8IPD Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8IPD_001 | 1/2/37:44 | No text annotation | homologous HL_8C3A_001 NA | |
| HL_8IPD_002 | 1/2/68:73 | No text annotation | homologous HL_8C3A_002 NA | |
| HL_8IPD_003 | 1/2/89:95 | No text annotation | homologous HL_8C3A_003 NA | |
| HL_8IPD_004 | 1/2/131:137 | No text annotation | geometric HL_2Y8W_001 HL_40612.1 | |
| HL_8IPD_005 | 1/2/204:211 | T-loop with 2 stacked bulged bases | homologous HL_5TBW_005 NA | |
| HL_8IPD_006 | 1/2/222:226 | No text annotation | homologous HL_5TBW_006 NA | |
| HL_8IPD_007 | 1/2/230:238 | T-loop with unstacked turn | homologous HL_8C3A_007 NA | |
| HL_8IPD_008 | 1/2/289:298 | No text annotation | homologous HL_5TBW_008 NA | |
| HL_8IPD_009 | 1/2/314:323 | Pseudoknot geometry | homologous HL_8C3A_009 NA | |
| HL_8IPD_080 | 1/2/368:373 | GNRA | homologous HL_8C3A_010 NA | |
| HL_8IPD_081 | 1/2/393:398 | GNRA | homologous HL_8C3A_011 NA | |
| HL_8IPD_083 | 1/2/1364:1373 | No text annotation | ||
| HL_8IPD_019 | 1/2/1389:1394 | GNRA | homologous HL_8C3A_016 NA | |
| HL_8IPD_021 | 1/2/1436:1448 | No text annotation | ||
| HL_8IPD_022 | 1/2/1480:1484 | No text annotation | ||
| HL_8IPD_024 | 1/2/1593:1602 | No text annotation | homologous HL_8C3A_020 NA | |
| HL_8IPD_025 | 1/2/1627:1635 | No text annotation | homologous HL_8C3A_021 NA | |
| HL_8IPD_026 | 1/2/1673:1682 | No text annotation | ||
| HL_8IPD_029 | 1/2/1864:1870 | Other HL | geometric HL_4V9F_039 HL_67772.1 | |
| HL_8IPD_030 | 1/2/1886:1893 | No text annotation | homologous HL_5TBW_026 NA | |
| HL_8IPD_031 | 1/2/1978:1988 | No text annotation | homologous HL_8C3A_027 NA | |
| HL_8IPD_032 | 1/2/2006:2013 | GNRA wlth tandem sheared | homologous HL_8C3A_028 NA | |
| HL_8IPD_033 | 1/2/2257:2261 | Mini UNCG | geometric HL_4V9F_041 HL_90436.2 | |
| HL_8IPD_034 | 1/2/2317:2322 | GNRA | homologous HL_8C3A_030 NA | |
| HL_8IPD_035 | 1/2/2376:2384 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_031 NA | |
| HL_8IPD_036 | 1/2/2420:2426 | Pseudoknot geometry with 3' bulge | homologous HL_5TBW_032 NA | |
| HL_8IPD_037 | 1/2/2458:2463 | GNRA variation | homologous HL_8C3A_033 NA | |
| HL_8IPD_039 | 1/2/2523:2532 | No text annotation | geometric HL_5TBW_035 NA | |
| HL_8IPD_041 | 1/2/2578:2583 | GNRA | homologous HL_8C3A_036 NA | |
| HL_8IPD_042 | 1/2/2624:2632 | No text annotation | homologous HL_8C3A_037 NA | |
| HL_8IPD_043 | 1/2/2664:2670 | Other HL | geometric HL_4V9F_039 HL_67772.1 | |
| HL_8IPD_044 | 1/2/2704:2712 | No text annotation | geometric HL_5NFV_001 HL_69752.4 | |
| HL_8IPD_045 | 1/2/2738:2742 | No text annotation | homologous HL_8C3A_040 NA | |
| HL_8IPD_046 | 1/2/2792:2799 | No text annotation | homologous HL_8C3A_041 NA | |
| HL_8IPD_047 | 1/2/2810:2816 | GNRA | homologous HL_5TBW_042 NA | |
| HL_8IPD_048 | 1/2/2872:2877 | UNCG | geometric HL_4PMI_004 HL_61337.2 | |
| HL_8IPD_050 | 1/2/3614:3618 | No text annotation | ||
| HL_8IPD_051 | 1/2/3639:3649 | No text annotation | homologous HL_8C3A_046 NA | |
| HL_8IPD_052 | 1/2/3668:3674 | GNRA | geometric HL_4PQV_001 HL_34789.2 | |
| HL_8IPD_053 | 1/2/3724:3729 | GNRA | homologous HL_8C3A_048 NA | |
| HL_8IPD_054 | 1/2/3873:3882 | No text annotation | geometric HL_8C3A_006 NA | |
| HL_8IPD_088 | 1/2/4098:4111 | No text annotation | ||
| HL_8IPD_059 | 1/2/4250:4258 | No text annotation | homologous HL_5TBW_056 NA | |
| HL_8IPD_062 | 1/2/4352:4362 | No text annotation | geometric HL_2ZZM_002 HL_33487.1 | |
| HL_8IPD_084 | 1/2/4412:4430 | No text annotation | ||
| HL_8IPD_064 | 1/2/4474:4481 | No text annotation | homologous HL_5TBW_062 NA | |
| HL_8IPD_065 | 1/2/4497:4503 | Mini UNCG | geometric HL_4ZLD_001 HL_12626.2 | |
| HL_8IPD_066 | 1/2/4540:4545 | GNRA | homologous HL_5TBW_064 NA | |
| HL_8IPD_067 | 1/2/4603:4608 | GNRA | geometric HL_5J7L_197 NA | |
| HL_8IPD_068 | 1/2/4646:4651 | Ribsomal LSU H95 | homologous HL_8C3A_067 NA | |
| HL_8IPD_069 | 1/2/4688:4702 | No text annotation | geometric HL_5TBW_067 NA | |
| HL_8IPD_071 | 1/2/4907:4914 | No text annotation | geometric HL_5XUZ_001 HL_69752.4 | |
| HL_8IPD_072 | 1/2/4975:4983 | No text annotation | geometric HL_5J7L_201 NA | |
| HL_8IPD_076 | 1/8/47:56 | Pseudoknot with intercalation | geometric HL_4V9F_001 HL_17803.1 | |
| HL_8IPD_077 | 1/8/68:90 | No text annotation | homologous HL_8C3A_075 NA | |
| HL_8IPD_078 | 1/8/107:112 | No text annotation | homologous HL_5TBW_075 NA | |
| HL_8IPD_079 | 1/8/122:128 | No text annotation | geometric HL_4V88_198 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8IPD_010 | GNRA with extra cWW | ||
| HL_8IPD_011 | No text annotation | ||
| HL_8IPD_012 | No text annotation | ||
| HL_8IPD_013 | No text annotation | ||
| HL_8IPD_014 | No text annotation | ||
| HL_8IPD_082 | No text annotation | ||
| HL_8IPD_087 | No text annotation | ||
| HL_8IPD_015 | No text annotation | ||
| HL_8IPD_016 | No text annotation | ||
| HL_8IPD_017 | No text annotation | ||
| HL_8IPD_018 | No text annotation | ||
| HL_8IPD_020 | No text annotation | ||
| HL_8IPD_023 | GNRA | ||
| HL_8IPD_027 | No text annotation | ||
| HL_8IPD_028 | No text annotation | ||
| HL_8IPD_038 | No text annotation | ||
| HL_8IPD_040 | No text annotation | ||
| HL_8IPD_049 | No text annotation | ||
| HL_8IPD_055 | No text annotation | ||
| HL_8IPD_056 | No text annotation | ||
| HL_8IPD_057 | Externally structured | ||
| HL_8IPD_058 | No text annotation | ||
| HL_8IPD_060 | No text annotation | ||
| HL_8IPD_061 | GNRA | ||
| HL_8IPD_063 | No text annotation | ||
| HL_8IPD_085 | No text annotation | ||
| HL_8IPD_070 | No text annotation | ||
| HL_8IPD_086 | No text annotation | ||
| HL_8IPD_073 | No text annotation | ||
| HL_8IPD_074 | No text annotation | ||
| HL_8IPD_075 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8IPD_001 | 1/2/6:7, 1/8/149:151 | Single bulged C | homologous IL_8C3A_002 NA | |
| IL_8IPD_002 | 1/2/12:14, 1/8/143:144 | Single bulged U | homologous IL_8C3A_003 NA | |
| IL_8IPD_003 | 1/2/16:18, 1/8/139:141 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_01003.2 | |
| IL_8IPD_004 | 1/2/26:27, 1/2/55:57 | No text annotation | homologous IL_8C3A_004 NA | |
| IL_8IPD_005 | 1/2/30:37, 1/2/44:52 | 9x8 Sarcin-Ricin; G-bulge | geometric IL_4WF9_008 IL_93502.1 | |
| IL_8IPD_006 | 1/2/81:88, 1/2/96:102 | No text annotation | homologous IL_8C3A_006 NA | |
| IL_8IPD_007 | 1/2/118:122, 1/2/147:153 | No text annotation | ||
| IL_8IPD_008 | 1/2/125:126, 1/2/142:144 | Single bulged C | geometric IL_1DQF_001 NA | |
| IL_8IPD_009 | 1/2/169:173, 1/2/263:266 | No text annotation | ||
| IL_8IPD_010 | 1/2/180:189, 1/2/252:256 | No text annotation | ||
| IL_8IPD_011 | 1/2/195:196, 1/2/244:246 | Single bulged C | geometric IL_1S03_006 IL_05642.2 | |
| IL_8IPD_012 | 1/2/199:201, 1/2/214:215 | Single bulged U | homologous IL_8C3A_013 NA | |
| IL_8IPD_013 | 1/2/339:342, 1/8/32:33 | Minor groove platform, major groove intercalation | geometric IL_1U9S_005 IL_55206.1 | |
| IL_8IPD_014 | 1/2/348:350, 1/8/25:26 | Single bulged A | homologous IL_8C3A_014 NA | |
| IL_8IPD_015 | 1/2/387:390, 1/2/401:414 | No text annotation | geometric IL_8C3A_015 NA | |
| IL_8IPD_016 | 1/2/415:421, 1/8/13:19 | Triple sheared with non-canonical cWW | homologous IL_5TBW_015 NA | |
| IL_8IPD_017 | 1/2/443:446, 1/2/1300:1304 | No text annotation | geometric IL_6AZ4_001 NA | |
| IL_8IPD_018 | 1/2/448:450, 1/2/1297:1298 | Single bulged C | geometric IL_4C7O_003 IL_05642.2 | |
| IL_8IPD_019 | 1/2/459:460, 1/2/695:697 | Single bulged C | geometric IL_3W3S_001 IL_05642.2 | |
| IL_8IPD_020 | 1/2/462:464, 1/2/691:693 | Isolated non-canonical cWW pair | geometric IL_4J50_002 IL_01003.2 | |
| IL_8IPD_021 | 1/2/466:472, 1/2/682:689 | No text annotation | ||
| IL_8IPD_022 | 1/2/482:485, 1/2/671:672 | Major groove intercalation | geometric IL_1U9S_003 IL_71421.2 | |
| IL_8IPD_023 | 1/2/487:488, 1/2/665:669 | Minor groove platform | geometric IL_5J7L_247 NA | |
| IL_8IPD_024 | 1/2/491:499, 1/2/655:662 | No text annotation | ||
| IL_8IPD_025 | 1/2/500:505, 1/2/653:654 | Multiple bulged bases | geometric IL_1R3E_001 IL_05670.1 | |
| IL_8IPD_026 | 1/2/508:510, 1/2/649:650 | Single bulged A | geometric IL_2VPL_002 IL_14190.2 | |
| IL_8IPD_029 | 1/2/709:710, 1/2/1286:1288 | Single bulged G | geometric IL_4LFB_036 IL_28408.2 | |
| IL_8IPD_030 | 1/2/723:724, 1/2/942:945 | Multiple bulged bases | geometric IL_7V9E_001 NA | |
| IL_8IPD_031 | 1/2/727:731, 1/2/938:939 | No text annotation | ||
| IL_8IPD_032 | 1/2/732:735, 1/2/928:937 | No text annotation | ||
| IL_8IPD_033 | 1/2/737:740, 1/2/924:926 | No text annotation | ||
| IL_8IPD_034 | 1/2/740:742, 1/2/922:924 | Isolated non-canonical cWW pair | geometric IL_4M4O_001 IL_01003.2 | |
| IL_8IPD_035 | 1/2/745:752, 1/2/911:919 | No text annotation | geometric IL_5TBW_020 NA | |
| IL_8IPD_038 | 1/2/1073:1074, 1/2/1237:1239 | Single bulged A | geometric IL_4R4V_003 IL_14190.2 | |
| IL_8IPD_040 | 1/2/1082:1084, 1/2/1213:1217 | Isolated cWH basepair | geometric IL_4KQ0_005 IL_10892.2 | |
| IL_8IPD_041 | 1/2/1086:1087, 1/2/1209:1211 | Single bulged C | geometric IL_3W3S_001 IL_05642.2 | |
| IL_8IPD_045 | 1/2/1244:1245, 1/2/1265:1267 | Single bulged G | geometric IL_4V88_442 NA | |
| IL_8IPD_047 | 1/2/1357:1360, 1/2/1379:1382 | No text annotation | ||
| IL_8IPD_176 | 1/2/1357:1361, 1/2/1376:1382 | No text annotation | ||
| IL_8IPD_048 | 1/2/1360:1361, 1/2/1376:1379 | Major groove intercalation | geometric IL_1U9S_003 IL_71421.2 | |
| IL_8IPD_050 | 1/2/1425:1429, 1/2/1455:1460 | No text annotation | geometric IL_3BBM_001 IL_47352.2 | |
| IL_8IPD_051 | 1/2/1431:1434, 1/2/1450:1453 | Double sheared | geometric IL_1SA9_002 IL_58355.2 | |
| IL_8IPD_052 | 1/2/1467:1468, 1/2/1496:1498 | Single bulged A | homologous IL_8C3A_026 NA | |
| IL_8IPD_054 | 1/2/1479:1480, 1/2/1484:1486 | No text annotation | ||
| IL_8IPD_177 | 1/2/1520:1522, 1/2/1655:1657 | Isolated non-canonical cWW pair | homologous IL_8P9A_255 IL_01003.2 | |
| IL_8IPD_178 | 1/2/1522:1526, 1/2/1648:1655 | No text annotation | homologous IL_8P9A_256 IL_73855.1 | |
| IL_8IPD_056 | 1/2/1545:1546, 1/2/1612:1614 | Single bulged A | geometric IL_7RQB_019 NA | |
| IL_8IPD_057 | 1/2/1550:1551, 1/2/1576:1578 | Single bulged G | homologous IL_8C3A_032 NA | |
| IL_8IPD_058 | 1/2/1551:1555, 1/2/1572:1576 | Triple sheared | homologous IL_8C3A_033 NA | |
| IL_8IPD_179 | 1/2/1586:1589, 1/2/1605:1607 | Major groove platform with extra cWW | homologous IL_8C3A_034 NA | |
| IL_8IPD_060 | 1/2/1590:1592, 1/2/1603:1604 | Single bulged U | geometric IL_7A0S_075 IL_97561.2 | |
| IL_8IPD_061 | 1/2/1624:1626, 1/2/1636:1640 | No text annotation | homologous IL_8C3A_036 NA | |
| IL_8IPD_062 | 1/2/1671:1673, 1/2/1682:1684 | Isolated non-canonical cWW pair | homologous IL_5TBW_034 NA | |
| IL_8IPD_063 | 1/2/1686:1688, 1/2/1848:1851 | No text annotation | ||
| IL_8IPD_065 | 1/2/1723:1725, 1/2/1838:1839 | Single bulged G | homologous IL_8C3A_040 NA | |
| IL_8IPD_067 | 1/2/1858:1860, 1/2/1874:1876 | Isolated non-canonical cWW pair | homologous IL_8C3A_049 NA | |
| IL_8IPD_180 | 1/2/1860:1862, 1/2/1872:1874 | No text annotation | homologous IL_8P9A_275 NA | |
| IL_8IPD_181 | 1/2/1905:1909, 1/2/2067:2071 | UAA/GAN | homologous IL_8C3A_051 NA | |
| IL_8IPD_070 | 1/2/1911:1918, 1/2/2064:2065 | SSU/LSU pseudoknot | geometric IL_7RQB_037 NA | |
| IL_8IPD_071 | 1/2/1918:1920, 1/2/2063:2064 | No text annotation | ||
| IL_8IPD_072 | 1/2/1920:1922, 1/2/2062:2063 | No text annotation | ||
| IL_8IPD_073 | 1/2/1926:1933, 1/2/2053:2058 | No text annotation | homologous IL_8C3A_054 NA | |
| IL_8IPD_075 | 1/2/1946:1948, 1/2/2035:2036 | Single bulged U | homologous IL_5TBW_053 NA | |
| IL_8IPD_076 | 1/2/1957:1965, 1/2/2022:2026 | Kink-turn | homologous IL_8C3A_057 NA | |
| IL_8IPD_078 | 1/2/1973:1977, 1/2/1989:1993 | No text annotation | homologous IL_8C3A_058 NA | |
| IL_8IPD_079 | 1/2/2001:2005, 1/2/2014:2016 | Major groove platform with extra cWW | geometric IL_1MMS_002 NA | |
| IL_8IPD_080 | 1/2/2083:2085, 1/2/2272:2273 | Single bulged C | geometric IL_4C7O_003 IL_05642.2 | |
| IL_8IPD_081 | 1/2/2290:2292, 1/2/2342:2345 | No text annotation | homologous IL_8C3A_061 NA | |
| IL_8IPD_083 | 1/2/2299:2301, 1/2/2334:2335 | Single bulged A | homologous IL_8C3A_062 NA | |
| IL_8IPD_084 | 1/2/2302:2309, 1/2/2329:2333 | Kink-turn | homologous IL_5TBW_059 NA | |
| IL_8IPD_085 | 1/2/2312:2314, 1/2/2325:2326 | Single bulged A | geometric IL_7RQB_033 NA | |
| IL_8IPD_182 | 1/2/2358:2364, 1/2/3858:3863 | No text annotation | homologous IL_8C3A_065 NA | |
| IL_8IPD_087 | 1/2/2415:2419, 1/2/2427:2429 | Minor groove platform | geometric IL_5J7L_041 NA | |
| IL_8IPD_088 | 1/2/2446:2450, 1/2/2509:2514 | UAA/GAN | homologous IL_8C3A_067 NA | |
| IL_8IPD_092 | 1/2/2542:2547, 1/2/2772:2774 | Decoding loop related | geometric IL_3C3Z_002 IL_53541.1 | |
| IL_8IPD_093 | 1/2/2549:2550, 1/2/2768:2770 | Single bulged U | geometric IL_2A64_002 IL_97561.2 | |
| IL_8IPD_096 | 1/2/2589:2593, 1/2/2752:2756 | Triple sheared | homologous IL_8P9A_295 IL_15190.2 | |
| IL_8IPD_097 | 1/2/2613:2614, 1/2/2724:2726 | Single bulged A | geometric IL_7A0S_012 IL_14190.2 | |
| IL_8IPD_098 | 1/2/2614:2615, 1/2/2722:2724 | Single stack bend | homologous IL_8C3A_076 NA | |
| IL_8IPD_099 | 1/2/2646:2648, 1/2/2685:2688 | Isolated tHS basepair with bulges | geometric IL_4V9F_076 IL_87316.1 | |
| IL_8IPD_100 | 1/2/2651:2653, 1/2/2681:2682 | Single bulged G | geometric IL_7D7W_002 IL_28408.2 | |
| IL_8IPD_101 | 1/2/2656:2662, 1/2/2672:2678 | Kink-turn | homologous IL_5TBW_073 NA | |
| IL_8IPD_102 | 1/2/2832:2838, 1/2/3850:3853 | No text annotation | homologous IL_8C3A_080 NA | |
| IL_8IPD_103 | 1/2/2844:2846, 1/2/3842:3844 | No text annotation | homologous IL_8C3A_081 NA | |
| IL_8IPD_104 | 1/2/2847:2850, 1/2/3840:3841 | Major groove platform; stack outside cWW | geometric IL_5TBW_076 NA | |
| IL_8IPD_184 | 1/2/2847:2855, 1/2/3837:3841 | No text annotation | homologous IL_8P9A_305 IL_80252.1 | |
| IL_8IPD_105 | 1/2/2850:2855, 1/2/3837:3840 | No text annotation | homologous IL_8C3A_083 NA | |
| IL_8IPD_106 | 1/2/2867:2872, 1/2/2877:2883 | No text annotation | homologous IL_8C3A_084 NA | |
| IL_8IPD_107 | 1/2/2889:2891, 1/2/3610:3612 | Isolated non-canonical cWW pair | homologous IL_5TBW_079 NA | |
| IL_8IPD_108 | 1/2/2896:2897, 1/2/3602:3605 | No text annotation | homologous IL_8C3A_086 NA | |
| IL_8IPD_111 | 1/2/3632:3633, 1/2/3827:3829 | Single bulged A | homologous IL_8C3A_087 NA | |
| IL_8IPD_112 | 1/2/3660:3665, 1/2/3677:3684 | Kink-turn related | homologous IL_5TBW_083 NA | |
| IL_8IPD_114 | 1/2/3700:3703, 1/2/3749:3750 | Minor groove platform, major groove intercalation | geometric IL_5J7L_314 NA | |
| IL_8IPD_116 | 1/2/3708:3710, 1/2/3741:3742 | Single stack bend | homologous IL_8C3A_091 NA | |
| IL_8IPD_120 | 1/2/3895:3898, 1/2/4563:4565 | No text annotation | homologous IL_8C3A_096 NA | |
| IL_8IPD_122 | 1/2/3900:3901, 1/2/4558:4561 | Major groove platform | geometric IL_7RQB_078 NA | |
| IL_8IPD_123 | 1/2/3913:3915, 1/2/4388:4389 | Single bulged U | homologous IL_8C3A_098 NA | |
| IL_8IPD_124 | 1/2/3916:3917, 1/2/4384:4387 | Minor groove platform | homologous IL_5TBW_094 NA | |
| IL_8IPD_126 | 1/2/3927:3929, 1/2/4181:4184 | No text annotation | homologous IL_8C3A_100 NA | |
| IL_8IPD_127 | 1/2/4082:4088, 1/2/4161:4164 | No text annotation | homologous IL_5TBW_096 NA | |
| IL_8IPD_185 | 1/2/4241:4243, 1/2/4267:4283 | No text annotation | ||
| IL_8IPD_133 | 1/2/4347:4350, 1/2/4364:4365 | Multiple bulged bases | geometric IL_4V88_392 NA | |
| IL_8IPD_134 | 1/2/4412:4418, 1/2/4426:4430 | No text annotation | ||
| IL_8IPD_135 | 1/2/4456:4458, 1/2/4520:4524 | Isolated non-canonical cWW with bulges | geometric IL_5TBW_108 NA | |
| IL_8IPD_136 | 1/2/4458:4459, 1/2/4517:4520 | No text annotation | homologous IL_8C3A_117 NA | |
| IL_8IPD_137 | 1/2/4466:4468, 1/2/4489:4491 | Isolated non-canonical cWW pair | homologous IL_8C3A_118 NA | |
| IL_8IPD_187 | 1/2/4466:4470, 1/2/4485:4491 | No text annotation | ||
| IL_8IPD_138 | 1/2/4468:4470, 1/2/4485:4489 | No text annotation | ||
| IL_8IPD_140 | 1/2/4495:4497, 1/2/4503:4505 | Isolated non-canonical cWW pair | homologous IL_5TBW_112 NA | |
| IL_8IPD_141 | 1/2/4537:4538, 1/2/4547:4549 | Minor groove platform | geometric IL_7A0S_028 IL_34520.2 | |
| IL_8IPD_142 | 1/2/4580:4582, 1/2/4721:4723 | No text annotation | geometric IL_3ICQ_003 NA | |
| IL_8IPD_143 | 1/2/4582:4585, 1/2/4717:4721 | Other IL | geometric IL_4WF9_054 IL_74317.1 | |
| IL_8IPD_188 | 1/2/4590:4592, 1/2/4618:4620 | Isolated non-canonical cWW pair | homologous IL_8P9A_343 IL_71625.2 | |
| IL_8IPD_144 | 1/2/4596:4603, 1/2/4608:4614 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_8C3A_125 NA | |
| IL_8IPD_146 | 1/2/4624:4629, 1/2/4669:4673 | No text annotation | ||
| IL_8IPD_189 | 1/2/4632:4637, 1/2/4662:4666 | No text annotation | homologous IL_8P9A_346 IL_98200.1 | |
| IL_8IPD_148 | 1/2/4638:4640, 1/2/4659:4661 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10892.2 | |
| IL_8IPD_149 | 1/2/4641:4642, 1/2/4655:4658 | Multiple bulged bases | homologous IL_5TBW_119 NA | |
| IL_8IPD_190 | 1/2/4681:4685, 1/2/4705:4709 | UAA/GAN | homologous IL_8P9A_348 IL_08938.1 | |
| IL_8IPD_151 | 1/2/4739:4742, 1/2/4958:4960 | Isolated non-canonical cWW pair | homologous IL_8C3A_130 NA | |
| IL_8IPD_152 | 1/2/4743:4746, 1/2/4954:4957 | Tandem non-canonical cWW pairs | geometric IL_5TBW_100 NA | |
| IL_8IPD_153 | 1/2/4749:4751, 1/2/4948:4951 | No text annotation | ||
| IL_8IPD_154 | 1/2/4756:4765, 1/2/4869:4877 | No text annotation | ||
| IL_8IPD_155 | 1/2/4769:4771, 1/2/4863:4865 | Isolated non-canonical cWW pair | geometric IL_1YZ9_001 NA | |
| IL_8IPD_156 | 1/2/4885:4889, 1/2/4930:4934 | Triple non-canonical cWW pairs | geometric IL_8S95_002 IL_71154.2 | |
| IL_8IPD_157 | 1/2/4891:4896, 1/2/4924:4928 | No text annotation | ||
| IL_8IPD_158 | 1/2/4899:4901, 1/2/4920:4921 | Single bulged C | geometric IL_1DQF_001 NA | |
| IL_8IPD_159 | 1/2/4972:4975, 1/2/4983:4986 | Tandem non-canonical cWW pairs | homologous IL_8C3A_135 NA | |
| IL_8IPD_160 | 1/2/4992:4994, 1/2/5057:5059 | Isolated non-canonical cWW pair | geometric IL_3D0U_006 IL_01003.2 | |
| IL_8IPD_161 | 1/2/4996:4997, 1/2/5053:5055 | Single bulged C | geometric IL_1KUQ_002 IL_05642.2 | |
| IL_8IPD_162 | 1/2/5000:5002, 1/2/5045:5050 | No text annotation | homologous IL_8C3A_138 NA | |
| IL_8IPD_163 | 1/2/5003:5009, 1/2/5039:5044 | No text annotation | ||
| IL_8IPD_164 | 1/2/5012:5014, 1/2/5035:5036 | Single bulged C | geometric IL_4WF9_035 IL_05642.2 | |
| IL_8IPD_165 | 1/2/5014:5017, 1/2/5032:5035 | Double sheared; A in syn | homologous IL_8C3A_141 NA | |
| IL_8IPD_170 | 1/3/71:79, 1/3/97:104 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_8C3A_148 NA | |
| IL_8IPD_191 | 1/3/71:82, 1/3/94:104 | No text annotation | ||
| IL_8IPD_171 | 1/3/79:82, 1/3/94:97 | Tandem non-canonical cWW pairs | geometric IL_6JDV_002 IL_15225.2 | |
| IL_8IPD_172 | 1/3/82:85, 1/3/92:94 | Decoding loop related | geometric IL_5Z1I_003 NA | |
| IL_8IPD_173 | 1/8/64:66, 1/8/92:95 | Isolated non-canonical cWW pair | homologous IL_5TBW_145 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8IPD_027 | No text annotation | ||
| IL_8IPD_174 | No text annotation | ||
| IL_8IPD_028 | Stack and bulge | ||
| IL_8IPD_036 | Isolated non-canonical cWW pair | ||
| IL_8IPD_037 | Isolated non-canonical cWW pair | ||
| IL_8IPD_039 | No text annotation | ||
| IL_8IPD_042 | No text annotation | ||
| IL_8IPD_175 | No text annotation | ||
| IL_8IPD_043 | No text annotation | ||
| IL_8IPD_044 | No text annotation | ||
| IL_8IPD_046 | Isolated non-canonical cWW pair | ||
| IL_8IPD_049 | Isolated cWH basepair | ||
| IL_8IPD_053 | Single stack bend with SAM intercalation | ||
| IL_8IPD_055 | No text annotation | ||
| IL_8IPD_059 | No text annotation | ||
| IL_8IPD_064 | No text annotation | ||
| IL_8IPD_066 | Single bulged G | ||
| IL_8IPD_068 | No text annotation | ||
| IL_8IPD_069 | No text annotation | ||
| IL_8IPD_074 | No text annotation | ||
| IL_8IPD_077 | Isolated non-canonical cWW pair | ||
| IL_8IPD_082 | Isolated non-canonical cWW pair | ||
| IL_8IPD_086 | Tandem non-canonical cWW pairs | ||
| IL_8IPD_089 | Minor groove platform | ||
| IL_8IPD_183 | No text annotation | ||
| IL_8IPD_090 | No text annotation | ||
| IL_8IPD_091 | Isolated non-canonical cWW pair | ||
| IL_8IPD_094 | Isolated non-canonical cWW pair | ||
| IL_8IPD_095 | No text annotation | ||
| IL_8IPD_109 | No text annotation | ||
| IL_8IPD_110 | No text annotation | ||
| IL_8IPD_113 | Isolated non-canonical cWW pair | ||
| IL_8IPD_115 | Major groove intercalation | ||
| IL_8IPD_117 | No text annotation | ||
| IL_8IPD_118 | No text annotation | ||
| IL_8IPD_119 | Isolated non-canonical cWW pair | ||
| IL_8IPD_121 | Isolated non-canonical cWW pair | ||
| IL_8IPD_125 | Isolated non-canonical cWW pair | ||
| IL_8IPD_128 | No text annotation | ||
| IL_8IPD_186 | No text annotation | ||
| IL_8IPD_129 | Tandem non-canonical cWW pairs | ||
| IL_8IPD_130 | Isolated non-canonical cWW pair | ||
| IL_8IPD_131 | Single stack bend | ||
| IL_8IPD_132 | Isolated non-canonical cWW pair | ||
| IL_8IPD_139 | Stack and bulge | ||
| IL_8IPD_145 | Isolated non-canonical cWW pair | ||
| IL_8IPD_147 | Triple sheared related | ||
| IL_8IPD_150 | UAA/GAN with extra cWW | ||
| IL_8IPD_166 | Single bulged A | ||
| IL_8IPD_167 | Minor groove platform related | ||
| IL_8IPD_168 | No text annotation | ||
| IL_8IPD_169 | Symmetric double minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8IPD_001 | 1/2/112:116, 1/2/155:160, 1/2/275:278 | No text annotation | ||
| J3_8IPD_012 | 1/2/351:367, 1/2/374:379, 1/8/21:24 | No text annotation | homologous J3_8P9A_045 J3_07616.1 | |
| J3_8IPD_013 | 1/2/380:387, 1/2/414:415, 1/8/19:20 | No text annotation | geometric J3_5TBW_002 NA | |
| J3_8IPD_014 | 1/2/380:390, 1/2/401:415, 1/8/19:20 | No text annotation | homologous J3_8P9A_047 J3_17917.1 | |
| J3_8IPD_015 | 1/2/451:455, 1/2/701:705, 1/2/1292:1296 | No text annotation | ||
| J3_8IPD_016 | 1/2/712:713, 1/2/955:976, 1/2/1278:1284 | No text annotation | ||
| J3_8IPD_002 | 1/2/1531:1537, 1/2/1622:1624, 1/2/1640:1643 | No text annotation | homologous J3_5TBW_004 NA | |
| J3_8IPD_003 | 1/2/1546:1548, 1/2/1580:1584, 1/2/1609:1612 | No text annotation | homologous J3_8C3A_004 NA | |
| J3_8IPD_017 | 1/2/1726:1727, 1/2/1802:1806, 1/2/1832:1837 | No text annotation | homologous J3_8P9A_051 J3_84137.1 | |
| J3_8IPD_004 | 1/2/1969:1971, 1/2/1995:2001, 1/2/2016:2018 | No text annotation | homologous J3_5TBW_007 NA | |
| J3_8IPD_005 | 1/2/2393:2399, 1/2/2805:2807, 1/2/2819:2822 | No text annotation | homologous J3_8C3A_006 NA | |
| J3_8IPD_006 | 1/2/2402:2405, 1/2/2785:2791, 1/2/2800:2802 | No text annotation | homologous J3_8P9A_054 J3_76012.1 | |
| J3_8IPD_018 | 1/2/2440:2445, 1/2/2515:2519, 1/2/2536:2537 | No text annotation | homologous J3_8P9A_055 J3_94309.1 | |
| J3_8IPD_019 | 1/2/2451:2456, 1/2/2465:2476, 1/2/2501:2508 | No text annotation | homologous J3_8CRE_016 NA | |
| J3_8IPD_007 | 1/2/2551:2555, 1/2/2572:2575, 1/2/2757:2767 | No text annotation | ||
| J3_8IPD_020 | 1/2/2575:2576, 1/2/2585:2589, 1/2/2756:2757 | No text annotation | homologous J3_8C3A_054 NA | |
| J3_8IPD_021 | 1/2/2598:2602, 1/2/2737:2738, 1/2/2742:2747 | No text annotation | homologous J3_8P9A_058 J3_08594.1 | |
| J3_8IPD_008 | 1/2/3937:3939, 1/2/4074:4078, 1/2/4168:4173 | Kink-turn 3-way junction | geometric J3_5J7L_044 NA | |
| J3_8IPD_022 | 1/2/4091:4097, 1/2/4112:4129, 1/2/4155:4158 | No text annotation | ||
| J3_8IPD_009 | 1/2/4463:4466, 1/2/4491:4493, 1/2/4507:4513 | No text annotation | homologous J3_8C3A_011 NA | |
| J3_8IPD_023 | 1/2/4751:4754, 1/2/4879:4883, 1/2/4936:4948 | No text annotation | ||
| J3_8IPD_010 | 1/2/4970:4972, 1/2/4986:4991, 1/2/5060:5063 | No text annotation | ||
| J3_8IPD_024 | 1/3/9:14, 1/3/65:66, 1/3/109:110 | No text annotation | homologous J3_8C3A_059 NA | |
| J3_8IPD_025 | 1/8/44:45, 1/8/58:64, 1/8/95:99 | No text annotation | homologous J3_8C3A_060 NA | |
| J4_8IPD_001 | 1/2/111:112, 1/2/278:283, 1/2/304:310, 1/2/327:330 | No text annotation | homologous J4_8P9A_012 J4_94698.1 | |
| J4_8IPD_002 | 1/2/196:199, 1/2/215:222, 1/2/226:228, 1/2/240:244 | No text annotation | ||
| J4_8IPD_008 | 1/2/981:983, 1/2/1070:1072, 1/2/1240:1243, 1/2/1268:1273 | No text annotation | ||
| J4_8IPD_004 | 1/2/2365:2371, 1/2/2389:2391, 1/2/2824:2829, 1/2/3856:3857 | No text annotation | ||
| J4_8IPD_005 | 1/2/2406:2410, 1/2/2434:2439, 1/2/2538:2539, 1/2/2777:2784 | No text annotation | homologous J4_8P9A_015 J4_47264.1 | |
| J4_8IPD_006 | 1/2/2618:2619, 1/2/2637:2642, 1/2/2692:2698, 1/2/2718:2719 | No text annotation | ||
| J4_8IPD_007 | 1/2/4587:4590, 1/2/4620:4621, 1/2/4676:4678, 1/2/4712:4715 | No text annotation | ||
| J5_8IPD_001 | 1/2/19:21, 1/8/35:42, 1/8/101:106, 1/8/113:114, 1/8/136:138 | No text annotation | homologous J5_8P9A_010 J5_27223.1 | |
| J5_8IPD_002 | 1/2/1335:1340, 1/2/1516:1519, 1/2/1658:1661, 1/2/2288:2290, 1/2/2345:2351 | No text annotation | homologous J5_8C3A_002 NA | |
| J5_8IPD_003 | 1/2/2855:2863, 1/2/2887:2888, 1/2/3613:3614, 1/2/3618:3626, 1/2/3835:3837 | No text annotation | homologous J5_8C3A_004 NA | |
| J6_8IPD_001 | 1/2/21:26, 1/2/57:67, 1/2/74:78, 1/2/105:109, 1/2/332:339, 1/8/33:35 | No text annotation | ||
| J6_8IPD_002 | 1/2/1352:1355, 1/2/1384:1388, 1/2/1395:1399, 1/2/1418:1421, 1/2/1464:1466, 1/2/1499:1504 | No text annotation | ||
| J7_8IPD_001 | 1/2/1666:1671, 1/2/1684:1685, 1/2/1852:1855, 1/2/1879:1884, 1/2/1895:1899, 1/2/2077:2078, 1/2/2278:2283 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8IPD_011 | No text annotation | ||
| J4_8IPD_003 | No text annotation |
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