RNA 3D Hub //

5APO Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/5/38:45
homologous
HL_5TBW_113		NA
1/5/69:74
homologous
HL_5TBW_114		NA
1/5/90:96
homologous
HL_5TBW_115		NA
1/5/132:136
homologous
HL_5TBW_116		NA
1/5/194:201
homologous
HL_5TBW_117		NA
1/5/208:212
homologous
HL_5TBW_118		NA
1/5/216:224
homologous
HL_5TBW_119		NA
1/5/278:287
homologous
HL_5TBW_120		NA
1/5/303:312
homologous
HL_5TBW_121		NA
1/5/357:362
homologous
HL_5TBW_122		NA
1/5/382:387
homologous
HL_5TBW_123		NA
1/5/543:548
geometric
HL_1U1Y_001		NA

HL_16568.1*
1/5/599:604
homologous
HL_5TBW_125		NA
1/5/640:649
homologous
HL_5TBW_126		NA
1/5/686:694
homologous
HL_5TBW_127		NA
1/5/707:712
homologous
HL_5TBW_128		NA
1/5/732:737
homologous
HL_5TBW_129		NA
1/5/763:768
homologous
HL_5TBW_130		NA
1/5/844:849
homologous
HL_5TBW_131		NA
1/5/876:885
homologous
HL_5TBW_132		NA
1/5/910:918
homologous
HL_5TBW_133		NA
1/5/958:963
homologous
HL_5TBW_134		NA
1/5/1076:1083
geometric
HL_5TBW_024		NA

HL_54035.7*
1/5/1126:1132
homologous
HL_5TBW_137		NA
1/5/1148:1155
homologous
HL_5TBW_138		NA
1/5/1239:1249
homologous
HL_5TBW_139		NA
1/5/1267:1274
homologous
HL_5TBW_140		NA
1/5/1347:1357
homologous
HL_5TBW_141		NA
1/5/1403:1408
homologous
HL_5TBW_142		NA
1/5/1462:1470
homologous
HL_5TBW_143		NA
1/5/1506:1512
homologous
HL_5TBW_144		NA
1/5/1544:1549
homologous
HL_5TBW_145		NA
1/5/1567:1571
geometric
HL_4O26_001		NA

HL_61984.1*
1/5/1599:1608
homologous
HL_5TBW_147		NA
1/5/1634:1639
homologous
HL_5TBW_148		NA
1/5/1680:1688
homologous
HL_5TBW_149		NA
1/5/1719:1725
homologous
HL_5TBW_150		NA
1/5/1759:1766
geometric
HL_6D12_002		NA

HL_82678.2*
1/5/1792:1796
homologous
HL_5TBW_152		NA
1/5/1844:1851
homologous
HL_5TBW_153		NA
1/5/1862:1868
homologous
HL_5TBW_154		NA
1/5/1923:1928
homologous
HL_5TBW_155		NA
1/5/2110:2114
homologous
HL_5TBW_157		NA
1/5/2135:2145
homologous
HL_5TBW_158		NA
1/5/2164:2170
homologous
HL_5TBW_159		NA
1/5/2220:2225
homologous
HL_5TBW_160		NA
1/5/2292:2300
homologous
HL_5TBW_162		NA
1/5/2369:2378
homologous
HL_5TBW_163		NA
1/5/2535:2544NANA
1/5/2568:2573NANA
1/5/2616:2624
homologous
HL_5TBW_167		NA
1/5/2633:2645
homologous
HL_5TBW_168		NA
1/5/2673:2681
homologous
HL_5TBW_169		NA
1/5/2693:2700
homologous
HL_5TBW_170		NA
1/5/2724:2732
homologous
HL_5TBW_171		NA
1/5/2744:2749
homologous
HL_5TBW_172		NA
1/5/2776:2784
homologous
HL_5TBW_173		NA
1/5/2840:2848
homologous
HL_5TBW_174		NA
1/5/2897:2904
homologous
HL_5TBW_175		NA
1/5/2920:2926
geometric
HL_5TBW_063		NA

HL_26055.6*
1/5/2963:2968
homologous
HL_5TBW_177		NA
1/5/3025:3030
homologous
HL_5TBW_178		NA
1/5/3068:3073
homologous
HL_5TBW_179		NA
1/5/3110:3124
homologous
HL_5TBW_180		NA
1/5/3194:3197
homologous
HL_5TBW_181		NA
1/5/3240:3247
homologous
HL_5TBW_182		NA
1/5/3303:3311
homologous
HL_5TBW_183		NA
1/5/3350:3353
geometric
HL_5U30_001		NA

HL_69353.7*
1/7/36:41NANA
1/7/88:93NANA
1/8/69:89NANA
1/8/108:114
homologous
HL_5TBW_075		NA

HL_06569.2*
1/8/124:129
homologous
HL_5TBW_076		NA

HL_60357.1*

Problematic loops

#loop idProblemSequence
HL_5APO_023NA
HL_5APO_044NA
HL_5APO_051NA

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/5/7:8,
1/8/150:152		Single bulged C
homologous
IL_5TBW_002		NA

IL_61258.10*
1/5/13:15,
1/8/144:145		Single bulged U
homologous
IL_5TBW_003		NA

IL_83039.11*
1/5/27:28,
1/5/56:58
homologous
IL_5TBW_240		NA
1/5/31:38,
1/5/45:53		tSH-tHW-tHH-tHS
geometric
IL_5TBW_005		NA

IL_22863.1*
1/5/82:89,
1/5/97:103
homologous
IL_5TBW_242		NA
1/5/123:124,
1/5/144:149
geometric
IL_5TBW_007		NA

IL_19724.1*
1/5/125:127,
1/5/141:143
homologous
IL_5TBW_244		NA
1/5/163:165,
1/5/257:258
homologous
IL_5TBW_245		NA
1/5/169:170,
1/5/248:253		NANA
1/5/177:178,
1/5/238:241		Major groove platform
geometric
IL_7A0S_073		NA

IL_80663.10*
1/5/189:191,
1/5/204:205
homologous
IL_5TBW_248		NA
1/5/337:339,
1/8/25:26		Single bulged A
homologous
IL_5TBW_013		NA

IL_80007.16*
1/5/376:379,
1/5/390:403
homologous
IL_5TBW_250		NA
1/5/404:410,
1/8/13:19		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015		NA

IL_66414.5*
1/5/428:431,
1/5/628:631		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002		NA

IL_85877.10*
1/5/512:513,
1/5/577:579
homologous
IL_5TBW_254		NA
1/5/517:525,
1/5/567:573
homologous
IL_5TBW_255		NA
1/5/531:538,
1/5/553:561
homologous
IL_5TBW_256		NA
1/5/668:670,
1/5/792:794
homologous
IL_5TBW_257		NA
1/5/680:684,
1/5/696:700
homologous
IL_5TBW_258		NA
1/5/725:728,
1/5/741:745
homologous
IL_5TBW_259		NA
1/5/752:753,
1/5/779:781
homologous
IL_5TBW_260		NA
1/5/755:756,
1/5/775:777
homologous
IL_5TBW_261		NA
1/5/758:763,
1/5/768:773
geometric
IL_5TBW_026		NA

IL_19954.1*
1/5/803:805,
1/5/938:940
homologous
IL_5TBW_263		NA
1/5/805:809,
1/5/931:938
geometric
IL_5TBW_028		NA

IL_17470.5*
1/5/828:829,
1/5/895:897		Single bulged A
geometric
IL_4V9F_025		NA

IL_80007.16*
1/5/833:834,
1/5/859:861		Single bulged G
geometric
IL_5TBW_029		NA

IL_99645.1*
1/5/834:838,
1/5/855:859
homologous
IL_5TBW_266		NA
1/5/869:872,
1/5/888:890
homologous
IL_5TBW_267		NA
1/5/873:875,
1/5/886:887
homologous
IL_5TBW_268		NA
1/5/907:909,
1/5/919:923		Multiple bulged bases
geometric
IL_5TBW_033		NA

IL_90991.5*
1/5/954:956,
1/5/965:967
homologous
IL_5TBW_270		NA
1/5/969:970,
1/5/1111:1113
homologous
IL_5TBW_271		NA
1/5/977:982,
1/5/1101:1104		NANA
1/5/983:985,
1/5/1099:1100
homologous
IL_5TBW_273		NA
1/5/991:997,
1/5/1052:1058		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5TBW_038		NA

IL_93830.2*
1/5/997:998,
1/5/1050:1052
homologous
IL_5TBW_275		NA
1/5/999:1004,
1/5/1046:1049
homologous
IL_5TBW_276		NA
1/5/1006:1009,
1/5/1041:1044
homologous
IL_5TBW_277		NA
1/5/1009:1011,
1/5/1039:1041
geometric
IL_4LFB_059		NA

IL_01312.13*
1/5/1069:1071,
1/5/1087:1089
homologous
IL_5TBW_280		NA
1/5/1074:1076,
1/5/1083:1084
homologous
IL_5TBW_281		NA
1/5/1120:1122,
1/5/1136:1138
homologous
IL_5TBW_282		NA
1/5/1123:1125,
1/5/1133:1135
homologous
IL_5TBW_283		NA
1/5/1167:1171,
1/5/1328:1332
homologous
IL_5TBW_284		NA
1/5/1173:1180,
1/5/1325:1326		SSU/LSU pseudoknot
geometric
IL_5TBW_049		NA

IL_15861.6*
1/5/1180:1182,
1/5/1324:1325
homologous
IL_5TBW_286		NA
1/5/1187:1194,
1/5/1314:1319
homologous
IL_5TBW_287		NA
1/5/1194:1205,
1/5/1299:1314
geometric
IL_5TBW_052		NA

IL_94878.1*
1/5/1207:1209,
1/5/1296:1297
homologous
IL_5TBW_289		NA
1/5/1218:1226,
1/5/1283:1287
homologous
IL_5TBW_290		NA
1/5/1234:1238,
1/5/1250:1254
homologous
IL_5TBW_291		NA
1/5/1262:1266,
1/5/1275:1277
homologous
IL_5TBW_292		NA
1/5/1376:1378,
1/5/1428:1431
homologous
IL_5TBW_293		NA
1/5/1385:1387,
1/5/1420:1421
homologous
IL_5TBW_294		NA
1/5/1388:1395,
1/5/1415:1419
homologous
IL_5TBW_295		NA
1/5/1398:1400,
1/5/1411:1412
homologous
IL_5TBW_296		NA
1/5/1444:1450,
1/5/2354:2359
homologous
IL_5TBW_297		NA
1/5/1492:1495,
1/5/1835:1836		Major groove platform; stack outside cWW
geometric
IL_4V9F_050		NA

IL_70995.6*
1/5/1501:1505,
1/5/1513:1515		C-loop
geometric
IL_7RQB_051		NA

IL_63596.4*
1/5/1532:1536,
1/5/1585:1590
homologous
IL_5TBW_299		NA
1/5/1565:1566,
1/5/1572:1574		Minor groove platform
geometric
IL_2QWY_009		NA

IL_06437.11*
1/5/1618:1621,
1/5/1824:1826
homologous
IL_5TBW_300		NA
1/5/1623:1625,
1/5/1818:1822		Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010		NA

IL_01312.13*
1/5/1627:1631,
1/5/1811:1816
homologous
IL_5TBW_302		NA
1/5/1645:1649,
1/5/1806:1810
homologous
IL_5TBW_303		NA
1/5/1661:1663,
1/5/1786:1788
homologous
IL_5TBW_304		NA
1/5/1669:1670,
1/5/1778:1780		Single bulged C
geometric
IL_5TBW_069		NA

IL_61258.10*
1/5/1670:1671,
1/5/1776:1778
homologous
IL_5TBW_306		NA
1/5/1694:1698,
1/5/1747:1752
homologous
IL_5TBW_307		NA
1/5/1702:1707,
1/5/1737:1743
homologous
IL_5TBW_308		NA
1/5/1711:1717,
1/5/1727:1733
homologous
IL_5TBW_309		NA
1/5/1883:1889,
1/5/2346:2349
homologous
IL_5TBW_310		NA
1/5/1895:1897,
1/5/2338:2340
homologous
IL_5TBW_311		NA
1/5/1898:1901,
1/5/2336:2337		Major groove platform; stack outside cWW
geometric
IL_5TBW_076		NA

IL_80663.10*
1/5/1901:1906,
1/5/2333:2336
homologous
IL_5TBW_313		NA
1/5/1918:1923,
1/5/1928:1934		tSH-tSH-tHH-tHS
geometric
IL_4V9F_063		NA

IL_66584.5*
1/5/1940:1942,
1/5/2106:2108
homologous
IL_5TBW_315		NA
1/5/1947:1948,
1/5/2098:2101
homologous
IL_5TBW_316		NA
1/5/2128:2129,
1/5/2323:2325
homologous
IL_5TBW_318		NA
1/5/2156:2161,
1/5/2173:2180
homologous
IL_5TBW_319		NA
1/5/2196:2199,
1/5/2245:2246
homologous
IL_5TBW_320		NA
1/5/2200:2201,
1/5/2241:2244
homologous
IL_5TBW_321		NA
1/5/2204:2206,
1/5/2237:2238		Single bulged U
geometric
IL_6UFG_004		NA

IL_83039.11*
1/5/2276:2278,
1/5/2307:2310		Intercalated cWW
geometric
IL_4WF9_047		NA

IL_04038.4*
1/5/2278:2288,
1/5/2304:2307		NANA
1/5/2391:2394,
1/5/2986:2988
homologous
IL_5TBW_327		NA
1/5/2396:2398,
1/5/2981:2984
homologous
IL_5TBW_328		NA
1/5/2409:2411,
1/5/2811:2812
homologous
IL_5TBW_329		NA
1/5/2411:2412,
1/5/2809:2811		NANA
1/5/2412:2413,
1/5/2807:2809		NANA
1/5/2423:2425,
1/5/2604:2607
homologous
IL_5TBW_331		NA
1/5/2435:2437,
1/5/2510:2512
geometric
IL_4P3U_012		NA

IL_01312.13*
1/5/2520:2526,
1/5/2584:2587
homologous
IL_5TBW_332		NA
1/5/2614:2615,
1/5/2625:2627
homologous
IL_5TBW_333		NA
1/5/2666:2668,
1/5/2686:2690		Isolated tHS basepair with bulges
geometric
IL_5TBW_099		NA

IL_38958.6*
1/5/2714:2717,
1/5/2739:2741
geometric
IL_4V88_455		NA

IL_01312.13*
1/5/2718:2721,
1/5/2735:2738
homologous
IL_5TBW_335		NA
1/5/2770:2773,
1/5/2787:2788
homologous
IL_5TBW_336		NA
1/5/2823:2824,
1/5/2865:2867
homologous
IL_5TBW_337		NA
1/5/2824:2826,
1/5/2863:2865
geometric
IL_5TBW_103		NA

IL_05265.1*
1/5/2826:2828,
1/5/2862:2863		Major groove platform
geometric
IL_4V9F_083		NA

IL_95601.1*
1/5/2828:2830,
1/5/2858:2862
homologous
IL_5TBW_340		NA
1/5/2835:2839,
1/5/2849:2853
homologous
IL_5TBW_341		NA
1/5/2876:2877,
1/5/2949:2951
homologous
IL_5TBW_342		NA
1/5/2879:2881,
1/5/2943:2947
homologous
IL_5TBW_343		NA
1/5/2881:2882,
1/5/2940:2943		Multiple bulged bases
geometric
IL_5TBW_109		NA

IL_13730.12*
1/5/2889:2891,
1/5/2912:2914
homologous
IL_5TBW_345		NA
1/5/2891:2892,
1/5/2909:2912		Minor groove platform with intercalation
geometric
IL_5TBW_111		NA

IL_95601.1*
1/5/2918:2920,
1/5/2926:2928
homologous
IL_5TBW_347		NA
1/5/2960:2961,
1/5/2970:2972
homologous
IL_5TBW_348		NA
1/5/3004:3007,
1/5/3139:3144
homologous
IL_5TBW_349		NA
1/5/3012:3014,
1/5/3040:3042
homologous
IL_5TBW_350		NA
1/5/3018:3025,
1/5/3030:3036		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116		NA

IL_04346.5*
1/5/3047:3051,
1/5/3091:3094
homologous
IL_5TBW_352		NA
1/5/3054:3059,
1/5/3084:3088
homologous
IL_5TBW_353		NA
1/5/3063:3064,
1/5/3077:3080
homologous
IL_5TBW_354		NA
1/5/3103:3107,
1/5/3127:3131
homologous
IL_5TBW_355		NA
1/5/3164:3166,
1/5/3284:3286		UG cWW
geometric
IL_4LFB_061		NA

IL_01312.13*
1/5/3168:3170,
1/5/3280:3282
homologous
IL_5TBW_357		NA
1/5/3177:3179,
1/5/3210:3211
homologous
IL_5TBW_358		NA
1/5/3179:3188,
1/5/3204:3210
geometric
IL_5TBW_124		NA

IL_56867.1*
1/5/3193:3194,
1/5/3197:3199		Single bulged U
geometric
IL_5TBW_125		NA

IL_83039.11*
1/5/3225:3229,
1/5/3258:3260
homologous
IL_5TBW_361		NA
1/5/3233:3235,
1/5/3252:3254
homologous
IL_5TBW_362		NA
1/5/3235:3238,
1/5/3249:3252		Tandem non-canonical cWW pairs
geometric
IL_6MWN_005		NA

IL_85877.10*
1/5/3300:3303,
1/5/3311:3314		Tandem non-canonical cWW pairs
geometric
IL_5TBW_129		NA

IL_85877.10*
1/5/3318:3320,
1/5/3387:3388
homologous
IL_5TBW_365		NA
1/5/3324:3325,
1/5/3381:3383
homologous
IL_5TBW_366		NA
1/5/3328:3330,
1/5/3373:3378
homologous
IL_5TBW_367		NA
1/5/3332:3337,
1/5/3367:3371
homologous
IL_5TBW_368		NA
1/5/3340:3342,
1/5/3363:3364		Single bulged U
geometric
IL_6UFH_004		NA

IL_83039.11*
1/5/3342:3345,
1/5/3360:3363
homologous
IL_5TBW_370		NA
1/5/3349:3350,
1/5/3353:3356
homologous
IL_5TBW_371		NA
1/7/15:16,
1/7/63:65		NANA
1/7/21:27,
1/7/53:58		NANA
1/7/28:29,
1/7/49:52		NANA
1/7/29:30,
1/7/47:49		NANA
1/7/32:36,
1/7/41:45		NANA
1/7/72:80,
1/7/100:106		NANA
1/7/84:87,
1/7/94:96		NANA
1/8/44:64,
1/8/96:100
geometric
IL_5TBW_144		NA

IL_23735.1*
1/8/64:66,
1/8/93:96		Isolated non-canonical cWW with bulges
homologous
IL_5TBW_145		NA

IL_55456.1*
1/8/68:69,
1/8/89:91		Single bulged U
homologous
IL_5TBW_146		NA

IL_83039.11*

Problematic loops

#loop idProblemSequence
IL_5APO_001
geometric
IL_3ICQ_003
IL_5APO_017NA
IL_5APO_092
geometric
IL_4V9F_017
IL_5APO_096
geometric
IL_4V88_419
IL_5APO_100
geometric
IL_4WF9_042
IL_5APO_125
geometric
IL_4YHW_001

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/5/113:123,
1/5/149:158,
1/5/263:267
homologous
J3_5TBW_030		NA
1/5/814:820,
1/5/905:907,
1/5/923:926
homologous
J3_5TBW_033		NA
1/5/829:831,
1/5/863:867,
1/5/892:895		NANA
1/5/1230:1232,
1/5/1256:1262,
1/5/1277:1279		NANA
1/5/1479:1485,
1/5/1857:1859,
1/5/1871:1874
homologous
J3_5TBW_037		NA
1/5/1488:1491,
1/5/1837:1843,
1/5/1852:1854
homologous
J3_5TBW_038		NA
1/5/2432:2435,
1/5/2512:2517,
1/5/2590:2597
homologous
J3_5TBW_041		NA
1/5/2529:2532,
1/5/2547:2563,
1/5/2578:2581		NANA
1/5/2664:2666,
1/5/2690:2692,
1/5/2701:2706
homologous
J3_5TBW_042		NA
1/5/2886:2889,
1/5/2914:2916,
1/5/2930:2936		NANA
1/5/3298:3300,
1/5/3314:3318,
1/5/3388:3390		NANA

Problematic loops

No problematic loops


Coloring options:
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