RNA 3D Hub //

3J7Q Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J7Q_0771/5/30:52No text annotation
HL_3J7Q_0011/5/37:44No text annotation
geometric
HL_4WF9_006
HL_30068.2
HL_3J7Q_0021/5/68:73No text annotation
homologous
HL_5TBW_002
NA
HL_3J7Q_0031/5/89:95No text annotation
homologous
HL_8C3A_003
NA
HL_3J7Q_0041/5/131:137No text annotation
homologous
HL_8C3A_004
NA
HL_3J7Q_0051/5/204:211T-loop with 2 stacked bulged bases
homologous
HL_8C3A_005
NA
HL_3J7Q_0061/5/222:226No text annotation
homologous
HL_8C3A_006
NA
HL_3J7Q_0071/5/230:238T-loop with unstacked turn
homologous
HL_8C3A_007
NA
HL_3J7Q_0791/5/285:302No text annotation
HL_3J7Q_0081/5/289:298No text annotation
HL_3J7Q_0091/5/314:323Pseudoknot geometry
homologous
HL_5TBW_009
NA
HL_3J7Q_0101/5/368:373GNRA
homologous
HL_8C3A_010
NA
HL_3J7Q_0111/5/393:398GNRA
homologous
HL_5TBW_011
NA
HL_3J7Q_0811/5/996:1047No text annotation
HL_3J7Q_0821/5/1172:1189No text annotation
HL_3J7Q_0121/5/1178:1183GNRA
geometric
HL_5J7L_007
HL_37824.7
HL_3J7Q_0131/5/1252:1258GNRA
geometric
HL_4LFB_012
HL_37824.7
HL_3J7Q_0141/5/1317:1326T-loop with 2 stacked bulged bases
homologous
HL_8C3A_014
NA
HL_3J7Q_0151/5/1364:1373No text annotation
HL_3J7Q_0161/5/1406:1411No text annotation
HL_3J7Q_0171/5/1436:1448No text annotation
HL_3J7Q_0181/5/1479:1486No text annotation
geometric
HL_2ZNI_001
HL_75660.5
HL_3J7Q_0191/5/1561:1566GNRA
homologous
HL_5TBW_019
NA
HL_3J7Q_0201/5/1593:1602No text annotation
geometric
HL_4V9F_024
HL_88205.2
HL_3J7Q_0211/5/1627:1635No text annotation
homologous
HL_8C3A_021
NA
HL_3J7Q_0221/5/1675:1680Externally structured
homologous
HL_8C3A_022
NA
HL_3J7Q_0231/5/1763:1769GNRA
geometric
HL_3RG5_007
HL_37824.7
HL_3J7Q_0241/5/1814:1823No text annotation
HL_3J7Q_0921/5/1864:1870GNRA
homologous
HL_8P9A_137
HL_37824.7
HL_3J7Q_0261/5/1886:1893No text annotation
homologous
HL_5TBW_026
NA
HL_3J7Q_0851/5/1978:1988No text annotation
HL_3J7Q_0281/5/2006:2013GNRA wlth tandem sheared
homologous
HL_8C3A_028
NA
HL_3J7Q_0291/5/2130:2244Mini UNCG
geometric
HL_8C3A_198
NA
HL_3J7Q_0301/5/2317:2322GNRA
homologous
HL_8C3A_030
NA
HL_3J7Q_0311/5/2376:2384T-loop with 2 stacked bulged bases
homologous
HL_8C3A_031
NA
HL_3J7Q_0321/5/2420:2426Pseudoknot geometry with 3' bulge
homologous
HL_5TBW_032
NA
HL_3J7Q_0331/5/2458:2463GNRA variation
homologous
HL_8C3A_033
NA
HL_3J7Q_0341/5/2487:2491No text annotation
geometric
HL_4O26_001
HL_35941.1
HL_3J7Q_0351/5/2522:2533No text annotation
HL_3J7Q_0361/5/2558:2569No text annotation
HL_3J7Q_0371/5/2578:2583GNRA
homologous
HL_8C3A_036
NA
HL_3J7Q_0861/5/2622:2634No text annotation
geometric
HL_5E6M_001
HL_99769.3
HL_3J7Q_0381/5/2623:2633No text annotation
HL_3J7Q_0391/5/2664:2670No text annotation
homologous
HL_8C3A_038
NA
HL_3J7Q_0401/5/2705:2710No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_3J7Q_0411/5/2738:2742No text annotation
homologous
HL_8C3A_040
NA
HL_3J7Q_0421/5/2792:2799No text annotation
geometric
HL_5TBW_041
NA
HL_3J7Q_0431/5/2810:2816GNRA
homologous
HL_5TBW_042
NA
HL_3J7Q_0441/5/2872:2877UNCG
geometric
HL_4PMI_004
HL_34617.5
HL_3J7Q_0871/5/2910:3584No text annotation
HL_3J7Q_0451/5/3614:3618No text annotation
homologous
HL_5TBW_045
NA
HL_3J7Q_0461/5/3639:3649No text annotation
homologous
HL_5TBW_046
NA
HL_3J7Q_0471/5/3667:3675No text annotation
geometric
HL_2Y9H_005
HL_86870.2
HL_3J7Q_0481/5/3724:3729GNRA
homologous
HL_8C3A_048
NA
HL_3J7Q_0491/5/3757:3767No text annotation
homologous
HL_5TBW_049
NA
HL_3J7Q_0881/5/3781:3811No text annotation
HL_3J7Q_0501/5/3795:3805No text annotation
HL_3J7Q_0511/5/3873:3882No text annotation
homologous
HL_5TBW_051
NA
HL_3J7Q_0531/5/4102:4107UNCG
geometric
HL_4PDB_001
HL_34617.5
HL_3J7Q_0541/5/4139:4145No text annotation
geometric
HL_6D12_001
HL_48417.5
HL_3J7Q_0551/5/4193:4201No text annotation
homologous
HL_8C3A_055
NA
HL_3J7Q_0561/5/4210:4222No text annotation
homologous
HL_8C3A_056
NA
HL_3J7Q_0571/5/4250:4258No text annotation
homologous
HL_8C3A_057
NA
HL_3J7Q_0581/5/4301:4309No text annotation
homologous
HL_8C3A_059
NA
HL_3J7Q_0591/5/4321:4326GNRA
homologous
HL_5TBW_059
NA
HL_3J7Q_0891/5/4347:4365No text annotation
HL_3J7Q_0601/5/4352:4362No text annotation
geometric
HL_4V83_139
NA
HL_3J7Q_0901/5/4412:4430No text annotation
HL_3J7Q_0611/5/4417:4425No text annotation
homologous
HL_5TBW_061
NA
HL_3J7Q_0621/5/4473:4481No text annotation
geometric
HL_5TBW_070
NA
HL_3J7Q_0631/5/4495:4505No text annotation
HL_3J7Q_0641/5/4540:4545GNRA
homologous
HL_5TBW_064
NA
HL_3J7Q_0651/5/4603:4608GNRA
homologous
HL_8C3A_066
NA
HL_3J7Q_0661/5/4644:4653No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_3J7Q_0671/5/4688:4702No text annotation
homologous
HL_8C3A_068
NA
HL_3J7Q_0681/5/4907:4914No text annotation
HL_3J7Q_0691/5/4972:4986No text annotation
HL_3J7Q_0701/5/5021:5028No text annotation
geometric
HL_8C3A_018
NA
HL_3J7Q_0711/7/36:41No text annotation
homologous
HL_5TBW_185
NA
HL_3J7Q_0721/7/86:91GNRA
homologous
HL_5TBW_186
NA
HL_3J7Q_0731/8/47:56Pseudoknot with intercalation
geometric
HL_4V9F_001
HL_93438.2
HL_3J7Q_0741/8/68:90No text annotation
homologous
HL_8C3A_075
NA
HL_3J7Q_0751/8/107:112No text annotation
HL_3J7Q_0761/8/121:129No text annotation
geometric
HL_4V88_194
NA

Problematic loops

#loop idProblemSequence
HL_3J7Q_078No text annotation
HL_3J7Q_080No text annotation
HL_3J7Q_083No text annotation
HL_3J7Q_084No text annotation
HL_3J7Q_025tRNA anticodon loop
HL_3J7Q_027No text annotation
HL_3J7Q_052No text annotation
HL_3J7Q_091No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J7Q_0011/5/6:7,
1/8/149:151		Single bulged C
homologous
IL_8C3A_002
NA
IL_3J7Q_1561/5/11:14,
1/8/143:145		Isolated non-canonical cWW pair
geometric
IL_4KNQ_003
IL_87907.2
IL_3J7Q_0021/5/12:14,
1/8/143:144		Single bulged U
homologous
IL_8P9A_232
IL_89505.4
IL_3J7Q_0031/5/16:18,
1/8/139:141		No text annotation
IL_3J7Q_1571/5/16:19,
1/8/138:141		Tandem non-canonical cWW pairs
geometric
IL_1D4R_003
IL_85033.2
IL_3J7Q_0041/5/26:29,
1/5/53:57		No text annotation
IL_3J7Q_0051/5/30:37,
1/5/44:52		9x8 Sarcin-Ricin; G-bulge
geometric
IL_4WF9_008
IL_84694.2
IL_3J7Q_0061/5/81:88,
1/5/96:102		No text annotation
homologous
IL_8C3A_006
NA
IL_3J7Q_0071/5/117:122,
1/5/147:154		No text annotation
IL_3J7Q_1591/5/123:127,
1/5/141:146		Partly complementary
geometric
IL_6CZR_167
NA
IL_3J7Q_0081/5/124:126,
1/5/142:145		No text annotation
IL_3J7Q_0091/5/160:161,
1/5/274:276		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_3J7Q_0101/5/168:173,
1/5/263:267		No text annotation
IL_3J7Q_0111/5/180:184,
1/5/253:256		No text annotation
geometric
IL_1GID_008
NA
IL_3J7Q_0121/5/184:189,
1/5/252:253		Major groove intercalation
geometric
IL_1NBS_009
IL_82107.4
IL_3J7Q_0131/5/199:201,
1/5/214:215		Single bulged U
homologous
IL_8C3A_013
NA
IL_3J7Q_0141/5/339:342,
1/8/32:33		Minor groove platform
geometric
IL_7RQB_073
NA
IL_3J7Q_0151/5/348:350,
1/8/25:26		Single bulged A
homologous
IL_5TBW_013
NA
IL_3J7Q_0161/5/387:390,
1/5/401:414		No text annotation
geometric
IL_5TBW_014
NA
IL_3J7Q_0171/5/415:421,
1/8/13:19		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA
IL_3J7Q_0181/5/443:446,
1/5/1300:1304		No text annotation
geometric
IL_7MLW_007
IL_99358.1
IL_3J7Q_0191/5/459:460,
1/5/695:697		Single bulged C
geometric
IL_1KUQ_002
IL_61258.15
IL_3J7Q_0201/5/462:464,
1/5/691:693		Isolated non-canonical cWW pair
geometric
IL_4AOB_005
IL_87907.2
IL_3J7Q_1971/5/464:473,
1/5/681:691		No text annotation
IL_3J7Q_0211/5/482:487,
1/5/669:672		No text annotation
IL_3J7Q_1621/5/482:496,
1/5/657:672		No text annotation
IL_3J7Q_0221/5/487:493,
1/5/661:669		No text annotation
IL_3J7Q_0231/5/493:496,
1/5/657:661		No text annotation
IL_3J7Q_0241/5/497:499,
1/5/655:656		No text annotation
IL_3J7Q_0251/5/500:505,
1/5/653:654		Single stack bend
geometric
IL_4V9F_005
IL_90729.1
IL_3J7Q_0261/5/508:510,
1/5/649:650		Single bulged A
geometric
IL_1U63_004
IL_31462.6
IL_3J7Q_1631/5/512:515,
1/5/646:647		Multiple bulged bases
geometric
IL_3MXH_004
IL_82107.4
IL_3J7Q_0281/5/708:709,
1/5/1287:1289		No text annotation
IL_3J7Q_0291/5/722:724,
1/5/942:946		No text annotation
IL_3J7Q_0301/5/726:731,
1/5/938:940		No text annotation
IL_3J7Q_0311/5/731:735,
1/5/928:938		No text annotation
IL_3J7Q_0321/5/735:737,
1/5/927:928		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_3J7Q_0331/5/740:742,
1/5/922:924		Isolated non-canonical cWW pair
geometric
IL_4V88_385
NA
IL_3J7Q_0341/5/745:750,
1/5/912:919		No text annotation
IL_3J7Q_1981/5/745:755,
1/5/908:919		No text annotation
IL_3J7Q_0351/5/750:755,
1/5/908:912		No text annotation
IL_3J7Q_1651/5/989:992,
1/5/1051:1064		No text annotation
IL_3J7Q_0371/5/1074:1079,
1/5/1221:1236		No text annotation
IL_3J7Q_0381/5/1081:1082,
1/5/1217:1219		No text annotation
IL_3J7Q_0391/5/1082:1085,
1/5/1212:1217		No text annotation
IL_3J7Q_0401/5/1086:1087,
1/5/1209:1211		Single bulged C
geometric
IL_7KGA_001
IL_61258.15
IL_3J7Q_1661/5/1094:1097,
1/5/1198:1202		No text annotation
geometric
IL_1HYS_004
IL_64231.5
IL_3J7Q_0411/5/1097:1098,
1/5/1197:1199		Multiple bulged bases
geometric
IL_7Q80_001
IL_84476.1
IL_3J7Q_0421/5/1172:1177,
1/5/1184:1189		No text annotation
IL_3J7Q_0431/5/1357:1361,
1/5/1376:1382		No text annotation
IL_3J7Q_0441/5/1425:1429,
1/5/1455:1460		No text annotation
IL_3J7Q_0451/5/1431:1434,
1/5/1450:1453		Double sheared
geometric
IL_4WF9_087
IL_09705.15
IL_3J7Q_0461/5/1467:1468,
1/5/1496:1498		Single bulged A
homologous
IL_8C3A_026
NA
IL_3J7Q_0471/5/1474:1478,
1/5/1487:1490		No text annotation
IL_3J7Q_0481/5/1520:1526,
1/5/1648:1657		No text annotation
IL_3J7Q_0491/5/1550:1551,
1/5/1576:1578		Single bulged G
geometric
IL_4V9F_026
IL_00225.13
IL_3J7Q_0501/5/1551:1555,
1/5/1572:1576		Triple sheared
homologous
IL_8C3A_033
NA
IL_3J7Q_0511/5/1586:1589,
1/5/1605:1607		Major groove platform with extra cWW
homologous
IL_8C3A_034
NA
IL_3J7Q_0521/5/1590:1592,
1/5/1603:1604		Single bulged U
homologous
IL_8C3A_035
NA
IL_3J7Q_0531/5/1624:1626,
1/5/1636:1640		Multiple bulged bases
geometric
IL_5J7L_265
IL_06549.2
IL_3J7Q_0541/5/1672:1674,
1/5/1681:1682		Single stack bend
geometric
IL_4V83_236
IL_90729.1
IL_3J7Q_0551/5/1686:1688,
1/5/1848:1851		No text annotation
IL_3J7Q_0561/5/1732:1737,
1/5/1792:1797		5x5 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_7A0S_027
NA
IL_3J7Q_0571/5/1737:1738,
1/5/1790:1792		Minor groove platform
homologous
IL_8C3A_042
NA
IL_3J7Q_0581/5/1739:1744,
1/5/1786:1789		C-loop with bulged stacked A's
homologous
IL_8C3A_043
NA
IL_3J7Q_0591/5/1746:1749,
1/5/1781:1784		Tandem non-canonical cWW pairs
geometric
IL_5TBW_041
NA
IL_3J7Q_1691/5/1746:1759,
1/5/1773:1784		No text annotation
IL_3J7Q_0601/5/1749:1751,
1/5/1779:1781		Isolated non-canonical cWW pair
homologous
IL_8C3A_045
NA
IL_3J7Q_0611/5/1751:1759,
1/5/1773:1779		No text annotation
IL_3J7Q_0621/5/1761:1763,
1/5/1769:1771		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_87907.2
IL_3J7Q_1711/5/1855:1860,
1/5/1874:1879		No text annotation
geometric
IL_5TBW_476
NA
IL_3J7Q_0631/5/1858:1860,
1/5/1874:1876		Isolated non-canonical cWW pair
homologous
IL_8C3A_049
NA
IL_3J7Q_0651/5/1905:1909,
1/5/2067:2071		UAA/GAN
homologous
IL_8C3A_051
NA
IL_3J7Q_0661/5/1911:1918,
1/5/2064:2065		Multiple bulged bases
geometric
IL_1R3E_002
IL_84476.1
IL_3J7Q_0671/5/1918:1920,
1/5/2063:2064		No text annotation
IL_3J7Q_0681/5/1920:1922,
1/5/2062:2063		No text annotation
geometric
IL_8CRE_390
IL_61258.15
IL_3J7Q_0691/5/1924:1933,
1/5/2053:2060		No text annotation
IL_3J7Q_0701/5/1933:1944,
1/5/2038:2053		No text annotation
geometric
IL_5TBW_052
NA
IL_3J7Q_0711/5/1945:1950,
1/5/2033:2037		No text annotation
IL_3J7Q_0721/5/1957:1967,
1/5/2020:2026		No text annotation
IL_3J7Q_0731/5/1973:1977,
1/5/1989:1993		No text annotation
homologous
IL_8C3A_058
NA
IL_3J7Q_0741/5/2001:2005,
1/5/2014:2016		Major groove platform with extra cWW
homologous
IL_8C3A_059
NA
IL_3J7Q_1751/5/2082:2085,
1/5/2272:2274		Isolated non-canonical cWW pair
geometric
IL_7A0S_042
IL_87907.2
IL_3J7Q_0751/5/2083:2085,
1/5/2272:2273		No text annotation
IL_3J7Q_1761/5/2087:2128,
1/5/2246:2270		No text annotation
IL_3J7Q_0761/5/2290:2292,
1/5/2342:2345		No text annotation
homologous
IL_8P9A_285
IL_42997.3
IL_3J7Q_1991/5/2290:2294,
1/5/2340:2345		Partly complementary
geometric
IL_7VYX_008
IL_49751.4
IL_3J7Q_0771/5/2299:2301,
1/5/2334:2335		Single bulged A
homologous
IL_8C3A_062
NA
IL_3J7Q_0781/5/2302:2309,
1/5/2329:2333		Kink-turn
homologous
IL_5TBW_059
NA
IL_3J7Q_0791/5/2310:2314,
1/5/2325:2328		No text annotation
IL_3J7Q_2001/5/2311:2315,
1/5/2324:2327		No text annotation
geometric
IL_8UIW_002
IL_77658.1
IL_3J7Q_0801/5/2358:2364,
1/5/3858:3863		7x6 Sarcin-Ricin; G-bulge
homologous
IL_8P9A_289
IL_26307.2
IL_3J7Q_0811/5/2415:2419,
1/5/2427:2429		C-loop
geometric
IL_7A0S_047
IL_83150.2
IL_3J7Q_0821/5/2446:2450,
1/5/2509:2514		UAA/GAN
homologous
IL_8C3A_067
NA
IL_3J7Q_0831/5/2477:2479,
1/5/2499:2500		Single stack bend
geometric
IL_4WF9_007
IL_90729.1
IL_3J7Q_0841/5/2542:2547,
1/5/2772:2774		Isolated non-canonical cWW pair
geometric
IL_5TBW_145
NA
IL_3J7Q_0851/5/2589:2593,
1/5/2752:2756		Triple sheared
homologous
IL_5TBW_067
NA
IL_3J7Q_2011/5/2598:2605,
1/5/2734:2747		No text annotation
IL_3J7Q_0861/5/2613:2614,
1/5/2724:2726		Single bulged C
homologous
IL_5TBW_069
NA
IL_3J7Q_0871/5/2614:2615,
1/5/2722:2724		Single stack bend
geometric
IL_4WF9_007
IL_90729.1
IL_3J7Q_0881/5/2642:2648,
1/5/2685:2692		No text annotation
IL_3J7Q_0891/5/2651:2653,
1/5/2681:2682		Single bulged G
geometric
IL_7D7W_002
IL_00225.13
IL_3J7Q_2021/5/2655:2662,
1/5/2672:2679		No text annotation
IL_3J7Q_0901/5/2656:2662,
1/5/2672:2678		No text annotation
IL_3J7Q_1821/5/2702:2705,
1/5/2710:2714		Tandem non-canonical cWW pairs
geometric
IL_4EYA_010
IL_51479.1
IL_3J7Q_0911/5/2703:2705,
1/5/2710:2713		No text annotation
IL_3J7Q_0921/5/2832:2838,
1/5/3850:3853		No text annotation
homologous
IL_5TBW_074
NA
IL_3J7Q_2031/5/2841:2846,
1/5/3842:3847		No text annotation
IL_3J7Q_0931/5/2844:2846,
1/5/3842:3844		No text annotation
homologous
IL_8C3A_081
NA
IL_3J7Q_0941/5/2847:2850,
1/5/3840:3841		Major groove platform; stack outside cWW
geometric
IL_5TBW_076
NA
IL_3J7Q_1841/5/2847:2855,
1/5/3837:3841		No text annotation
homologous
IL_8P9A_305
IL_22854.4
IL_3J7Q_0951/5/2850:2855,
1/5/3837:3840		No text annotation
homologous
IL_8C3A_083
NA
IL_3J7Q_0961/5/2867:2872,
1/5/2877:2883		No text annotation
homologous
IL_8C3A_084
NA
IL_3J7Q_0971/5/2889:2891,
1/5/3610:3612		Isolated non-canonical cWW pair
homologous
IL_8C3A_085
NA
IL_3J7Q_1851/5/2893:2897,
1/5/3602:3608		No text annotation
IL_3J7Q_0981/5/2894:2897,
1/5/3602:3607		No text annotation
IL_3J7Q_0991/5/2901:2905,
1/5/3589:3598		No text annotation
IL_3J7Q_1001/5/3632:3633,
1/5/3827:3829		Single bulged A
homologous
IL_5TBW_082
NA
IL_3J7Q_1011/5/3660:3665,
1/5/3677:3684		Kink-turn related
homologous
IL_5TBW_083
NA
IL_3J7Q_1021/5/3700:3703,
1/5/3749:3750		No text annotation
homologous
IL_8C3A_089
NA
IL_3J7Q_1031/5/3704:3705,
1/5/3745:3748		Multiple bulged bases
homologous
IL_8C3A_090
NA
IL_3J7Q_1861/5/3708:3724,
1/5/3729:3742		No text annotation
IL_3J7Q_1041/5/3780:3781,
1/5/3811:3814		Bulged stacked bases
geometric
IL_4V9F_070
IL_22551.4
IL_3J7Q_1051/5/3781:3795,
1/5/3805:3811		No text annotation
IL_3J7Q_1061/5/3895:3902,
1/5/4558:4565		No text annotation
IL_3J7Q_1071/5/3913:3915,
1/5/4388:4389		Single bulged U
homologous
IL_5TBW_093
NA
IL_3J7Q_1081/5/3916:3917,
1/5/4384:4387		Minor groove platform
homologous
IL_5TBW_094
NA
IL_3J7Q_1091/5/3927:3929,
1/5/4181:4184		Isolated tHS basepair with bulges
homologous
IL_5TBW_095
NA
IL_3J7Q_1871/5/4078:4088,
1/5/4161:4168		No text annotation
IL_3J7Q_1101/5/4079:4088,
1/5/4161:4167		No text annotation
IL_3J7Q_1111/5/4095:4098,
1/5/4111:4113		No text annotation
geometric
IL_4N0T_004
IL_99358.1
IL_3J7Q_1121/5/4191:4192,
1/5/4202:4204		Single bulged A
homologous
IL_5TBW_098
NA
IL_3J7Q_1881/5/4238:4243,
1/5/4267:4286		No text annotation
IL_3J7Q_1131/5/4239:4243,
1/5/4267:4285		No text annotation
IL_3J7Q_1141/5/4243:4245,
1/5/4263:4267		Isolated tHS basepair with bulges
homologous
IL_5TBW_099
NA
IL_3J7Q_1151/5/4291:4293,
1/5/4317:4318		Single bulged A
geometric
IL_4V88_399
NA
IL_3J7Q_1161/5/4295:4298,
1/5/4312:4315		Tandem non-canonical cWW pairs
homologous
IL_5TBW_100
NA
IL_3J7Q_1171/5/4347:4351,
1/5/4363:4365		No text annotation
geometric
IL_8C3A_419
NA
IL_3J7Q_1181/5/4400:4401,
1/5/4442:4444		Major groove platform
homologous
IL_8P9A_329
IL_48076.6
IL_3J7Q_1191/5/4401:4403,
1/5/4440:4442		Isolated non-canonical cWW pair
geometric
IL_5TBW_103
NA
IL_3J7Q_1201/5/4403:4405,
1/5/4439:4440		Major groove platform
geometric
IL_5TBW_104
NA
IL_3J7Q_1211/5/4405:4407,
1/5/4435:4439		Major groove minor groove platform with extra cWW
homologous
IL_5TBW_105
NA
IL_3J7Q_1221/5/4412:4416,
1/5/4426:4430		Triple sheared
homologous
IL_5TBW_106
NA
IL_3J7Q_1231/5/4453:4454,
1/5/4526:4528		Major groove platform
geometric
IL_4V9F_086
IL_07039.3
IL_3J7Q_1891/5/4453:4458,
1/5/4520:4528		No text annotation
IL_3J7Q_1241/5/4456:4458,
1/5/4520:4524		No text annotation
IL_3J7Q_1251/5/4458:4459,
1/5/4517:4520		No text annotation
homologous
IL_8C3A_117
NA
IL_3J7Q_1261/5/4472:4473,
1/5/4481:4483		No text annotation
IL_3J7Q_1901/5/4534:4540,
1/5/4545:4552		No text annotation
IL_3J7Q_1271/5/4535:4538,
1/5/4547:4551		No text annotation
IL_3J7Q_1281/5/4577:4579,
1/5/4723:4726		No text annotation
geometric
IL_8C3A_419
NA
IL_3J7Q_1291/5/4579:4582,
1/5/4721:4723		No text annotation
IL_3J7Q_1301/5/4582:4585,
1/5/4717:4721		Double sheared
homologous
IL_5TBW_114
NA
IL_3J7Q_1311/5/4590:4592,
1/5/4618:4620		Isolated non-canonical cWW pair
homologous
IL_8C3A_124
NA
IL_3J7Q_1321/5/4596:4603,
1/5/4608:4614		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_3J7Q_1331/5/4624:4629,
1/5/4669:4673		No text annotation
IL_3J7Q_1341/5/4632:4637,
1/5/4662:4666		UAA/GAN related
geometric
IL_5TBW_118
NA
IL_3J7Q_1351/5/4638:4640,
1/5/4659:4661		Isolated cWH basepair
geometric
IL_3R1C_012
IL_10167.6
IL_3J7Q_1921/5/4638:4642,
1/5/4655:4661		No text annotation
IL_3J7Q_1361/5/4641:4642,
1/5/4655:4658		Multiple bulged bases
homologous
IL_5TBW_119
NA
IL_3J7Q_1371/5/4681:4685,
1/5/4705:4709		UAA/GAN
homologous
IL_8C3A_129
NA
IL_3J7Q_1931/5/4740:4746,
1/5/4954:4959		No text annotation
IL_3J7Q_1941/5/4755:4765,
1/5/4869:4878		No text annotation
IL_3J7Q_1401/5/4768:4772,
1/5/4863:4866		Tandem non-canonical cWW pairs
geometric
IL_7A0S_040
IL_77658.1
IL_3J7Q_1411/5/4891:4896,
1/5/4924:4928		No text annotation
IL_3J7Q_1421/5/4899:4901,
1/5/4920:4921		No text annotation
IL_3J7Q_1431/5/4992:4994,
1/5/5057:5059		Isolated non-canonical cWW pair
geometric
IL_3D0U_006
IL_87907.2
IL_3J7Q_1441/5/4996:5000,
1/5/5050:5055		No text annotation
IL_3J7Q_1951/5/4996:5010,
1/5/5038:5055		No text annotation
IL_3J7Q_1451/5/5000:5002,
1/5/5045:5050		No text annotation
homologous
IL_8C3A_138
NA
IL_3J7Q_1461/5/5002:5010,
1/5/5038:5045		No text annotation
IL_3J7Q_1471/5/5012:5014,
1/5/5035:5036		Single bulged U
homologous
IL_8C3A_140
NA
IL_3J7Q_1481/5/5014:5017,
1/5/5032:5035		Double sheared; A in syn
homologous
IL_8C3A_141
NA
IL_3J7Q_1491/7/15:16,
1/7/62:64		Single bulged C
geometric
IL_3W3S_001
IL_61258.15
IL_3J7Q_1961/7/15:18,
1/7/60:64		Tandem non-canonical cWW pairs
geometric
IL_1MFQ_004
IL_85033.2
IL_3J7Q_1501/7/21:27,
1/7/52:57		Minor groove platform related
homologous
IL_5TBW_373
NA
IL_3J7Q_1511/7/28:29,
1/7/48:51		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_357
IL_68140.4
IL_3J7Q_1521/7/32:36,
1/7/41:45		Symmetric double minor groove platform
geometric
IL_7RQB_114
NA
IL_3J7Q_1531/7/71:78,
1/7/98:104		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5TBW_377
NA
IL_3J7Q_1541/7/79:81,
1/7/95:97		Isolated non-canonical cWW pair
geometric
IL_4Y1M_005
IL_07785.1
IL_3J7Q_1551/7/82:85,
1/7/92:94		Isolated non-canonical cWW pair
homologous
IL_5TBW_378
NA

Problematic loops

#loop idProblemSequence
IL_3J7Q_158No text annotation
IL_3J7Q_160No text annotation
IL_3J7Q_161No text annotation
IL_3J7Q_027Isolated non-canonical cWW with bulges
IL_3J7Q_164No text annotation
IL_3J7Q_036No text annotation
IL_3J7Q_167Triple sheared with non-canonical cWW
IL_3J7Q_168No text annotation
IL_3J7Q_170Tandem non-canonical cWW pairs
IL_3J7Q_064No text annotation
IL_3J7Q_172No text annotation
IL_3J7Q_173No text annotation
IL_3J7Q_174No text annotation
IL_3J7Q_177Tandem non-canonical cWW pairs with near WC pairs
IL_3J7Q_178Isolated non-canonical cWW pair
IL_3J7Q_179No text annotation
IL_3J7Q_180No text annotation
IL_3J7Q_181No text annotation
IL_3J7Q_183No text annotation
IL_3J7Q_191No text annotation
IL_3J7Q_138No text annotation
IL_3J7Q_139No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J7Q_0011/5/112:116,
1/5/155:160,
1/5/276:278		No text annotation
J3_3J7Q_0151/5/194:199,
1/5/215:228,
1/5/240:247		No text annotation
J3_3J7Q_0161/5/351:367,
1/5/374:379,
1/8/21:24		No text annotation
homologous
J3_8P9A_045
J3_30040.2
J3_3J7Q_0021/5/380:387,
1/5/414:415,
1/8/19:20		No text annotation
homologous
J3_5TBW_002
NA
J3_3J7Q_0251/5/443:458,
1/5/698:704,
1/5/1293:1304		No text annotation
J3_3J7Q_0181/5/708:713,
1/5/955:978,
1/5/1276:1289		No text annotation
J3_3J7Q_0031/5/1531:1537,
1/5/1622:1624,
1/5/1640:1643		No text annotation
homologous
J3_8C3A_003
NA
J3_3J7Q_0191/5/1531:1537,
1/5/1622:1626,
1/5/1636:1643		No text annotation
J3_3J7Q_0041/5/1545:1548,
1/5/1580:1584,
1/5/1609:1614		No text annotation
homologous
J3_5TBW_005
NA
J3_3J7Q_0051/5/1969:1971,
1/5/1995:2001,
1/5/2016:2018		No text annotation
homologous
J3_5TBW_007
NA
J3_3J7Q_0061/5/2393:2399,
1/5/2805:2807,
1/5/2819:2822		No text annotation
homologous
J3_8C3A_006
NA
J3_3J7Q_0071/5/2402:2405,
1/5/2785:2792,
1/5/2799:2802		No text annotation
J3_3J7Q_0081/5/2440:2445,
1/5/2515:2519,
1/5/2536:2537		No text annotation
homologous
J3_5TBW_010
NA
J3_3J7Q_0261/5/2450:2456,
1/5/2465:2476,
1/5/2501:2509		No text annotation
J3_3J7Q_0271/5/2549:2556,
1/5/2571:2575,
1/5/2757:2770		No text annotation
J3_3J7Q_0091/5/2575:2578,
1/5/2583:2589,
1/5/2756:2757		No text annotation
J3_3J7Q_0101/5/3934:3939,
1/5/4074:4078,
1/5/4168:4176		No text annotation
J3_3J7Q_0111/5/4091:4095,
1/5/4113:4129,
1/5/4155:4158		No text annotation
J3_3J7Q_0221/5/4091:4099,
1/5/4110:4129,
1/5/4155:4158		No text annotation
J3_3J7Q_0231/5/4463:4470,
1/5/4485:4493,
1/5/4507:4513		No text annotation
J3_3J7Q_0241/5/4748:4754,
1/5/4879:4888,
1/5/4931:4952		No text annotation
J3_3J7Q_0121/5/4970:4972,
1/5/4986:4991,
1/5/5060:5063		No text annotation
J3_3J7Q_0131/7/6:14,
1/7/65:66,
1/7/109:113		No text annotation
J3_3J7Q_0141/8/44:45,
1/8/58:66,
1/8/92:99		No text annotation
J4_3J7Q_0011/5/194:199,
1/5/215:222,
1/5/226:228,
1/5/240:247		No text annotation
J4_3J7Q_0061/5/980:983,
1/5/1070:1074,
1/5/1236:1246,
1/5/1264:1274		No text annotation
J4_3J7Q_0071/5/2406:2410,
1/5/2434:2439,
1/5/2538:2539,
1/5/2777:2784		No text annotation
homologous
J4_8CRE_004
J4_69051.6
J4_3J7Q_0041/5/2618:2619,
1/5/2637:2642,
1/5/2692:2698,
1/5/2718:2719		No text annotation
J4_3J7Q_0051/5/4587:4590,
1/5/4620:4621,
1/5/4676:4678,
1/5/4712:4715		No text annotation
J5_3J7Q_0011/5/111:116,
1/5/155:160,
1/5/276:283,
1/5/304:310,
1/5/327:330		No text annotation
J5_3J7Q_0101/5/1335:1341,
1/5/1515:1519,
1/5/1658:1661,
1/5/2288:2290,
1/5/2345:2351		No text annotation
J5_3J7Q_0031/5/1352:1355,
1/5/1384:1399,
1/5/1418:1421,
1/5/1464:1466,
1/5/1499:1504		No text annotation
J5_3J7Q_0111/5/2358:2371,
1/5/2389:2399,
1/5/2805:2807,
1/5/2819:2829,
1/5/3856:3863		No text annotation
J5_3J7Q_0051/5/2847:2863,
1/5/2887:2888,
1/5/3613:3614,
1/5/3618:3626,
1/5/3835:3841		No text annotation
J5_3J7Q_0061/5/2855:2863,
1/5/2887:2888,
1/5/3613:3614,
1/5/3618:3626,
1/5/3835:3837		No text annotation
homologous
J5_8C3A_004
NA
J5_3J7Q_0071/5/3903:3911,
1/5/4391:4405,
1/5/4439:4453,
1/5/4528:4534,
1/5/4552:4557		No text annotation
J5_3J7Q_0081/5/3920:3923,
1/5/4188:4192,
1/5/4202:4205,
1/5/4227:4228,
1/5/4375:4381		No text annotation
J5_3J7Q_0091/5/4228:4237,
1/5/4287:4291,
1/5/4318:4319,
1/5/4328:4345,
1/5/4367:4375		No text annotation
J6_3J7Q_0011/5/3634:3638,
1/5/3650:3657,
1/5/3687:3698,
1/5/3752:3755,
1/5/3769:3780,
1/5/3814:3826		No text annotation
J7_3J7Q_0021/5/1666:1674,
1/5/1681:1685,
1/5/1852:1855,
1/5/1879:1885,
1/5/1894:1901,
1/5/2075:2081,
1/5/2275:2283		No text annotation
J8_3J7Q_0011/5/3920:3923,
1/5/4188:4192,
1/5/4202:4205,
1/5/4227:4237,
1/5/4287:4291,
1/5/4318:4319,
1/5/4328:4345,
1/5/4367:4381		No text annotation
J10_3J7Q_0011/5/19:26,
1/5/57:67,
1/5/74:78,
1/5/105:109,
1/5/332:339,
1/8/33:45,
1/8/58:66,
1/8/92:106,
1/8/113:114,
1/8/136:138		No text annotation
J10_3J7Q_0021/5/19:29,
1/5/53:67,
1/5/74:78,
1/5/105:109,
1/5/332:339,
1/8/33:45,
1/8/58:66,
1/8/92:106,
1/8/113:114,
1/8/136:138		No text annotation

Problematic loops

#loop idProblemSequence
J3_3J7Q_017No text annotation
J3_3J7Q_020No text annotation
J3_3J7Q_021No text annotation
J4_3J7Q_002No text annotation
J4_3J7Q_003No text annotation
J5_3J7Q_002No text annotation
J5_3J7Q_004No text annotation
J7_3J7Q_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1539 s