1/A/176:178, 1/A/200:202 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_44465.1 | |
| IL_1VW3_010 | 1/A/223:224, 1/A/252:254 | Single stack bend | geometric IL_5J7L_249 IL_90729.1 | |
| IL_1VW3_011 | 1/A/228:234, 1/A/241:248 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_250 IL_04346.10 | |
| IL_1VW3_013 | 1/A/279:285, 1/A/293:298 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_4V9F_007 IL_26307.2 | |
| IL_1VW3_014 | 1/A/433:436, 1/A/453:456 | No text annotation | ||
| IL_1VW3_015 | 1/A/463:465, 1/A/474:476 | No text annotation | geometric IL_7RQB_015 NA | |
| IL_1VW3_016 | 1/A/581:583, 1/A/697:699 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_87907.2 | |
| IL_1VW3_017 | 1/A/583:587, 1/A/690:697 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_1VW3_018 | 1/A/606:607, 1/A/654:656 | Single bulged A | geometric IL_5J7L_261 IL_31462.5 | |
| IL_1VW3_019 | 1/A/611:612, 1/A/619:621 | Single bulged G | geometric IL_4WF9_023 IL_00225.13 | |
| IL_1VW3_020 | 1/A/629:632, 1/A/647:649 | Major groove platform with extra cWW | geometric IL_7RQB_022 NA | |
| IL_1VW3_021 | 1/A/666:669, 1/A/677:682 | No text annotation | ||
| IL_1VW3_023 | 1/A/734:738, 1/A/858:861 | Tandem non-canonical cWW pairs | geometric IL_5J7L_033 IL_85033.2 | |
| IL_1VW3_024 | 1/A/738:740, 1/A/855:858 | No text annotation | ||
| IL_1VW3_025 | 1/A/780:785, 1/A/841:846 | 5x5 Sarcin-Ricin with intercalated A; G-bulge | geometric IL_7A0S_027 NA | |
| IL_1VW3_026 | 1/A/785:786, 1/A/839:841 | Minor groove platform related | geometric IL_7TZS_003 IL_51454.2 | |
| IL_1VW3_027 | 1/A/787:791, 1/A/835:838 | C-loop | geometric IL_4V88_443 NA | |
| IL_1VW3_028 | 1/A/797:799, 1/A/828:829 | Single bulged A | geometric IL_5TBW_060 NA | |
| IL_1VW3_030 | 1/A/807:809, 1/A/817:818 | Single stack bend | geometric IL_4V9F_005 IL_90729.1 | |
| IL_1VW3_031 | 1/A/877:879, 1/A/890:892 | Isolated non-canonical cWW pair | geometric IL_5TBW_042 NA | |
| IL_1VW3_032 | 1/A/919:922, 1/A/1179:1181 | Major groove platform with extra pair | geometric IL_5TBW_091 NA | |
| IL_1VW3_033 | 1/A/924:928, 1/A/1173:1177 | UAA/GAN | geometric IL_4WF9_036 IL_38507.2 | |
| IL_1VW3_034 | 1/A/943:949, 1/A/1106:1120 | Kink-turn related | geometric IL_4WF9_039 IL_57188.5 | |
| IL_1VW3_035 | 1/A/1230:1232, 1/A/1280:1283 | Isolated cWS basepair | geometric IL_5J7L_286 IL_42997.3 | |
| IL_1VW3_036 | 1/A/1237:1244, 1/A/1268:1275 | No text annotation | ||
| IL_1VW3_038 | 1/A/1295:1302, 1/A/1911:1917 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_289 IL_04346.10 | |
| IL_1VW3_039 | 1/A/1355:1362, 1/A/1403:1409 | No text annotation | ||
| IL_1VW3_040 | 1/A/1364:1368, 1/A/1397:1401 | UAA/GAN | geometric IL_5J7L_292 IL_89021.2 | |
| IL_1VW3_041 | 1/A/1370:1372, 1/A/1394:1395 | Single bulged A | geometric IL_4WF9_006 IL_31462.5 | |
| IL_1VW3_045 | 1/A/1492:1493, 1/A/1515:1521 | No text annotation | ||
| IL_1VW3_046 | 1/A/1603:1608, 1/A/1904:1906 | No text annotation | geometric IL_5J7L_304 IL_12566.4 | |
| IL_1VW3_047 | 1/A/1615:1617, 1/A/1895:1897 | Isolated tWW turn | geometric IL_5J7L_305 IL_67095.2 | |
| IL_1VW3_048 | 1/A/1618:1621, 1/A/1893:1894 | Major groove platform; stack outside cWW | geometric IL_7RQB_066 NA | |
| IL_1VW3_049 | 1/A/1621:1626, 1/A/1890:1893 | Intercalated tWH | geometric IL_5J7L_307 IL_76758.2 | |
| IL_1VW3_050 | 1/A/1635:1636, 1/A/1658:1668 | No text annotation | ||
| IL_1VW3_051 | 1/A/1638:1643, 1/A/1649:1656 | No text annotation | ||
| IL_1VW3_052 | 1/A/1677:1678, 1/A/1880:1882 | Single bulged A | geometric IL_7RQB_069 NA | |
| IL_1VW3_053 | 1/A/1705:1711, 1/A/1721:1729 | Kink-turn related | geometric IL_4V9F_065 IL_17069.5 | |
| IL_1VW3_054 | 1/A/1745:1748, 1/A/1803:1804 | Major groove minor groove platform; mini C-loop | geometric IL_5J7L_029 IL_68140.4 | |
| IL_1VW3_055 | 1/A/1749:1750, 1/A/1799:1802 | Major groove intercalation | geometric IL_5TBW_085 NA | |
| IL_1VW3_056 | 1/A/1754:1757, 1/A/1793:1795 | No text annotation | geometric IL_4V84_070 NA | |
| IL_1VW3_057 | 1/A/1757:1764, 1/A/1786:1793 | No text annotation | ||
| IL_1VW3_058 | 1/A/1764:1766, 1/A/1785:1786 | Single stack bend | geometric IL_5TBW_375 NA | |
| IL_1VW3_060 | 1/A/1833:1834, 1/A/1864:1867 | Bulged stacked bases | geometric IL_4V9F_070 IL_22551.3 | |
| IL_1VW3_061 | 1/A/1834:1845, 1/A/1861:1864 | No text annotation | geometric IL_4WF9_077 IL_42218.2 | |
| IL_1VW3_062 | 1/A/1950:1952, 1/A/2884:2885 | Major groove platform | geometric IL_5J7L_320 IL_48076.6 | |
| IL_1VW3_063 | 1/A/1954:1956, 1/A/2879:2882 | No text annotation | geometric IL_4V9F_073 IL_83389.2 | |
| IL_1VW3_064 | 1/A/1967:1969, 1/A/2708:2709 | Single bulged U | geometric IL_4WF9_080 IL_89505.4 | |
| IL_1VW3_065 | 1/A/1970:1971, 1/A/2704:2707 | Minor groove platform | geometric IL_4V9F_075 IL_51454.2 | |
| IL_1VW3_066 | 1/A/1981:1983, 1/A/2262:2265 | Isolated tHS basepair with bulges | geometric IL_5J7L_325 IL_85599.2 | |
| IL_1VW3_067 | 1/A/1988:1991, 1/A/2256:2257 | Multiple bulged bases | geometric IL_1R3E_002 IL_84476.1 | |
| IL_1VW3_069 | 1/A/2287:2288, 1/A/2304:2306 | No text annotation | ||
| IL_1VW3_070 | 1/A/2437:2440, 1/A/2608:2610 | No text annotation | ||
| IL_1VW3_071 | 1/A/2468:2472, 1/A/2578:2581 | No text annotation | ||
| IL_1VW3_072 | 1/A/2617:2620, 1/A/2631:2634 | Double sheared | geometric IL_1SAQ_002 NA | |
| IL_1VW3_073 | 1/A/2668:2670, 1/A/2681:2682 | Major groove intercalation | geometric IL_1U9S_003 IL_82107.4 | |
| IL_1VW3_074 | 1/A/2720:2721, 1/A/2762:2764 | Major groove platform | geometric IL_7A0S_084 IL_48076.6 | |
| IL_1VW3_075 | 1/A/2723:2725, 1/A/2759:2760 | Major groove platform | geometric IL_4WF9_091 IL_48076.6 | |
| IL_1VW3_076 | 1/A/2725:2727, 1/A/2755:2759 | Major groove minor groove platform with extra cWW | geometric IL_5J7L_337 IL_51387.2 | |
| IL_1VW3_077 | 1/A/2731:2736, 1/A/2746:2751 | tSH-tHW-tHS-cWW | geometric IL_6DVK_004 IL_76308.6 | |
| IL_1VW3_078 | 1/A/2773:2774, 1/A/2847:2849 | Major groove platform | geometric IL_7A0S_088 IL_07039.3 | |
| IL_1VW3_079 | 1/A/2776:2778, 1/A/2841:2845 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 IL_07785.1 | |
| IL_1VW3_080 | 1/A/2778:2779, 1/A/2838:2841 | No text annotation | geometric IL_5J7L_341 IL_42626.2 | |
| IL_1VW3_081 | 1/A/2788:2789, 1/A/2807:2810 | Major groove platform with intercalation | geometric IL_7RQB_099 NA | |
| IL_1VW3_082 | 1/A/2858:2859, 1/A/2868:2870 | Single bulged A | geometric IL_7A0S_002 IL_31462.5 | |
| IL_1VW3_083 | 1/A/2902:2906, 1/A/3112:3116 | Triple sheared | geometric IL_7RQB_075 NA | |
| IL_1VW3_084 | 1/A/2919:2925, 1/A/2930:2935 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_5J7L_346 IL_16458.4 | |
| IL_1VW3_085 | 1/A/2947:2951, 1/A/3061:3063 | C-loop | geometric IL_7RQB_104 NA | |
| IL_1VW3_086 | 1/A/2954:2959, 1/A/3053:3058 | No text annotation | ||
| IL_1VW3_087 | 1/A/2962:2963, 1/A/3047:3050 | Multiple bulged bases | geometric IL_5J7L_349 IL_42626.2 | |
| IL_1VW3_088 | 1/A/2970:2971, 1/A/3038:3040 | Single bulged A | geometric IL_7RQB_101 NA | |
| IL_1VW3_090 | 1/A/3073:3078, 1/A/3099:3104 | UAA/GAN with extra cWW | geometric IL_7RQB_107 NA | |
| IL_1VW3_091 | 1/A/3123:3126, 1/A/3259:3260 | Multiple bulged bases | geometric IL_1R3E_002 IL_84476.1 | |
| IL_1VW3_093 | 1/A/3161:3162, 1/A/3242:3244 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_1VW3_094 | 1/A/3162:3168, 1/A/3229:3242 | No text annotation | ||
| IL_1VW3_095 | 1/A/3169:3173, 1/A/3193:3228 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_1VW3_022 | No text annotation | ||
| IL_1VW3_029 | No text annotation | ||
| IL_1VW3_042 | Tandem non-canonical cWW pairs | ||
| IL_1VW3_043 | Isolated non-canonical cWW pair | ||
| IL_1VW3_044 | Tandem non-canonical cWW pairs | ||
| IL_1VW3_068 | Isolated non-canonical cWW pair | ||
| IL_1VW3_089 | No text annotation | ||
| IL_1VW3_092 | Isolated non-canonical cWW with bulges |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_1VW3_001 | 1/A/592:598, 1/A/664:666, 1/A/682:685 | No text annotation | geometric J3_8VTW_001 NA | |
| J3_1VW3_002 | 1/A/607:609, 1/A/623:627, 1/A/651:654 | No text annotation | geometric J3_8VTW_002 NA | |
| J3_1VW3_003 | 1/A/1329:1334, 1/A/1577:1580, 1/A/1590:1594 | No text annotation | ||
| J3_1VW3_004 | 1/A/1337:1340, 1/A/1557:1563, 1/A/1572:1574 | No text annotation | geometric J3_4V9F_006 J3_19545.2 | |
| J3_1VW3_005 | 1/A/1426:1432, 1/A/1489:1491, 1/A/1522:1527 | No text annotation | ||
| J3_1VW3_006 | 1/A/1626:1635, 1/A/1668:1672, 1/A/1887:1890 | No text annotation | ||
| J3_1VW3_007 | 1/A/1993:1995, 1/A/2091:2095, 1/A/2249:2254 | No text annotation | ||
| J3_1VW3_008 | 1/A/2783:2786, 1/A/2812:2814, 1/A/2828:2834 | No text annotation | geometric J3_5J7L_046 J3_32601.5 |
Problematic loops
No problematic loops
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