RNA 3D Hub //

2YKR Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_2YKR_0011/A/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_2YKR_0331/A/77:92No text annotation
HL_2YKR_0031/A/158:163GNRA
homologous
HL_6CZR_074
NA
HL_2YKR_0041/A/186:191GNRA
homologous
HL_5J7L_004
HL_37824.8
HL_2YKR_0051/A/207:212No text annotation
HL_2YKR_0391/A/259:267GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_2YKR_0071/A/296:301GNRA
homologous
HL_5J7L_007
HL_37824.8
HL_2YKR_0081/A/320:333No text annotation
homologous
HL_5J7L_008
HL_81205.3
HL_2YKR_0351/A/342:347UNCG
homologous
HL_6CZR_080
NA
HL_2YKR_0361/A/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_2YKR_0111/A/419:424UNCG
homologous
HL_4LFB_011
HL_34617.5
HL_2YKR_0121/A/459:473No text annotation
HL_2YKR_0131/A/522:527GNRA variation
geometric
HL_1JID_001
HL_37824.8
HL_2YKR_0141/A/617:623GNRA-like with tWH
homologous
HL_5J7L_014
HL_10453.3
HL_2YKR_0151/A/689:698No text annotation
homologous
HL_5J7L_015
HL_75293.5
HL_2YKR_0161/A/726:731GNRA
homologous
HL_4LFB_016
HL_37824.8
HL_2YKR_0171/A/786:796No text annotation
HL_2YKR_0181/A/840:846No text annotation
geometric
HL_8VM9_005
HL_32346.4
HL_2YKR_0191/A/862:867GNRA
homologous
HL_5J7L_019
HL_37824.8
HL_2YKR_0201/A/897:902GNRA
homologous
HL_5J7L_020
HL_37824.8
HL_2YKR_0211/A/963:972No text annotation
HL_2YKR_0221/A/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.8
HL_2YKR_0231/A/1028:1033No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_2YKR_0241/A/1076:1081GNRA
homologous
HL_6CZR_095
NA
HL_2YKR_0251/A/1089:1096T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_2YKR_0381/A/1134:1140No text annotation
homologous
HL_5J7L_025
HL_87954.2
HL_2YKR_0271/A/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_2YKR_0281/A/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.8
HL_2YKR_0291/A/1314:1323No text annotation
HL_2YKR_0301/A/1356:1366No text annotation
homologous
HL_5J7L_029
HL_06226.4
HL_2YKR_0401/A/1449:1454UNCG
homologous
HL_5J7L_030
HL_34617.5
HL_2YKR_0321/A/1515:1520GNRA
homologous
HL_4LFB_032
HL_37824.8

Problematic loops

#loop idProblemSequence
HL_2YKR_002No text annotation
HL_2YKR_034GNRA with extra near cWW
HL_2YKR_006tRNA D-loop
HL_2YKR_009No text annotation
HL_2YKR_010tRNA anticodon loop
HL_2YKR_037No text annotation
HL_2YKR_026No text annotation
HL_2YKR_031No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_2YKR_1051/A/30:32,
1/A/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_2YKR_0021/A/44:45,
1/A/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_2YKR_1061/A/54:56,
1/A/356:357		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_2YKR_0861/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_6CZR_117
NA
IL_2YKR_0061/A/67:69,
1/A/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_2YKR_0871/A/70:73,
1/A/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_2YKR_0081/A/75:76,
1/A/93:95		No text annotation
IL_2YKR_0101/A/128:136,
1/A/227:233		No text annotation
IL_2YKR_0881/A/144:146,
1/A/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_2YKR_1071/A/147:153,
1/A/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_2YKR_0901/A/202:206,
1/A/213:215		No text annotation
IL_2YKR_0151/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_2YKR_0911/A/249:252,
1/A/274:275		No text annotation
homologous
IL_6CZR_405
NA
IL_2YKR_0191/A/292:293,
1/A/304:308		No text annotation
IL_2YKR_0221/A/367:369,
1/A/392:393		Single bulged U
geometric
IL_5J7L_279
IL_89505.4
IL_2YKR_0231/A/370:376,
1/A/387:391		No text annotation
IL_2YKR_0251/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_2YKR_0261/A/446:450,
1/A/483:488		tSH-tHW-tWW
geometric
IL_5J7L_022
IL_88269.4
IL_2YKR_1081/A/446:455,
1/A/477:488		No text annotation
IL_2YKR_0271/A/450:455,
1/A/477:483		No text annotation
IL_2YKR_0291/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_2YKR_0311/A/515:521,
1/A/528:536		No text annotation
IL_2YKR_0321/A/569:575,
1/A/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_2YKR_0341/A/580:584,
1/A/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_2YKR_0361/A/594:596,
1/A/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_2YKR_0371/A/597:598,
1/A/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_2YKR_1091/A/605:612,
1/A/628:633		No text annotation
IL_2YKR_1101/A/654:655,
1/A/751:754		Major groove platform; stack outside cWW
geometric
IL_9DFE_065
IL_50694.7
IL_2YKR_0971/A/658:659,
1/A/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_2YKR_0421/A/662:666,
1/A/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_2YKR_0981/A/673:677,
1/A/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
IL_49751.4
IL_2YKR_0441/A/683:688,
1/A/699:707		Kink-turn
homologous
IL_4LFB_031
IL_95727.1
IL_2YKR_0461/A/772:779,
1/A/803:807		No text annotation
IL_2YKR_1111/A/774:783,
1/A/799:805		No text annotation
IL_2YKR_0471/A/779:783,
1/A/799:803		tSH-tHW-tHS
geometric
IL_4LFB_033
IL_17136.7
IL_2YKR_0491/A/887:895,
1/A/904:910		9x7 Sarcin-Ricin with inserted C; G-bulge
homologous
IL_6CZR_146
NA
IL_2YKR_1121/A/922:923,
1/A/1393:1395		Single bulged A
homologous
IL_4LFB_035
IL_31462.7
IL_2YKR_0511/A/924:927,
1/A/1390:1392		No text annotation
IL_2YKR_0521/A/933:935,
1/A/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_2YKR_1131/A/993:997,
1/A/1044:1045		Minor groove platform
geometric
IL_5J7L_043
IL_47078.3
IL_2YKR_1141/A/998:999,
1/A/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_2YKR_0581/A/1048:1050,
1/A/1208:1209		Single bulged U
homologous
IL_4LFB_042
IL_89505.4
IL_2YKR_0591/A/1052:1058,
1/A/1199:1206		No text annotation
geometric
IL_4V88_510
NA
IL_2YKR_0601/A/1060:1061,
1/A/1195:1197		Single bulged A
homologous
IL_5J7L_049
IL_31462.7
IL_2YKR_0621/A/1121:1128,
1/A/1144:1152		No text annotation
IL_2YKR_0631/A/1129:1132,
1/A/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_2YKR_1001/A/1158:1162,
1/A/1174:1181		No text annotation
IL_2YKR_1151/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_4LFB_051
IL_09129.2
IL_2YKR_0671/A/1255:1258,
1/A/1277:1282		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_2YKR_0681/A/1259:1263,
1/A/1272:1276		No text annotation
IL_2YKR_0691/A/1303:1308,
1/A/1329:1334		No text annotation
homologous
IL_5J7L_057
IL_85536.2
IL_2YKR_0731/A/1399:1401,
1/A/1501:1504		No text annotation
homologous
IL_5J7L_058
IL_61438.4
IL_2YKR_0741/A/1401:1404,
1/A/1497:1501		No text annotation
geometric
IL_4V88_464
NA
IL_2YKR_0751/A/1405:1407,
1/A/1494:1496		Isolated non-canonical cWW pair
geometric
IL_5Z1I_001
NA
IL_2YKR_1021/A/1405:1409,
1/A/1491:1496		Partly complementary
homologous
IL_6CZR_167
NA
IL_2YKR_0761/A/1407:1409,
1/A/1491:1494		No text annotation
IL_2YKR_0771/A/1412:1416,
1/A/1484:1488		Partly complementary
geometric
IL_8D29_010
IL_49751.4
IL_2YKR_0781/A/1416:1419,
1/A/1481:1484		Double sheared
geometric
IL_1SA9_002
IL_09705.15
IL_2YKR_1161/A/1430:1435,
1/A/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_2YKR_1041/A/1440:1442,
1/A/1460:1461		No text annotation
geometric
IL_8C3A_483
NA
IL_2YKR_0841/A/1445:1448,
1/A/1455:1457		No text annotation

Problematic loops

#loop idProblemSequence
IL_2YKR_001Isolated non-canonical cWW pair
IL_2YKR_003Minor groove platform with extra cWW
IL_2YKR_004Isolated non-canonical cWW pair
IL_2YKR_005Isolated non-canonical cWW pair
IL_2YKR_007No text annotation
IL_2YKR_009No text annotation
IL_2YKR_011Tandem non-canonical cWW pairs
IL_2YKR_089No text annotation
IL_2YKR_012No text annotation
IL_2YKR_013No text annotation
IL_2YKR_014No text annotation
IL_2YKR_016No text annotation
IL_2YKR_017Isolated non-canonical cWW pair
IL_2YKR_018Isolated non-canonical cWW pair
IL_2YKR_020No text annotation
IL_2YKR_021Isolated non-canonical cWW pair
IL_2YKR_092No text annotation
IL_2YKR_024Tandem non-canonical cWW pairs
IL_2YKR_093No text annotation
IL_2YKR_094No text annotation
IL_2YKR_028No text annotation
IL_2YKR_030No text annotation
IL_2YKR_095No text annotation
IL_2YKR_033No text annotation
IL_2YKR_035Isolated non-canonical cWW pair
IL_2YKR_038Tandem non-canonical cWW pairs with near WC pairs
IL_2YKR_039No text annotation
IL_2YKR_096No text annotation
IL_2YKR_040No text annotation
IL_2YKR_041No text annotation
IL_2YKR_043No text annotation
IL_2YKR_045Isolated non-canonical cWW pair
IL_2YKR_099No text annotation
IL_2YKR_048Self complementary
IL_2YKR_050No text annotation
IL_2YKR_053Decoding loop related
IL_2YKR_054Isolated non-canonical cWW pair
IL_2YKR_055Isolated non-canonical cWW pair
IL_2YKR_056No text annotation
IL_2YKR_057No text annotation
IL_2YKR_061Isolated non-canonical cWW pair
IL_2YKR_064No text annotation
IL_2YKR_065No text annotation
IL_2YKR_101No text annotation
IL_2YKR_066No text annotation
IL_2YKR_070No text annotation
IL_2YKR_071Self complementary
IL_2YKR_072Isolated non-canonical cWW pair
IL_2YKR_079Isolated non-canonical cWW pair
IL_2YKR_080Isolated non-canonical cWW pair
IL_2YKR_085No text annotation
IL_2YKR_103No text annotation
IL_2YKR_082No text annotation
IL_2YKR_083No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_2YKR_0011/A/46:52,
1/A/359:367,
1/A/393:395		No text annotation
homologous
J3_4LFB_014
J3_46317.4
J3_2YKR_0111/A/586:588,
1/A/651:654,
1/A/754:755		No text annotation
geometric
J3_5J7L_002
J3_56052.5
J3_2YKR_0221/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_2YKR_0121/A/672:673,
1/A/717:725,
1/A/732:734		No text annotation
J3_2YKR_0161/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_2YKR_0031/A/936:939,
1/A/1344:1350,
1/A/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_2YKR_0171/A/943:946,
1/A/1235:1237,
1/A/1337:1340		No text annotation
homologous
J3_5J7L_005
J3_52655.4
J3_2YKR_0051/A/953:962,
1/A/973:984,
1/A/1221:1228		No text annotation
J3_2YKR_0061/A/990:993,
1/A/1045:1047,
1/A/1210:1215		No text annotation
homologous
J3_4LFB_005
J3_82572.1
J3_2YKR_0231/A/990:997,
1/A/1044:1047,
1/A/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_2YKR_0241/A/1003:1006,
1/A/1023:1027,
1/A/1034:1037		No text annotation
J3_2YKR_0081/A/1061:1068,
1/A/1107:1113,
1/A/1187:1195		No text annotation
J3_2YKR_0131/A/1073:1074,
1/A/1083:1087,
1/A/1098:1102		No text annotation
J3_2YKR_0251/A/1116:1118,
1/A/1155:1158,
1/A/1181:1184		No text annotation
J3_2YKR_0261/A/1116:1118,
1/A/1155:1162,
1/A/1174:1184		No text annotation
J3_2YKR_0101/A/1237:1241,
1/A/1296:1303,
1/A/1334:1337		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J3_2YKR_0211/A/1237:1241,
1/A/1296:1308,
1/A/1329:1337		No text annotation
J4_2YKR_0011/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
J4_2YKR_0021/A/142:144,
1/A/178:184,
1/A/193:198,
1/A/219:221		No text annotation
homologous
J4_5J7L_002
J4_01665.1
J4_2YKR_0031/A/575:577,
1/A/764:769,
1/A/810:821,
1/A/879:880		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J5_2YKR_0011/A/36:39,
1/A/403:406,
1/A/436:442,
1/A/492:500,
1/A/545:548		No text annotation
homologous
J5_5J7L_002
J5_67416.1
J5_2YKR_0021/A/58:63,
1/A/104:113,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_6CZR_008
NA

Problematic loops

#loop idProblemSequence
J3_2YKR_014No text annotation
J3_2YKR_015No text annotation
J3_2YKR_002No text annotation
J3_2YKR_004No text annotation
J3_2YKR_018No text annotation
J3_2YKR_019No text annotation
J3_2YKR_007No text annotation
J3_2YKR_009No text annotation
J3_2YKR_020No text annotation

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