RNA 3D Hub //

8V87 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8V87_0011/1/38:45No text annotation
geometric
HL_2B3J_001
HL_41169.1
HL_8V87_0021/1/69:74No text annotation
geometric
HL_5TBW_002
NA
HL_8V87_0031/1/90:96No text annotation
geometric
HL_7A0S_008
HL_76371.1
HL_8V87_0041/1/132:136No text annotation
geometric
HL_5TBW_004
NA
HL_8V87_0051/1/194:201T-loop with 2 stacked bulged bases
geometric
HL_4V9F_010
HL_13999.1
HL_8V87_0061/1/208:212No text annotation
geometric
HL_5TBW_006
NA
HL_8V87_0071/1/216:224T-loop with unstacked turn
geometric
HL_5TBW_007
NA
HL_8V87_0081/1/278:287No text annotation
geometric
HL_5TBW_008
NA
HL_8V87_0101/1/357:362GNRA
geometric
HL_4V9F_015
HL_34789.1
HL_8V87_0111/1/382:387GNRA
geometric
HL_6JOO_001
NA
HL_8V87_0131/1/599:604GNRA
geometric
HL_5J7L_004
NA
HL_8V87_0141/1/640:649No text annotation
geometric
HL_8C3A_015
NA
HL_8V87_0151/1/686:694No text annotation
geometric
HL_5TBW_015
NA
HL_8V87_0201/1/911:916GNRA
geometric
HL_5Y7M_002
HL_34789.1
HL_8V87_0211/1/958:963UNCG variation
geometric
HL_2CZJ_007
NA
HL_8V87_0231/1/1126:1132Other HL
geometric
HL_4V9F_039
HL_67772.1
HL_8V87_0241/1/1148:1155No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_8V87_0251/1/1239:1249No text annotation
geometric
HL_5D8H_001
HL_20174.1
HL_8V87_0261/1/1267:1274GNRA wlth tandem sheared
geometric
HL_5D8H_002
HL_98423.1
HL_8V87_0281/1/1403:1408GNRA
geometric
HL_5TBW_030
NA
HL_8V87_0291/1/1462:1470T-loop with 2 bulged bases not stacked
geometric
HL_3F2X_004
HL_13999.1
HL_8V87_0301/1/1506:1512Pseudoknot geometry with 3' bulge
homologous
HL_8C3A_032
NA
HL_8V87_0311/1/1544:1549GNRA variation
geometric
HL_5TBW_033
NA
HL_8V87_0321/1/1565:1574No text annotation
HL_8V87_0331/1/1599:1608No text annotation
geometric
HL_5TBW_035
NA
HL_8V87_0341/1/1634:1639GNRA
geometric
HL_5TBW_036
NA
HL_8V87_0351/1/1680:1688No text annotation
geometric
HL_5TBW_037
NA
HL_8V87_0361/1/1719:1725No text annotation
geometric
HL_5TBW_038
NA
HL_8V87_0381/1/1792:1796No text annotation
geometric
HL_2Y9H_003
HL_75660.6
HL_8V87_0411/1/2369:2378No text annotation
geometric
HL_2ZZM_002
NA
HL_8V87_0621/1/2897:2904GNRA variation
homologous
HL_8P9A_173
HL_46665.1
HL_8V87_0451/1/2918:2928No text annotation
geometric
HL_7KI3_001
HL_75660.6
HL_8V87_0471/1/2963:2968No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_8V87_0481/1/3025:3030GNRA
geometric
HL_5J7L_003
NA
HL_8V87_0491/1/3068:3073Ribsomal LSU H95
geometric
HL_5TBW_066
NA
HL_8V87_0501/1/3110:3124No text annotation
geometric
HL_5TBW_067
NA
HL_8V87_0511/1/3194:3197No text annotation
geometric
HL_2Y8W_001
NA
HL_8V87_0521/1/3240:3247No text annotation
homologous
HL_8P9A_180
HL_31089.1
HL_8V87_0531/1/3303:3311No text annotation
geometric
HL_5TBW_070
NA
HL_8V87_0611/2/47:56Pseudoknot with intercalation
homologous
HL_8C3A_229
NA
HL_8V87_0551/2/69:89No text annotation
homologous
HL_8P9A_187
HL_68571.1
HL_8V87_0571/2/124:129No text annotation
homologous
HL_5TBW_076
NA
HL_8V87_0581/6/12:16No text annotation
geometric
HL_2Y9H_003
HL_75660.6
HL_8V87_0591/6/37:42UNCG
geometric
HL_5LYS_002
HL_61337.1

Problematic loops

#loop idProblemSequence
HL_8V87_009No text annotation
HL_8V87_012No text annotation
HL_8V87_016GNRA related
HL_8V87_017GNRA related
HL_8V87_018GNRA
HL_8V87_019No text annotation
HL_8V87_022No text annotation
HL_8V87_027Mini UNCG
HL_8V87_037No text annotation
HL_8V87_039Mini UNCG
HL_8V87_040No text annotation
HL_8V87_042No text annotation
HL_8V87_043UNCG variation
HL_8V87_044No text annotation
HL_8V87_046No text annotation
HL_8V87_054Mini UNCG
HL_8V87_056No text annotation
HL_8V87_060No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8V87_0011/1/7:8,
1/2/150:152		Single bulged C
homologous
IL_8C3A_002
NA
IL_8V87_0021/1/13:15,
1/2/144:145		Single bulged U
homologous
IL_8C3A_003
NA
IL_8V87_0031/1/27:28,
1/1/56:58		Single stack bend
geometric
IL_5TBW_004
NA
IL_8V87_0041/1/31:38,
1/1/45:53		tSH-tHW-tHH-tHS
geometric
IL_5TBW_005
NA
IL_8V87_0051/1/82:89,
1/1/97:103		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_007
IL_62167.1
IL_8V87_0061/1/123:124,
1/1/144:149		No text annotation
geometric
IL_5TBW_007
NA
IL_8V87_0071/1/125:127,
1/1/141:143		Isolated non-canonical cWW pair
geometric
IL_5TBW_008
NA
IL_8V87_0081/1/164:166,
1/1/256:257		Single bulged A
geometric
IL_3OXE_001
IL_14190.1
IL_8V87_0091/1/169:170,
1/1/248:253		No text annotation
IL_8V87_0101/1/177:178,
1/1/238:241		Minor groove platform
geometric
IL_4KQY_004
IL_94991.1
IL_8V87_0111/1/189:191,
1/1/204:205		Single bulged U
geometric
IL_5TBW_012
NA
IL_8V87_0121/1/337:339,
1/2/25:26		Single bulged A
homologous
IL_5TBW_013
NA
IL_8V87_0131/1/376:379,
1/1/390:403		No text annotation
geometric
IL_5TBW_014
NA
IL_8V87_0141/1/404:410,
1/2/13:19		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA
IL_8V87_0151/1/429:431,
1/1/628:630		Isolated non-canonical cWW pair
geometric
IL_1YZ9_001
NA
IL_8V87_0161/1/512:513,
1/1/577:579		Single bulged A
geometric
IL_5TBW_018
NA
IL_8V87_0171/1/517:525,
1/1/567:573		No text annotation
geometric
IL_5TBW_019
NA
IL_8V87_0181/1/531:538,
1/1/553:561		No text annotation
geometric
IL_5TBW_020
NA
IL_8V87_0201/1/668:670,
1/1/792:794		Isolated non-canonical cWW pair
geometric
IL_7A0S_020
IL_01003.1
IL_8V87_0211/1/680:684,
1/1/696:700		No text annotation
geometric
IL_5TBW_022
NA
IL_8V87_0221/1/725:728,
1/1/741:745		UAA/GAN variation
geometric
IL_5TBW_023
NA
IL_8V87_0241/1/803:805,
1/1/938:940		No text annotation
geometric
IL_7RQB_017
NA
IL_8V87_0251/1/805:809,
1/1/931:938		No text annotation
IL_8V87_0291/1/909:911,
1/1/916:919		No text annotation
geometric
IL_4P3T_002
NA
IL_8V87_0301/1/969:970,
1/1/1111:1113		Single stack bend
geometric
IL_5TBW_035
NA
IL_8V87_1111/1/977:981,
1/1/1102:1104		No text annotation
IL_8V87_0321/1/983:985,
1/1/1099:1100		Single bulged G
geometric
IL_5TBW_037
NA
IL_8V87_0331/1/1120:1122,
1/1/1136:1138		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.1
IL_8V87_0351/1/1167:1171,
1/1/1328:1332		UAA/GAN
geometric
IL_5TBW_048
NA
IL_8V87_0361/1/1173:1180,
1/1/1325:1326		SSU/LSU pseudoknot
geometric
IL_5TBW_049
NA
IL_8V87_0371/1/1180:1182,
1/1/1324:1325		Single bulged U
geometric
IL_5TBW_050
NA
IL_8V87_0381/1/1187:1194,
1/1/1314:1319		No text annotation
geometric
IL_5TBW_051
NA
IL_8V87_0401/1/1207:1209,
1/1/1296:1297		Single bulged U
geometric
IL_7KVT_002
IL_97561.1
IL_8V87_0411/1/1218:1226,
1/1/1283:1287		Kink-turn
geometric
IL_4V9F_042
IL_99692.3
IL_8V87_0421/1/1234:1238,
1/1/1250:1254		No text annotation
geometric
IL_4V9F_043
NA
IL_8V87_0431/1/1262:1266,
1/1/1275:1277		Major groove platform with extra cWW
geometric
IL_5D8H_003
IL_36931.1
IL_8V87_0441/1/1376:1378,
1/1/1428:1431		Isolated cWS basepair
geometric
IL_5TBW_057
NA
IL_8V87_0451/1/1385:1387,
1/1/1420:1421		Single bulged A
geometric
IL_5TBW_058
NA
IL_8V87_0461/1/1388:1395,
1/1/1415:1419		Kink-turn
geometric
IL_5TBW_059
NA
IL_8V87_0471/1/1398:1400,
1/1/1411:1412		Single bulged A
geometric
IL_4V9F_002
IL_14190.1
IL_8V87_0481/1/1444:1450,
1/1/2354:2359		7x6 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_061
NA
IL_8V87_0501/1/1501:1505,
1/1/1513:1515		C-loop
geometric
IL_5J7L_347
NA
IL_8V87_0511/1/1532:1536,
1/1/1585:1590		UAA/GAN
geometric
IL_5TBW_063
NA
IL_8V87_0521/1/1618:1621,
1/1/1824:1826		Other IL
geometric
IL_5TBW_064
NA
IL_8V87_0531/1/1623:1624,
1/1/1820:1822		Single bulged U
geometric
IL_2R8S_004
IL_97561.1
IL_8V87_0541/1/1625:1631,
1/1/1811:1819		No text annotation
IL_8V87_0551/1/1645:1649,
1/1/1806:1810		Triple sheared
geometric
IL_5TBW_067
NA
IL_8V87_0561/1/1661:1663,
1/1/1786:1788		Isolated non-canonical cWW pair
geometric
IL_5TBW_127
NA
IL_8V87_0571/1/1669:1670,
1/1/1778:1780		Single bulged C
geometric
IL_5TBW_069
NA
IL_8V87_0581/1/1670:1671,
1/1/1776:1778		Single stack bend
geometric
IL_5TBW_070
NA
IL_8V87_0591/1/1694:1698,
1/1/1747:1752		No text annotation
geometric
IL_5TBW_071
NA
IL_8V87_0601/1/1702:1707,
1/1/1737:1743		No text annotation
geometric
IL_5TBW_072
NA
IL_8V87_0611/1/1711:1717,
1/1/1727:1733		Kink-turn
geometric
IL_5TBW_073
NA
IL_8V87_0621/1/1883:1889,
1/1/2346:2349		No text annotation
IL_8V87_1121/1/2391:2394,
1/1/2986:2988		No text annotation
IL_8V87_0681/1/2410:2412,
1/1/2809:2811		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_01003.1
IL_8V87_0691/1/2412:2413,
1/1/2807:2809		Single bulged A
geometric
IL_4R4V_003
IL_14190.1
IL_8V87_0711/1/2423:2425,
1/1/2604:2607		Isolated tHS basepair with bulges
geometric
IL_5J7L_325
NA
IL_8V87_0771/1/2452:2463,
1/1/2492:2495		No text annotation
geometric
IL_4P3T_002
NA
IL_8V87_0781/1/2466:2469,
1/1/2476:2489		No text annotation
geometric
IL_3U4M_003
IL_75283.2
IL_8V87_0791/1/2835:2839,
1/1/2849:2853		Double sheared with non-canonical cWW
geometric
IL_1U6B_002
IL_87767.1
IL_8V87_0811/1/2889:2891,
1/1/2912:2914		Isolated non-canonical cWW pair
geometric
IL_5TBW_110
NA
IL_8V87_1131/1/2889:2892,
1/1/2909:2914		No text annotation
homologous
IL_8P9A_338
IL_07469.3
IL_8V87_0821/1/2891:2892,
1/1/2909:2912		Major groove platform with intercalation
geometric
IL_4V9F_089
IL_94991.1
IL_8V87_0831/1/2959:2961,
1/1/2970:2973		Isolated cWH basepair
geometric
IL_1L9A_007
NA
IL_8V87_0841/1/3004:3007,
1/1/3139:3144		Double sheared
geometric
IL_5TBW_114
NA
IL_8V87_0851/1/3012:3015,
1/1/3039:3042		Tandem non-canonical cWW pairs
geometric
IL_4EYA_008
IL_15225.1
IL_8V87_0861/1/3018:3025,
1/1/3030:3036		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_8V87_0871/1/3047:3051,
1/1/3091:3094		Major groove minor groove platform with tHH
geometric
IL_5TBW_117
NA
IL_8V87_1141/1/3054:3058,
1/1/3085:3088		No text annotation
IL_8V87_0891/1/3063:3064,
1/1/3077:3080		Multiple bulged bases
geometric
IL_5TBW_119
NA
IL_8V87_0901/1/3103:3107,
1/1/3127:3131		UAA/GAN
geometric
IL_5TBW_120
NA
IL_8V87_0911/1/3164:3166,
1/1/3284:3286		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_01003.1
IL_8V87_0921/1/3168:3170,
1/1/3280:3282		Isolated non-canonical cWW pair
geometric
IL_2O3Y_001
IL_71625.1
IL_8V87_0931/1/3177:3179,
1/1/3210:3211		Single bulged A
geometric
IL_5TBW_123
NA
IL_8V87_0941/1/3179:3188,
1/1/3204:3210		No text annotation
geometric
IL_5TBW_124
NA
IL_8V87_0951/1/3193:3194,
1/1/3197:3199		Single bulged U
geometric
IL_5TBW_125
NA
IL_8V87_0961/1/3225:3229,
1/1/3258:3260		No text annotation
geometric
IL_5TBW_126
NA
IL_8V87_0971/1/3233:3235,
1/1/3252:3254		Isolated non-canonical cWW pair
geometric
IL_5TBW_127
NA
IL_8V87_0981/1/3235:3238,
1/1/3249:3252		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
NA
IL_8V87_0991/1/3300:3303,
1/1/3311:3314		Tandem non-canonical cWW pairs
geometric
IL_5TBW_129
NA
IL_8V87_1001/1/3318:3320,
1/1/3387:3388		Single bulged U
geometric
IL_5J7L_279
NA
IL_8V87_1011/1/3324:3325,
1/1/3381:3383		Single bulged U
geometric
IL_5TBW_131
NA
IL_8V87_1021/1/3328:3330,
1/1/3373:3378		Isolated non-canonical cWW pair
geometric
IL_5TBW_132
NA
IL_8V87_1031/1/3332:3337,
1/1/3367:3371		tHS double platform
geometric
IL_4V9F_099
IL_48489.1
IL_8V87_1041/1/3340:3342,
1/1/3363:3364		Major groove intercalation
geometric
IL_1ET4_002
NA
IL_8V87_1061/2/44:64,
1/2/96:100		No text annotation
geometric
IL_5TBW_144
NA
IL_8V87_1071/2/64:66,
1/2/93:96		Isolated non-canonical cWW pair
homologous
IL_5TBW_145
NA
IL_8V87_1081/2/68:69,
1/2/89:91		Single bulged U
homologous
IL_5TBW_146
NA
IL_8V87_1091/6/26:27,
1/6/51:54		Multiple bulged bases
geometric
IL_4V88_392
NA
IL_8V87_1101/6/30:34,
1/6/45:48		No text annotation

Problematic loops

#loop idProblemSequence
IL_8V87_019Tandem non-canonical cWW pairs
IL_8V87_023Single bulged A
IL_8V87_026No text annotation
IL_8V87_027No text annotation
IL_8V87_028Major groove platform with extra cWW
IL_8V87_031No text annotation
IL_8V87_034Isolated non-canonical cWW pair
IL_8V87_039No text annotation
IL_8V87_049No text annotation
IL_8V87_063Isolated non-canonical cWW pair
IL_8V87_064Single bulged A
IL_8V87_065Single bulged G
IL_8V87_066No text annotation
IL_8V87_067No text annotation
IL_8V87_070No text annotation
IL_8V87_072No text annotation
IL_8V87_073No text annotation
IL_8V87_074Isolated cWS basepair
IL_8V87_075Minor groove platform
IL_8V87_076Single stack bend
IL_8V87_080Tandem non-canonical cWW pairs
IL_8V87_088No text annotation
IL_8V87_105Double sheared; A in syn

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8V87_0011/1/113:123,
1/1/149:158,
1/1/263:267		No text annotation
homologous
J3_8P9A_042
J3_69230.1
J3_8V87_0091/1/113:124,
1/1/144:158,
1/1/263:267		No text annotation
J3_8V87_0101/1/185:189,
1/1/205:214,
1/1/226:231		No text annotation
homologous
J3_8P9A_044
J3_97456.1
J3_8V87_0111/1/340:356,
1/1/363:368,
1/2/21:24		No text annotation
homologous
J3_8P9A_045
J3_07616.1
J3_8V87_0121/1/369:376,
1/1/403:404,
1/2/19:20		No text annotation
geometric
J3_8C3A_048
NA
J3_8V87_0131/1/369:379,
1/1/390:404,
1/2/19:20		No text annotation
homologous
J3_8C3A_049
NA
J3_8V87_0141/1/435:441,
1/1/493:495,
1/1/618:624		No text annotation
J3_8V87_0151/1/502:503,
1/1/588:597,
1/1/606:611		No text annotation
homologous
J3_8P9A_048
J3_86133.1
J3_8V87_0041/1/1230:1232,
1/1/1256:1262,
1/1/1277:1279		No text annotation
homologous
J3_8P9A_052
J3_37832.1
J3_8V87_0051/1/1479:1485,
1/1/1857:1859,
1/1/1871:1874		No text annotation
homologous
J3_8P9A_053
J3_05025.1
J3_8V87_0161/1/1526:1531,
1/1/1591:1595,
1/1/1612:1613		No text annotation
homologous
J3_8P9A_055
J3_94309.1
J3_8V87_0171/1/1537:1542,
1/1/1551:1560,
1/1/1579:1584		No text annotation
J3_8V87_0181/1/1631:1632,
1/1/1641:1645,
1/1/1810:1811		No text annotation
homologous
J3_8C3A_054
NA
J3_8V87_0191/1/1654:1658,
1/1/1791:1792,
1/1/1796:1801		No text annotation
homologous
J3_8C3A_055
NA
J3_8V87_0061/1/2879:2882,
1/1/2940:2942,
1/1/2945:2947		No text annotation
J3_8V87_0221/1/2886:2889,
1/1/2914:2916,
1/1/2930:2936		No text annotation
homologous
J3_8CRE_023
NA
J3_8V87_0231/1/3171:3176,
1/1/3212:3220,
1/1/3265:3279		No text annotation
J3_8V87_0081/1/3298:3300,
1/1/3314:3318,
1/1/3388:3390		No text annotation
homologous
J3_8P9A_065
J3_81015.1
J3_8V87_0211/2/44:45,
1/2/58:64,
1/2/96:100		No text annotation
homologous
J3_8C3A_060
NA
J4_8V87_0011/1/112:113,
1/1/267:272,
1/1/293:299,
1/1/316:319		No text annotation
homologous
J4_8P9A_012
J4_94698.1
J4_8V87_0021/1/185:189,
1/1/205:208,
1/1/212:214,
1/1/226:231		No text annotation
homologous
J4_8P9A_013
J4_43318.1
J4_8V87_0031/1/1492:1496,
1/1/1520:1525,
1/1/1614:1615,
1/1/1829:1836		No text annotation
homologous
J4_8P9A_015
J4_47264.1
J4_8V87_0041/1/1674:1675,
1/1/1693:1694,
1/1/1752:1753,
1/1/1772:1773		No text annotation
homologous
J4_8P9A_016
J4_75575.1
J4_8V87_0051/1/3010:3012,
1/1/3042:3043,
1/1/3098:3100,
1/1/3134:3136		No text annotation
homologous
J4_8P9A_020
J4_37757.1
J5_8V87_0011/1/20:22,
1/2/35:42,
1/2/102:107,
1/2/115:116,
1/2/137:139		No text annotation
homologous
J5_8C3A_001
NA
J5_8V87_0021/1/658:663,
1/1/799:802,
1/1/941:944,
1/1/1375:1376,
1/1/1431:1437		No text annotation
homologous
J5_8C3A_002
NA
J5_8V87_0031/1/675:678,
1/1/702:706,
1/1/713:721,
1/1/749:751,
1/1/782:787		No text annotation
homologous
J5_8P9A_012
J5_56629.1
J6_8V87_0011/1/22:27,
1/1/58:68,
1/1/75:79,
1/1/106:110,
1/1/321:331,
1/2/32:35		No text annotation
J7_8V87_0011/1/949:956,
1/1/965:968,
1/1/1114:1117,
1/1/1141:1146,
1/1/1157:1161,
1/1/1338:1339,
1/1/1365:1370		No text annotation

Problematic loops

#loop idProblemSequence
J3_8V87_002No text annotation
J3_8V87_003No text annotation
J3_8V87_007No text annotation
J3_8V87_020No text annotation

Coloring options:
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