RNA 3D Hub //

3J9M Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J9M_0011/A/1722:1729No text annotation
Not in a motif group		geometric
HL_4WF9_006
HL_06192.2
HL_3J9M_0021/A/1746:1752No text annotation
Not in a motif group		geometric
HL_5J7L_141
HL_67216.7
HL_3J9M_0031/A/1786:1791GNRA
Not in a motif group		homologous
HL_5J7L_147
HL_42097.1
HL_3J9M_0051/A/1831:1839No text annotation
Not in a motif group
HL_3J9M_0071/A/1884:1889No text annotation
Not in a motif group		geometric
HL_5J7L_143
HL_75407.1
HL_3J9M_0101/A/1988:1996No text annotation
Not in a motif group		geometric
HL_5TBW_021
HL_33817.1
HL_3J9M_0111/A/2035:2040No text annotation
Not in a motif group		geometric
HL_4WF9_025
HL_64365.1
HL_3J9M_0131/A/2107:2114GNRA
Not in a motif group		homologous
HL_4WF9_027
HL_42097.1
HL_3J9M_0141/A/2129:2136No text annotation
Not in a motif group		homologous
HL_5J7L_160
HL_64430.2
HL_3J9M_0151/A/2175:2185No text annotation
Not in a motif group		homologous
HL_6PRV_001
HL_07145.1
HL_3J9M_0161/A/2202:2209No text annotation
Not in a motif group		homologous
HL_6PRV_002
HL_84085.2
HL_3J9M_0171/A/2279:2286No text annotation
Not in a motif group
HL_3J9M_0181/A/2319:2324UNCG
Not in a motif group		geometric
HL_4U7U_001
HL_32369.1
HL_3J9M_0201/A/2400:2403No text annotation
Not in a motif group		geometric
HL_7A0S_039
HL_38927.2
HL_3J9M_0231/A/2518:2532No text annotation
Not in a motif group
HL_3J9M_0291/A/2812:2820No text annotation
Not in a motif group		homologous
HL_4WF9_049
HL_53171.2
HL_3J9M_0301/A/2828:2840No text annotation
Not in a motif group
HL_3J9M_0311/A/2862:2870No text annotation
Not in a motif group		geometric
HL_2ZZM_002
HL_23083.1
HL_3J9M_0321/A/2902:2907GNRA
Not in a motif group		geometric
HL_5B2P_001
HL_42097.1
HL_3J9M_0371/A/3126:3131GNRA
Not in a motif group		geometric
HL_3LQX_001
HL_42097.1
HL_3J9M_0381/A/3154:3159No text annotation
Not in a motif group
HL_3J9M_0391/A/3176:3193No text annotation
Not in a motif group
HL_3J9M_0401/A/3216:3224No text annotation
Not in a motif group		geometric
HL_7RQB_068
HL_27930.1
HL_3J9M_0411/AA/654:664No text annotation
Not in a motif group
HL_3J9M_0421/AA/701:708No text annotation
Not in a motif group
HL_3J9M_0431/AA/768:773Other HL
Not in a motif group		geometric
HL_5TBW_033
HL_76539.2
HL_3J9M_0441/AA/792:796No text annotation
Not in a motif group		geometric
HL_6U8D_003
HL_89098.1
HL_3J9M_0451/AA/804:809No text annotation
Not in a motif group		geometric
HL_5T16_002
HL_65572.2
HL_3J9M_0461/AA/842:847GNRA
Not in a motif group		geometric
HL_6DME_001
HL_42097.1
HL_3J9M_0471/AA/894:899Other HL
Not in a motif group		geometric
HL_1G1X_003
HL_87030.2
HL_3J9M_0481/AA/989:998No text annotation
Not in a motif group		geometric
HL_5J7L_015
HL_12326.1
HL_3J9M_0491/AA/1023:1028Other HL
Not in a motif group		geometric
HL_1G1X_005
HL_87030.2
HL_3J9M_0501/AA/1074:1084No text annotation
Not in a motif group		geometric
HL_5J7L_017
HL_12326.1
HL_3J9M_0521/AA/1150:1155No text annotation
Not in a motif group		geometric
HL_6AAX_001
HL_94803.1
HL_3J9M_0531/AA/1217:1226No text annotation
Not in a motif group		geometric
HL_2Y9H_003
HL_16173.1
HL_3J9M_0541/AA/1281:1287No text annotation
Not in a motif group		geometric
HL_5U3G_001
HL_87030.2
HL_3J9M_0551/AA/1310:1315No text annotation
Not in a motif group		geometric
HL_5TBW_022
HL_94803.1
HL_3J9M_0561/AA/1373:1379No text annotation
Not in a motif group		geometric
HL_2Y9H_003
HL_16173.1
HL_3J9M_0581/AA/1440:1450No text annotation
Not in a motif group		homologous
HL_6CZR_101
HL_96366.1
HL_3J9M_0591/AA/1522:1528No text annotation
Not in a motif group		geometric
HL_5M3H_001
HL_27930.1
HL_3J9M_0601/AA/1580:1585No text annotation
Not in a motif group		geometric
HL_5NFV_001
HL_76539.2
HL_3J9M_0621/B/1630:1638Guanidine riboswitch aptamer P2 hairpin
Not in a motif group		geometric
HL_5T83_002
HL_53597.2

Problematic loops

#loop idProblemSequence
HL_3J9M_004No text annotation
HL_3J9M_006T-loop with 2 stacked bulged bases
HL_3J9M_008No text annotation
HL_3J9M_009No text annotation
HL_3J9M_012No text annotation
HL_3J9M_019No text annotation
HL_3J9M_021No text annotation
HL_3J9M_022No text annotation
HL_3J9M_024No text annotation
HL_3J9M_025No text annotation
HL_3J9M_026No text annotation
HL_3J9M_027No text annotation
HL_3J9M_028No text annotation
HL_3J9M_033No text annotation
HL_3J9M_034No text annotation
HL_3J9M_035No text annotation
HL_3J9M_036GNRA
HL_3J9M_051No text annotation
HL_3J9M_057No text annotation
HL_3J9M_061No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J9M_0011/A/1682:1683,
1/A/1768:1770		Single bulged A
Not in a motif group		homologous
IL_7A0S_002
IL_37497.2
IL_3J9M_0021/A/1739:1745,
1/A/1753:1758		7x6 Sarcin-Ricin; G-bulge
Not in a motif group		geometric
IL_4V9F_106
IL_76042.2
IL_3J9M_0031/A/1845:1847,
1/A/1856:1858		No text annotation
Not in a motif group		homologous
IL_5J7L_257
IL_95997.1
IL_3J9M_0041/A/1862:1863,
1/A/2301:2303		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0051/A/1863:1865,
1/A/2300:2301		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0061/A/1875:1876,
1/A/1897:1899		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0071/A/1876:1879,
1/A/1895:1897		No text annotation
Not in a motif group		geometric
IL_4V84_070
IL_23164.1
IL_3J9M_0081/A/1880:1883,
1/A/1890:1894		No text annotation
Not in a motif group
IL_3J9M_0091/A/1904:1906,
1/A/2016:2018		No text annotation
Not in a motif group		geometric
IL_4WF9_020
IL_95997.1
IL_3J9M_0101/A/1906:1910,
1/A/2009:2016		tHW-tHW cross-strand stack
Not in a motif group		homologous
IL_5J7L_260
IL_17470.6
IL_3J9M_0111/A/1913:1915,
1/A/2004:2006		No text annotation
Not in a motif group		geometric
IL_5TBW_079
IL_95997.1
IL_3J9M_0121/A/1925:1927,
1/A/1977:1979		No text annotation
Not in a motif group		geometric
IL_5UNE_001
IL_53251.2
IL_3J9M_0131/A/1929:1930,
1/A/1973:1975		Single bulged A
Not in a motif group		homologous
IL_5J7L_261
IL_37497.2
IL_3J9M_0151/A/1985:1987,
1/A/1997:2001		Multiple bulged bases
Not in a motif group		homologous
IL_5J7L_265
IL_90991.6
IL_3J9M_0161/A/2032:2033,
1/A/2041:2043		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0171/A/2033:2035,
1/A/2040:2041		Single stack bend
Not in a motif group		geometric
IL_4LFB_041
IL_76488.2
IL_3J9M_0181/A/2046:2048,
1/A/2091:2094		Other IL
Not in a motif group		geometric
IL_5TBW_064
IL_84698.1
IL_3J9M_0191/A/2057:2063,
1/A/2076:2082		No text annotation
Not in a motif group
IL_3J9M_0201/A/2145:2147,
1/A/2254:2255		Single bulged C
Not in a motif group		homologous
IL_5J7L_276
IL_61258.12
IL_3J9M_0211/A/2149:2153,
1/A/2248:2252		UAA/GAN
Not in a motif group		homologous
IL_4WF9_036
IL_89002.2
IL_3J9M_0221/A/2168:2170,
1/A/2190:2192		Isolated near basepair
Not in a motif group		geometric
IL_2ZI0_001
IL_52767.2
IL_3J9M_0231/A/2170:2174,
1/A/2186:2190		No text annotation
Not in a motif group		geometric
IL_4V9F_043
IL_30542.3
IL_3J9M_0241/A/2197:2200,
1/A/2211:2212		No text annotation
Not in a motif group		homologous
IL_6PRV_002
NA
IL_3J9M_0251/A/2306:2313,
1/A/2674:2680		8x7 Sarcin-Ricin; G-bulge
Not in a motif group		homologous
IL_5J7L_289
IL_04346.7
IL_3J9M_0261/A/2329:2333,
1/A/2441:2448		No text annotation
Not in a motif group
IL_3J9M_0271/A/2456:2461,
1/A/2666:2668		No text annotation
Not in a motif group
IL_3J9M_0281/A/2465:2466,
1/A/2660:2662		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0291/A/2466:2469,
1/A/2658:2660		No text annotation
Not in a motif group
IL_3J9M_0301/A/2470:2473,
1/A/2656:2657		Major groove platform; stack outside cWW
Not in a motif group		geometric
IL_5J7L_306
IL_50694.2
IL_3J9M_0381/A/2712:2715,
1/A/3104:3106		Major groove platform with extra pair
Not in a motif group		geometric
IL_5TBW_091
IL_63450.2
IL_3J9M_0391/A/2717:2719,
1/A/3099:3102		No text annotation
Not in a motif group		homologous
IL_4WF9_079
IL_54678.5
IL_3J9M_0401/A/2730:2732,
1/A/2929:2930		Single bulged U
Not in a motif group		homologous
IL_7A0S_075
IL_83039.13
IL_3J9M_0411/A/2733:2734,
1/A/2925:2928		Minor groove platform
Not in a motif group		homologous
IL_5J7L_324
IL_42622.2
IL_3J9M_0421/A/2744:2746,
1/A/2802:2803		Minor groove platform
Not in a motif group		geometric
IL_7A0S_003
IL_42622.2
IL_3J9M_0431/A/2747:2748,
1/A/2799:2801		Single stack bend
Not in a motif group		geometric
IL_4V83_236
IL_76488.2
IL_3J9M_0441/A/2748:2750,
1/A/2798:2799		Single stack bend
Not in a motif group		geometric
IL_4LFB_041
IL_76488.2
IL_3J9M_0451/A/2849:2855,
1/A/2877:2889		No text annotation
Not in a motif group
IL_3J9M_0461/A/2856:2860,
1/A/2872:2876		Triple sheared
Not in a motif group		geometric
IL_5J7L_274
IL_56467.8
IL_3J9M_0581/A/3115:3117,
1/A/3139:3141		UG cWW
Not in a motif group		geometric
IL_4LFB_061
IL_95997.1
IL_3J9M_0591/A/3119:3126,
1/A/3131:3137		8x7 Sarcin-Ricin; G-bulge
Not in a motif group		geometric
IL_5TBW_116
IL_04346.7
IL_3J9M_0601/A/3148:3152,
1/A/3161:3163		Major groove minor groove platform with tHH
Not in a motif group		geometric
IL_4WF9_050
IL_37712.2
IL_3J9M_0611/AA/649:651,
1/AA/667:668		No text annotation
Not in a motif group
IL_3J9M_0621/AA/674:676,
1/AA/921:923		Intercalated cWW
Not in a motif group		geometric
IL_7A0S_044
IL_82842.2
IL_3J9M_0631/AA/685:686,
1/AA/859:861		Single bulged A
Not in a motif group		geometric
IL_5J7L_002
IL_37497.2
IL_3J9M_0641/AA/690:692,
1/AA/822:823		Single bulged A
Not in a motif group		geometric
IL_4R4V_004
IL_37497.2
IL_3J9M_0651/AA/694:696,
1/AA/819:820		Minor groove platform
Not in a motif group		geometric
IL_4LFB_004
IL_93353.1
IL_3J9M_0661/AA/727:729,
1/AA/744:747		Minor groove platform with extra cWW
Not in a motif group		geometric
IL_7RQB_031
IL_46796.1
IL_3J9M_0671/AA/729:732,
1/AA/742:744		Minor groove platform with extra cWW
Not in a motif group		geometric
IL_7RQB_031
IL_46796.1
IL_3J9M_0681/AA/756:761,
1/AA/779:786		Kink-turn with non-sequential stacking
Not in a motif group		geometric
IL_4LFB_011
IL_45067.2
IL_3J9M_0691/AA/762:765,
1/AA/777:778		Major groove platform; stack outside cWW
Not in a motif group		geometric
IL_1NTA_003
IL_50694.2
IL_3J9M_0701/AA/765:766,
1/AA/775:777		No text annotation
Not in a motif group
IL_3J9M_0711/AA/830:832,
1/AA/855:856		Single bulged U
Not in a motif group		geometric
IL_5J7L_017
IL_83039.13
IL_3J9M_0721/AA/834:838,
1/AA/852:853		C-loop
Not in a motif group		geometric
IL_5J7L_018
IL_75255.1
IL_3J9M_0731/AA/838:839,
1/AA/850:852		Single bulged A
Not in a motif group		geometric
IL_2QUX_002
IL_37497.2
IL_3J9M_0741/AA/876:885,
1/AA/910:913		No text annotation
Not in a motif group
IL_3J9M_0751/AA/887:893,
1/AA/900:908		No text annotation
Not in a motif group		geometric
IL_4V88_415
IL_55871.1
IL_3J9M_0761/AA/935:941,
1/AA/1133:1134		No text annotation
Not in a motif group		geometric
IL_5J7L_026
IL_69996.1
IL_3J9M_0771/AA/946:950,
1/AA/1044:1049		No text annotation
Not in a motif group
IL_3J9M_0781/AA/974:980,
1/AA/1008:1014		No text annotation
Not in a motif group
IL_3J9M_0791/AA/982:984,
1/AA/1004:1006		No text annotation
Not in a motif group		geometric
IL_5MWI_007
IL_95997.1
IL_3J9M_0801/AA/986:988,
1/AA/999:1002		No text annotation
Not in a motif group
IL_3J9M_0811/AA/1020:1022,
1/AA/1029:1030		Other IL
Not in a motif group		geometric
IL_3WBM_004
IL_76223.2
IL_3J9M_0821/AA/1062:1066,
1/AA/1092:1093		Left turn
Not in a motif group		geometric
IL_5J7L_036
IL_29346.1
IL_3J9M_0831/AA/1067:1071,
1/AA/1087:1091		tSH-tHW-tHS
Not in a motif group		geometric
IL_5J7L_037
IL_17136.1
IL_3J9M_0841/AA/1109:1111,
1/AA/1130:1132		No text annotation
Not in a motif group		geometric
IL_1Z7F_002
IL_95997.1
IL_3J9M_0851/AA/1139:1147,
1/AA/1158:1164		No text annotation
Not in a motif group
IL_3J9M_0861/AA/1175:1176,
1/AA/1477:1479		Single bulged A
Not in a motif group		geometric
IL_6CZR_147
IL_37497.2
IL_3J9M_0871/AA/1178:1180,
1/AA/1474:1475		Single bulged G
Not in a motif group		geometric
IL_6CZR_148
IL_00225.2
IL_3J9M_0881/AA/1186:1190,
1/AA/1464:1468		C-loop
Not in a motif group		geometric
IL_1KOG_007
IL_75255.1
IL_3J9M_0891/AA/1208:1209,
1/AA/1355:1357		Minor groove platform
Not in a motif group		geometric
IL_7A0S_028
IL_42622.2
IL_3J9M_0901/AA/1244:1252,
1/AA/1340:1345		No text annotation
Not in a motif group
IL_3J9M_0911/AA/1253:1255,
1/AA/1338:1339		Single bulged C
Not in a motif group		geometric
IL_6ZDP_001
IL_61258.12
IL_3J9M_0921/AA/1257:1261,
1/AA/1334:1336		Isolated cWS basepair
Not in a motif group		geometric
IL_4LFB_044
IL_76319.2
IL_3J9M_0931/AA/1262:1263,
1/AA/1329:1333		Minor groove platform
Not in a motif group		geometric
IL_3RW6_003
IL_93353.1
IL_3J9M_0941/AA/1265:1266,
1/AA/1325:1327		Single bulged A
Not in a motif group		geometric
IL_5J7L_049
IL_37497.2
IL_3J9M_0951/AA/1266:1268,
1/AA/1323:1325		No text annotation
Not in a motif group		geometric
IL_4LFB_047
IL_95997.1
IL_3J9M_0961/AA/1274:1277,
1/AA/1298:1301		Double sheared
Not in a motif group		geometric
IL_1SA9_002
IL_09705.9
IL_3J9M_0971/AA/1278:1279,
1/AA/1289:1297		No text annotation
Not in a motif group
IL_3J9M_0981/AA/1388:1393,
1/AA/1413:1418		No text annotation
Not in a motif group		geometric
IL_5J7L_057
IL_19954.2
IL_3J9M_0991/AA/1483:1485,
1/AA/1566:1569		No text annotation
Not in a motif group		geometric
IL_5J7L_058
IL_36143.3
IL_3J9M_1001/AA/1485:1488,
1/AA/1562:1566		No text annotation
Not in a motif group		geometric
IL_4V88_464
IL_99670.1
IL_3J9M_1011/AA/1489:1491,
1/AA/1559:1561		No text annotation
Not in a motif group		geometric
IL_5VCI_002
IL_95997.1
IL_3J9M_1021/AA/1491:1495,
1/AA/1554:1559		No text annotation
Not in a motif group
IL_3J9M_1031/AA/1500:1504,
1/AA/1546:1549		UAA/GAN related
Not in a motif group		geometric
IL_2R8S_002
IL_77691.1
IL_3J9M_1041/AA/1507:1510,
1/AA/1540:1543		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_5TBW_128
IL_30621.2
IL_3J9M_1051/AA/1510:1511,
1/AA/1538:1540		No text annotation
Not in a motif group
IL_3J9M_1061/AA/1511:1514,
1/AA/1535:1538		No text annotation
Not in a motif group
IL_3J9M_1081/B/1627:1629,
1/B/1639:1641		No text annotation
Not in a motif group		geometric
IL_4WF9_042
IL_95997.1

Problematic loops

#loop idProblemSequence
IL_3J9M_014Major groove platform with extra cWW
IL_3J9M_031Intercalated tWH
IL_3J9M_032No text annotation
IL_3J9M_033Single bulged A
IL_3J9M_034Major groove outside cWW, minor groove, intercalation pocket
IL_3J9M_035Major groove outside cWW, minor groove, intercalation pocket
IL_3J9M_036Multiple bulged bases
IL_3J9M_037No text annotation
IL_3J9M_047Single stack bend
IL_3J9M_048Major groove platform
IL_3J9M_049Major groove platform with extra pair
IL_3J9M_050Major groove minor groove platform with extra cWW
IL_3J9M_051No text annotation
IL_3J9M_052Minor groove platform
IL_3J9M_053Major groove platform
IL_3J9M_054Isolated non-canonical cWW with bulges
IL_3J9M_055No text annotation
IL_3J9M_056No text annotation
IL_3J9M_057Single bulged A
IL_3J9M_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J9M_0011/A/1678:1681,
1/A/1771:1785,
1/A/1792:1797		No text annotation
Not in a motif group
J3_3J9M_0021/A/1915:1921,
1/A/1983:1985,
1/A/2001:2004		No text annotation
Not in a motif group
J3_3J9M_0041/A/2336:2343,
1/A/2423:2427,
1/A/2436:2438		No text annotation
Not in a motif group
J3_3J9M_0051/A/2343:2345,
1/A/2368:2375,
1/A/2421:2423		No text annotation
Not in a motif group
J3_3J9M_0071/AA/677:680,
1/AA/866:872,
1/AA/917:920		No text annotation
Not in a motif group
J3_3J9M_0081/AA/687:690,
1/AA/823:830,
1/AA/856:858		No text annotation
Not in a motif group
J3_3J9M_0091/AA/973:974,
1/AA/1014:1020,
1/AA/1030:1031		No text annotation
Not in a motif group
J3_3J9M_0101/AA/1192:1194,
1/AA/1428:1434,
1/AA/1456:1462		No text annotation
Not in a motif group
J3_3J9M_0111/AA/1198:1201,
1/AA/1364:1366,
1/AA/1421:1424		No text annotation
Not in a motif group
J3_3J9M_0121/AA/1210:1216,
1/AA/1227:1238,
1/AA/1351:1354		No text annotation
Not in a motif group
J3_3J9M_0131/AA/1268:1273,
1/AA/1302:1308,
1/AA/1317:1323		No text annotation
Not in a motif group
J3_3J9M_0141/AA/1366:1370,
1/AA/1382:1388,
1/AA/1418:1421		No text annotation
Not in a motif group

Problematic loops

#loop idProblemSequence
J3_3J9M_003No text annotation
J3_3J9M_006No text annotation

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