RNA 3D Hub //

5XYU Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5XYU_0011/A/16:26No text annotation
homologous
HL_5J7L_001
NA
HL_5XYU_0041/A/191:196No text annotation
HL_5XYU_0311/A/259:267GNRA related
homologous
HL_5J7L_006
NA
HL_5XYU_0071/A/296:301GNRA
homologous
HL_4LFB_007
HL_34789.4
HL_5XYU_0081/A/320:333No text annotation
HL_5XYU_0091/A/342:347UNCG
homologous
HL_4LFB_009
HL_61337.3
HL_5XYU_0101/A/379:384GNRA
homologous
HL_4LFB_010
HL_34789.4
HL_5XYU_0131/A/502:507No text annotation
geometric
HL_5J7L_143
NA
HL_5XYU_0141/A/597:603GNRA-like with tWH
homologous
HL_4LFB_014
HL_86621.1
HL_5XYU_0301/A/664:686No text annotation
HL_5XYU_0151/A/669:678No text annotation
homologous
HL_4LFB_015
HL_38491.2
HL_5XYU_0161/A/706:711GNRA
homologous
HL_5J7L_016
NA
HL_5XYU_0171/A/766:776No text annotation
homologous
HL_5J7L_017
NA
HL_5XYU_0191/A/844:849GNRA
homologous
HL_5J7L_019
NA
HL_5XYU_0201/A/879:884GNRA
homologous
HL_4LFB_020
HL_34789.4
HL_5XYU_0211/A/945:954No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_5XYU_0221/A/995:1000GNRA
homologous
HL_4LFB_022
HL_34789.4
HL_5XYU_0231/A/1056:1061GNRA
homologous
HL_5J7L_023
NA
HL_5XYU_0251/A/1246:1251GNRA
homologous
HL_4LFB_028
HL_34789.4
HL_5XYU_0261/A/1296:1305T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
NA
HL_5XYU_0271/A/1338:1349No text annotation
homologous
HL_4LFB_030
HL_86432.1
HL_5XYU_0291/A/1499:1504GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_5XYU_002No text annotation
HL_5XYU_003No text annotation
HL_5XYU_005No text annotation
HL_5XYU_006tRNA D-loop
HL_5XYU_011No text annotation
HL_5XYU_012No text annotation
HL_5XYU_018No text annotation
HL_5XYU_024No text annotation
HL_5XYU_028No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5XYU_0011/A/34:36,
1/A/532:533		Single bulged G
homologous
IL_5J7L_001
NA
IL_5XYU_0021/A/48:49,
1/A/396:398		Single bulged A
homologous
IL_4LFB_002
IL_14190.2
IL_5XYU_0031/A/51:56,
1/A/359:361		No text annotation
geometric
IL_5J7L_003
NA
IL_5XYU_0041/A/58:60,
1/A/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_34520.3
IL_5XYU_0051/A/67:70,
1/A/99:100		Multiple bulged bases
homologous
IL_4LFB_005
IL_71421.2
IL_5XYU_0061/A/125:128,
1/A/231:232		Multiple bulged bases
homologous
IL_4LFB_007
IL_75289.1
IL_5XYU_0071/A/129:133,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_60988.2
IL_5XYU_0691/A/144:150,
1/A/165:172		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_5XYU_0611/A/183:188,
1/A/199:205		No text annotation
geometric
IL_5TBW_476
NA
IL_5XYU_0091/A/186:188,
1/A/199:202		Isolated cWS basepair
geometric
IL_4TS2_003
NA
IL_5XYU_0101/A/241:247,
1/A/277:285		No text annotation
IL_5XYU_0111/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_5XYU_0121/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_5XYU_0131/A/367:369,
1/A/392:393		Single bulged U
geometric
IL_5J7L_017
NA
IL_5XYU_0141/A/371:375,
1/A/389:390		C-loop
geometric
IL_5J7L_018
NA
IL_5XYU_0151/A/375:376,
1/A/387:389		Single bulged G
homologous
IL_5J7L_019
NA
IL_5XYU_0161/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_62329.1
IL_5XYU_0701/A/440:442,
1/A/472:477		No text annotation
geometric
IL_5J7L_021
NA
IL_5XYU_0181/A/446:450,
1/A/463:468		6x5 Sarcin-Ricin; G-bulge
homologous
IL_4LFB_018
IL_82100.1
IL_5XYU_0191/A/484:491,
1/A/520:521		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_11411.1
IL_5XYU_0211/A/549:555,
1/A/862:863		No text annotation
homologous
IL_5J7L_026
NA
IL_5XYU_0221/A/560:564,
1/A/737:741		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_5XYU_0241/A/574:576,
1/A/624:625		Major groove platform
homologous
IL_4LFB_024
IL_48076.8
IL_5XYU_0251/A/577:578,
1/A/620:623		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_73108.2
IL_5XYU_0711/A/585:591,
1/A/609:613		No text annotation
IL_5XYU_0271/A/634:635,
1/A/731:734		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_74641.2
IL_5XYU_0721/A/637:639,
1/A/726:729		No text annotation
IL_5XYU_0291/A/642:646,
1/A/720:723		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
NA
IL_5XYU_0731/A/653:657,
1/A/693:697		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
NA
IL_5XYU_0311/A/664:668,
1/A/679:686		Kink-turn
homologous
IL_5J7L_035
NA
IL_5XYU_0321/A/754:758,
1/A/784:785		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_5XYU_0331/A/759:763,
1/A/779:783		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_5XYU_0341/A/869:876,
1/A/887:892		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_5XYU_0651/A/904:905,
1/A/1376:1378		Single bulged A
homologous
IL_4LFB_035
IL_14190.2
IL_5XYU_0361/A/907:909,
1/A/1373:1374		Single bulged G
homologous
IL_4LFB_036
IL_28408.2
IL_5XYU_0371/A/915:917,
1/A/1363:1367		Minor groove platform
homologous
IL_4LFB_037
IL_61370.1
IL_5XYU_0381/A/1028:1030,
1/A/1189:1190		Single bulged U
homologous
IL_5J7L_046
NA
IL_5XYU_0391/A/1032:1036,
1/A/1185:1187		No text annotation
homologous
IL_6CZR_154
NA
IL_5XYU_0401/A/1037:1038,
1/A/1180:1184		Minor groove platform
homologous
IL_5J7L_048
NA
IL_5XYU_0411/A/1040:1041,
1/A/1176:1178		Single bulged A
geometric
IL_5J7L_049
NA
IL_5XYU_0421/A/1041:1043,
1/A/1174:1176		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.3
IL_5XYU_0451/A/1104:1108,
1/A/1125:1130		No text annotation
homologous
IL_5J7L_051
NA
IL_5XYU_0461/A/1236:1239,
1/A/1258:1263		180 degree turn
homologous
IL_5J7L_055
NA
IL_5XYU_0471/A/1240:1244,
1/A/1253:1257		Double sheared with non-canonical cWW
homologous
IL_5J7L_056
NA
IL_5XYU_0741/A/1285:1294,
1/A/1307:1316		No text annotation
IL_5XYU_0481/A/1382:1384,
1/A/1485:1488		No text annotation
homologous
IL_5J7L_058
NA
IL_5XYU_0491/A/1384:1387,
1/A/1481:1485		No text annotation
homologous
IL_5J7L_059
NA
IL_5XYU_0501/A/1388:1390,
1/A/1478:1480		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.3
IL_5XYU_0511/A/1390:1392,
1/A/1475:1478		Decoding loop related
geometric
IL_3C3Z_002
IL_53541.1
IL_5XYU_0521/A/1395:1397,
1/A/1470:1472		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_01003.3
IL_5XYU_0531/A/1399:1402,
1/A/1465:1468		Double sheared
homologous
IL_6CZR_169
NA
IL_5XYU_0551/A/1413:1418,
1/A/1450:1454		Triple sheared related
geometric
IL_4V9F_018
IL_67427.1
IL_5XYU_0751/A/1418:1420,
1/A/1448:1450		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_01003.3
IL_5XYU_0571/A/1423:1426,
1/A/1443:1445		Isolated tHS basepair with bulges
geometric
IL_7RQB_082
NA

Problematic loops

#loop idProblemSequence
IL_5XYU_058Isolated non-canonical cWW pair
IL_5XYU_059No text annotation
IL_5XYU_060No text annotation
IL_5XYU_008No text annotation
IL_5XYU_017No text annotation
IL_5XYU_062No text annotation
IL_5XYU_020No text annotation
IL_5XYU_023Not an internal loop
IL_5XYU_026No text annotation
IL_5XYU_028Tandem non-canonical cWW pairs
IL_5XYU_030No text annotation
IL_5XYU_063No text annotation
IL_5XYU_064No text annotation
IL_5XYU_035Isolated non-canonical cWW with bulges
IL_5XYU_066No text annotation
IL_5XYU_043Multiple bulged bases
IL_5XYU_044No text annotation
IL_5XYU_067No text annotation
IL_5XYU_054No text annotation
IL_5XYU_056Tandem non-canonical cWW pairs
IL_5XYU_068Triple non-canonical cWW pairs

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5XYU_0011/A/50:51,
1/A/361:367,
1/A/393:395		No text annotation
homologous
J3_5J7L_001
NA
J3_5XYU_0111/A/50:51,
1/A/361:369,
1/A/392:395		No text annotation
J3_5XYU_0121/A/50:56,
1/A/359:369,
1/A/392:395		No text annotation
J3_5XYU_0021/A/566:568,
1/A/631:634,
1/A/734:735		No text annotation
homologous
J3_5J7L_002
NA
J3_5XYU_0131/A/566:568,
1/A/631:635,
1/A/731:735		No text annotation
homologous
J3_5J7L_051
NA
J3_5XYU_0031/A/652:653,
1/A/697:705,
1/A/712:714		No text annotation
homologous
J3_6CZR_017
NA
J3_5XYU_0041/A/806:809,
1/A/839:843,
1/A/850:856		No text annotation
homologous
J3_5J7L_004
NA
J3_5XYU_0051/A/918:921,
1/A/1326:1332,
1/A/1355:1362		No text annotation
homologous
J3_4LFB_002
J3_85722.1
J3_5XYU_0061/A/925:928,
1/A/1216:1218,
1/A/1319:1322		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_5XYU_0071/A/935:944,
1/A/955:966,
1/A/1202:1209		No text annotation
J3_5XYU_0081/A/969:975,
1/A/1025:1027,
1/A/1191:1199		No text annotation
J3_5XYU_0091/A/1043:1048,
1/A/1087:1093,
1/A/1168:1174		No text annotation
homologous
J3_5J7L_008
NA
J3_5XYU_0101/A/1218:1222,
1/A/1278:1285,
1/A/1316:1319		No text annotation
homologous
J3_4LFB_009
J3_03192.1
J4_5XYU_0011/A/111:119,
1/A/238:240,
1/A/286:289,
1/A/311:312		No text annotation
J4_5XYU_0021/A/555:557,
1/A/744:749,
1/A/790:801,
1/A/861:862		No text annotation
homologous
J4_5J7L_003
NA
J5_5XYU_0041/A/40:43,
1/A/403:406,
1/A/436:440,
1/A/477:480,
1/A/525:528		No text annotation
J5_5XYU_0051/A/40:43,
1/A/403:406,
1/A/436:442,
1/A/472:480,
1/A/525:528		No text annotation
homologous
J5_5J7L_002
NA
J5_5XYU_0031/A/62:65,
1/A/102:109,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_4LFB_002
J5_58574.1

Problematic loops

#loop idProblemSequence
J5_5XYU_001No text annotation
J5_5XYU_002No text annotation

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