RNA 3D Hub //

7UPH Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7UPH_0011/I/11:21No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_7UPH_1111/I/80:87No text annotation
HL_7UPH_0031/I/157:162GNRA
homologous
HL_5J7L_003
HL_37824.7
HL_7UPH_0041/I/185:190GNRA
homologous
HL_5J7L_004
HL_37824.7
HL_7UPH_0051/I/202:213No text annotation
HL_7UPH_0061/I/258:266GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_7UPH_0071/I/295:300GNRA
homologous
HL_5J7L_007
HL_37824.7
HL_7UPH_0081/I/319:332No text annotation
homologous
HL_5J7L_008
HL_81205.3
HL_7UPH_0091/I/341:346UNCG
homologous
HL_5J7L_009
HL_34617.5
HL_7UPH_0101/I/378:383GNRA
homologous
HL_6CZR_081
NA
HL_7UPH_0111/I/418:423UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_7UPH_0121/I/461:469GNRA related
homologous
HL_5J7L_012
HL_81538.2
HL_7UPH_1021/I/521:526GNRA variation
homologous
HL_5J7L_205
HL_37824.7
HL_7UPH_0141/I/616:622No text annotation
homologous
HL_5J7L_014
HL_10453.3
HL_7UPH_0151/I/688:697No text annotation
homologous
HL_5J7L_015
HL_75293.5
HL_7UPH_0161/I/725:730GNRA
homologous
HL_6CZR_087
NA
HL_7UPH_0171/I/785:795No text annotation
homologous
HL_5J7L_017
HL_75293.5
HL_7UPH_1121/I/839:845No text annotation
HL_7UPH_0191/I/861:866GNRA
homologous
HL_5J7L_019
HL_37824.7
HL_7UPH_0201/I/896:901GNRA
homologous
HL_5J7L_020
HL_37824.7
HL_7UPH_0211/I/962:971No text annotation
homologous
HL_5J7L_021
HL_50779.4
HL_7UPH_0221/I/1006:1021No text annotation
homologous
HL_5J7L_022
NA
HL_7UPH_0231/I/1075:1080GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_7UPH_0241/I/1088:1095T-loop related
homologous
HL_5J7L_024
HL_77436.5
HL_7UPH_0251/I/1132:1140No text annotation
geometric
HL_7KI3_001
HL_75660.5
HL_7UPH_0261/I/1164:1170GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_7UPH_0271/I/1264:1269No text annotation
homologous
HL_6CZR_099
NA
HL_7UPH_0281/I/1313:1322T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
HL_02887.3
HL_7UPH_0291/I/1355:1365No text annotation
homologous
HL_4LFB_030
HL_06226.4
HL_7UPH_0301/I/1498:1501No text annotation
HL_7UPH_0311/I/1559:1568No text annotation
geometric
HL_5J7L_134
HL_35677.3
HL_7UPH_0321/I/1585:1597No text annotation
HL_7UPH_0331/I/1623:1628No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_7UPH_0341/I/1634:1645No text annotation
geometric
HL_2ZZM_002
HL_13963.3
HL_7UPH_0351/I/1658:1668No text annotation
geometric
HL_5J7L_138
HL_68257.1
HL_7UPH_0361/I/1694:1701No text annotation
geometric
HL_5TBW_001
NA
HL_7UPH_0371/I/1725:1730UNCG
geometric
HL_6JQ6_004
HL_34617.5
HL_7UPH_0381/I/1746:1752No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_7UPH_0391/I/1805:1812T-loop with 2 stacked bulged bases
geometric
HL_4WF9_010
HL_01609.3
HL_7UPH_0401/I/1819:1823No text annotation
geometric
HL_4WF9_011
HL_75660.5
HL_7UPH_0411/I/1827:1835T-loop with unstacked turn
geometric
HL_4V9F_012
HL_27670.2
HL_7UPH_0421/I/1881:1893No text annotation
geometric
HL_4WF9_013
HL_69139.1
HL_7UPH_0431/I/1910:1917Pseudoknot geometry
geometric
HL_4GXY_003
HL_65794.5
HL_7UPH_0441/I/1962:1967No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_7UPH_0451/I/1987:1993No text annotation
geometric
HL_3IGI_004
HL_04783.2
HL_7UPH_0461/I/2043:2050No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_7UPH_1051/I/2064:2077No text annotation
HL_7UPH_0471/I/2066:2075T-loop with 2 bulged bases not stacked
geometric
HL_3F2X_004
HL_01609.3
HL_7UPH_0481/I/2111:2117No text annotation
geometric
HL_5J7L_151
HL_80922.2
HL_7UPH_0491/I/2129:2134GNRA
geometric
HL_5M0J_001
HL_37824.7
HL_7UPH_1131/I/2141:2147No text annotation
homologous
HL_5J7L_153
HL_13529.1
HL_7UPH_0511/I/2212:2219GNRA wlth tandem sheared
geometric
HL_1MMS_002
HL_81538.2
HL_7UPH_0521/I/2244:2253No text annotation
geometric
HL_5J7L_155
HL_88205.2
HL_7UPH_1061/I/2279:2285No text annotation
geometric
HL_7A0S_023
HL_53890.2
HL_7UPH_0541/I/2324:2333No text annotation
HL_7UPH_1071/I/2380:2391No text annotation
HL_7UPH_0551/I/2381:2389No text annotation
HL_7UPH_1081/I/2449:2456GNRA
geometric
HL_5J7L_211
HL_37824.7
HL_7UPH_0571/I/2472:2479No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_7UPH_0581/I/2558:2568No text annotation
geometric
HL_1MMS_001
HL_19210.3
HL_7UPH_0591/I/2586:2593GNRA wlth tandem sheared
geometric
HL_4WF9_004
HL_81538.2
HL_7UPH_0601/I/2663:2674No text annotation
geometric
HL_4V9F_003
HL_75660.5
HL_7UPH_0611/I/2716:2721GNRA
geometric
HL_7A0S_031
HL_37824.7
HL_7UPH_0621/I/2775:2783No text annotation
geometric
HL_4WF9_011
HL_75660.5
HL_7UPH_0631/I/2818:2824Pseudoknot geometry with 3' bulge
geometric
HL_4V9F_035
HL_57176.2
HL_7UPH_0641/I/2857:2862GNRA
geometric
HL_5J7L_167
HL_37824.7
HL_7UPH_0651/I/2883:2892No text annotation
geometric
HL_4V9F_037
HL_81545.2
HL_7UPH_0661/I/2945:2953Mini UNCG
geometric
HL_5F9R_002
HL_48778.2
HL_7UPH_0671/I/2986:2992Mini UNCG
geometric
HL_1ZBH_001
HL_56334.1
HL_7UPH_0681/I/3025:3034No text annotation
HL_7UPH_0691/I/3059:3062Mini UNCG
geometric
HL_7A0S_039
HL_48778.2
HL_7UPH_0701/I/3106:3113No text annotation
geometric
HL_4WF9_038
HL_89567.2
HL_7UPH_0711/I/3124:3130GNRA
geometric
HL_3DIL_003
HL_30068.2
HL_7UPH_0721/I/3185:3190No text annotation
geometric
HL_4V9F_011
HL_75660.5
HL_7UPH_0731/I/3221:3227No text annotation
homologous
HL_5J7L_214
HL_08100.1
HL_7UPH_0741/I/3246:3250Externally structured
geometric
HL_8C3A_022
NA
HL_7UPH_0751/I/3271:3281No text annotation
geometric
HL_4WF9_043
HL_01962.2
HL_7UPH_0761/I/3298:3307No text annotation
HL_7UPH_0771/I/3361:3368No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_7UPH_0781/I/3404:3414Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_7UPH_0791/I/3443:3451No text annotation
geometric
HL_5J7L_182
HL_20167.2
HL_7UPH_0801/I/3521:3530No text annotation
geometric
HL_4WF9_047
HL_61996.2
HL_7UPH_0811/I/3637:3642No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_7UPH_0821/I/3703:3709No text annotation
geometric
HL_5J7L_185
HL_49922.4
HL_7UPH_0831/I/3742:3750No text annotation
geometric
HL_7A0S_052
HL_85367.2
HL_7UPH_0841/I/3758:3770No text annotation
geometric
HL_7RQB_054
NA
HL_7UPH_1141/I/3798:3806No text annotation
homologous
HL_9DFE_198
HL_50860.2
HL_7UPH_0861/I/3817:3826No text annotation
HL_7UPH_0871/I/3850:3855GNRA
geometric
HL_4Y1M_002
HL_37824.7
HL_7UPH_0881/I/3868:3873No text annotation
geometric
HL_361D_002
HL_13963.3
HL_7UPH_0891/I/3898:3907No text annotation
geometric
HL_7RQB_059
NA
HL_7UPH_0901/I/3965:3973No text annotation
geometric
HL_361D_002
HL_13963.3
HL_7UPH_1091/I/4022:4029Mini UNCG
geometric
HL_5VW1_002
HL_48778.2
HL_7UPH_0921/I/4045:4051No text annotation
geometric
HL_5TBW_063
NA
HL_7UPH_0931/I/4088:4093No text annotation
geometric
HL_4WF9_011
HL_75660.5
HL_7UPH_0941/I/4152:4157GNRA
geometric
HL_7A0S_005
HL_37824.7
HL_7UPH_1151/I/4195:4200Ribsomal LSU H95
homologous
HL_5J7L_198
HL_65794.5
HL_7UPH_0961/I/4239:4253No text annotation
geometric
HL_5J7L_199
HL_74055.2
HL_7UPH_0971/I/4290:4293Mini UNCG
geometric
HL_4V88_192
NA
HL_7UPH_0981/I/4313:4321No text annotation
geometric
HL_7A0S_067
HL_64690.6
HL_7UPH_0991/I/4419:4424No text annotation
geometric
HL_7A0S_011
HL_75660.5
HL_7UPH_1161/J/33:47No text annotation
homologous
HL_5J7L_215
HL_97756.2
HL_7UPH_1001/J/37:43No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_7UPH_1011/J/85:89Mini UNCG
homologous
HL_5J7L_204
HL_48778.2

Problematic loops

#loop idProblemSequence
HL_7UPH_002No text annotation
HL_7UPH_013No text annotation
HL_7UPH_018No text annotation
HL_7UPH_103No text annotation
HL_7UPH_104No text annotation
HL_7UPH_050No text annotation
HL_7UPH_053No text annotation
HL_7UPH_056GNRA with extra cWW
HL_7UPH_085No text annotation
HL_7UPH_091No text annotation
HL_7UPH_095No text annotation
HL_7UPH_110No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7UPH_0011/I/29:31,
1/I/551:552		Single bulged G
homologous
IL_5J7L_001
IL_00225.13
IL_7UPH_0021/I/43:44,
1/I/395:397		Single bulged A
homologous
IL_5J7L_002
IL_31462.6
IL_7UPH_0031/I/46:51,
1/I/358:360		No text annotation
homologous
IL_5J7L_003
IL_14177.2
IL_7UPH_0041/I/53:55,
1/I/355:356		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_7UPH_0051/I/62:65,
1/I/102:103		Multiple bulged bases
homologous
IL_5J7L_005
IL_82107.4
IL_7UPH_0061/I/66:68,
1/I/98:101		Minor groove platform with extra cWW
geometric
IL_5J7L_006
IL_90351.1
IL_7UPH_2151/I/69:72,
1/I/96:97		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_7UPH_0081/I/74:75,
1/I/92:94		Single bulged G
homologous
IL_5J7L_395
IL_00225.13
IL_7UPH_0091/I/127:130,
1/I/230:232		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
IL_57744.1
IL_7UPH_0101/I/131:135,
1/I/226:229		Minor groove platform related
homologous
IL_6CZR_120
NA
IL_7UPH_0111/I/143:145,
1/I/175:177		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_7UPH_0121/I/146:152,
1/I/167:174		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_7UPH_0131/I/241:246,
1/I/276:283		Kink-turn with non-sequential stacking
geometric
IL_4V88_402
NA
IL_7UPH_1791/I/248:251,
1/I/273:274		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_7UPH_0151/I/291:292,
1/I/303:307		C-loop
homologous
IL_6CZR_125
NA
IL_7UPH_0161/I/366:368,
1/I/391:392		Single bulged U
homologous
IL_5J7L_017
IL_89505.4
IL_7UPH_1801/I/370:374,
1/I/388:389		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_7UPH_0181/I/374:376,
1/I/385:388		Single bulged G, near cWW
homologous
IL_6CZR_128
NA
IL_7UPH_0191/I/408:415,
1/I/426:432		No text annotation
homologous
IL_5J7L_020
IL_28026.3
IL_7UPH_0201/I/439:441,
1/I/491:496		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_7UPH_0211/I/445:449,
1/I/482:487		tSH-tHW-tWW
geometric
IL_5J7L_022
IL_88269.4
IL_7UPH_0221/I/449:454,
1/I/476:482		No text annotation
homologous
IL_5J7L_023
IL_70801.1
IL_7UPH_0231/I/503:510,
1/I/539:540		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_7UPH_0241/I/514:520,
1/I/527:535		Kink-turn related
homologous
IL_5J7L_025
IL_54177.4
IL_7UPH_0251/I/568:574,
1/I/879:880		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_7UPH_0261/I/579:583,
1/I/756:760		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_7UPH_1821/I/592:595,
1/I/643:645		No text annotation
geometric
IL_7SZU_003
IL_55516.2
IL_7UPH_0271/I/593:595,
1/I/643:644		Major groove platform
homologous
IL_4LFB_024
IL_48076.6
IL_7UPH_0281/I/596:597,
1/I/639:642		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_68140.4
IL_7UPH_0291/I/604:611,
1/I/627:632		No text annotation
homologous
IL_5J7L_030
IL_78349.3
IL_7UPH_0301/I/653:654,
1/I/750:753		Major groove platform; stack outside cWW
homologous
IL_5J7L_031
IL_50694.7
IL_7UPH_1831/I/656:658,
1/I/745:748		No text annotation
IL_7UPH_0321/I/661:665,
1/I/739:742		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_7UPH_0331/I/672:677,
1/I/711:716		No text annotation
homologous
IL_4LFB_030
NA
IL_7UPH_0341/I/683:687,
1/I/698:705		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_7UPH_2161/I/773:777,
1/I/803:804		Left turn
homologous
IL_4LFB_032
IL_29346.2
IL_7UPH_0361/I/778:782,
1/I/798:802		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_7UPH_0371/I/886:893,
1/I/904:909		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
IL_41756.4
IL_7UPH_0381/I/921:922,
1/I/1392:1394		Single bulged A
homologous
IL_6CZR_147
NA
IL_7UPH_0391/I/923:926,
1/I/1389:1391		Isolated non-canonical cWW pair
geometric
IL_4Y1M_005
IL_07785.1
IL_7UPH_1841/I/924:927,
1/I/1388:1390		Isolated non-canonical cWW pair
geometric
IL_4ZC7_004
IL_87907.2
IL_7UPH_0401/I/932:934,
1/I/1379:1383		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_7UPH_0411/I/952:953,
1/I/1225:1227		No text annotation
homologous
IL_6CZR_150
NA
IL_7UPH_0431/I/1001:1005,
1/I/1022:1037		No text annotation
IL_7UPH_0441/I/1047:1049,
1/I/1207:1208		No text annotation
homologous
IL_6CZR_152
NA
IL_7UPH_2171/I/1051:1055,
1/I/1203:1205		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_7UPH_0461/I/1056:1057,
1/I/1198:1202		Minor groove platform
homologous
IL_4LFB_045
IL_95583.2
IL_7UPH_0471/I/1059:1060,
1/I/1194:1196		Single bulged U
homologous
IL_6CZR_156
NA
IL_7UPH_0481/I/1060:1062,
1/I/1192:1194		Isolated non-canonical cWW pair
geometric
IL_5J7L_050
IL_28037.2
IL_7UPH_0491/I/1123:1127,
1/I/1143:1148		No text annotation
homologous
IL_5J7L_051
IL_06691.1
IL_7UPH_2181/I/1128:1131,
1/I/1141:1142		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_7UPH_0511/I/1157:1160,
1/I/1174:1180		No text annotation
IL_7UPH_1861/I/1244:1252,
1/I/1283:1291		No text annotation
IL_7UPH_0521/I/1254:1257,
1/I/1276:1281		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_7UPH_0531/I/1258:1262,
1/I/1271:1275		Triple sheared
homologous
IL_5J7L_056
IL_17948.2
IL_7UPH_1871/I/1258:1264,
1/I/1269:1275		No text annotation
IL_7UPH_0541/I/1302:1307,
1/I/1328:1333		No text annotation
geometric
IL_5J7L_057
IL_85536.2
IL_7UPH_1881/I/1302:1308,
1/I/1327:1333		No text annotation
IL_7UPH_0551/I/1398:1400,
1/I/4405:4408		No text annotation
homologous
IL_5J7L_058
IL_61438.4
IL_7UPH_0561/I/1400:1403,
1/I/4401:4405		No text annotation
geometric
IL_4V88_464
NA
IL_7UPH_1891/I/1404:1406,
1/I/4398:4400		Isolated non-canonical cWW pair
homologous
IL_4LFB_069
IL_87907.2
IL_7UPH_2191/I/1406:1408,
1/I/4395:4398		Isolated non-canonical cWW pair
homologous
IL_4LFB_069
IL_87907.2
IL_7UPH_0581/I/1411:1413,
1/I/4390:4392		Isolated non-canonical cWW pair
geometric
IL_5J7L_061
IL_87907.2
IL_7UPH_0591/I/1415:1418,
1/I/4385:4388		Double sheared
geometric
IL_5J7L_062
IL_09705.15
IL_7UPH_0601/I/1429:1434,
1/I/4370:4374		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_7UPH_0611/I/1439:1441,
1/I/4364:4365		Single bulged A
homologous
IL_5J7L_064
IL_31462.6
IL_7UPH_0621/I/1443:1447,
1/I/4359:4362		No text annotation
IL_7UPH_0631/I/1448:1458,
1/I/4349:4358		No text annotation
IL_7UPH_1921/I/1461:1465,
1/I/4341:4346		tHS double platform
geometric
IL_5J7L_354
IL_70411.2
IL_7UPH_0651/I/1466:1470,
1/I/4337:4340		No text annotation
IL_7UPH_2201/I/1474:1476,
1/I/4332:4333		No text annotation
IL_7UPH_0671/I/1485:1488,
1/I/4300:4305		No text annotation
geometric
IL_5J7L_351
IL_29471.1
IL_7UPH_0681/I/1524:1530,
1/I/2010:2016		Triple sheared with non-canonical cWW
geometric
IL_7A0S_001
IL_04021.2
IL_7UPH_0691/I/1536:1537,
1/I/1942:1944		Single bulged A
geometric
IL_7A0S_002
IL_31462.6
IL_7UPH_0701/I/1543:1544,
1/I/1934:1936		Minor groove platform
geometric
IL_5J7L_247
IL_51454.3
IL_7UPH_0711/I/1581:1585,
1/I/1597:1605		No text annotation
homologous
IL_5J7L_248
IL_37015.1
IL_7UPH_0721/I/1688:1694,
1/I/1701:1708		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_04346.10
IL_7UPH_0731/I/1739:1745,
1/I/1753:1758		No text annotation
geometric
IL_8C3A_065
NA
IL_7UPH_0741/I/1769:1772,
1/I/1865:1870		No text annotation
IL_7UPH_0751/I/1774:1781,
1/I/1859:1863		No text annotation
homologous
IL_5J7L_253
IL_77870.1
IL_7UPH_2211/I/1786:1795,
1/I/1843:1854		No text annotation
IL_7UPH_0761/I/1790:1795,
1/I/1843:1850		No text annotation
IL_7UPH_0771/I/1981:1984,
1/I/1996:2009		No text annotation
geometric
IL_5J7L_255
IL_81516.2
IL_7UPH_1951/I/2036:2039,
1/I/2054:2057		Double sheared
geometric
IL_1SAQ_002
NA
IL_7UPH_0791/I/2064:2066,
1/I/2075:2077		Isolated non-canonical cWW pair
geometric
IL_7A0S_011
IL_07785.1
IL_7UPH_0801/I/2105:2110,
1/I/2118:2123		No text annotation
IL_7UPH_0811/I/2172:2174,
1/I/2306:2308		Isolated non-canonical cWW pair
geometric
IL_5TBW_027
NA
IL_7UPH_0821/I/2174:2178,
1/I/2299:2306		tHW-tHW cross-strand stack
geometric
IL_7A0S_015
IL_54041.2
IL_7UPH_0831/I/2197:2198,
1/I/2263:2265		Single bulged A
geometric
IL_4V9F_025
IL_31462.6
IL_7UPH_0841/I/2202:2203,
1/I/2228:2230		Single bulged G
geometric
IL_4WF9_023
IL_00225.13
IL_7UPH_1961/I/2202:2207,
1/I/2224:2230		No text annotation
geometric
IL_4V88_462
NA
IL_7UPH_0851/I/2203:2207,
1/I/2224:2228		Triple sheared
geometric
IL_7RQB_021
NA
IL_7UPH_0861/I/2238:2240,
1/I/2257:2258		Major groove platform
geometric
IL_5J7L_264
IL_48076.6
IL_7UPH_0871/I/2275:2277,
1/I/2287:2291		Multiple bulged bases
geometric
IL_7A0S_021
IL_06549.2
IL_7UPH_0881/I/2344:2347,
1/I/2427:2428		No text annotation
IL_7UPH_1971/I/2344:2348,
1/I/2424:2428		No text annotation
IL_7UPH_0891/I/2347:2348,
1/I/2424:2427		Stack outside cWW
geometric
IL_5J7L_268
IL_56987.1
IL_7UPH_0901/I/2348:2350,
1/I/2421:2424		No text annotation
geometric
IL_4V84_070
NA
IL_7UPH_0911/I/2356:2362,
1/I/2409:2415		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5J7L_270
IL_29198.2
IL_7UPH_0921/I/2362:2363,
1/I/2407:2409		Single bulged G
homologous
IL_5J7L_271
IL_00225.13
IL_7UPH_0931/I/2364:2368,
1/I/2403:2406		No text annotation
IL_7UPH_1981/I/2370:2372,
1/I/2399:2401		Isolated non-canonical cWW pair
geometric
IL_1T0E_002
IL_28037.2
IL_7UPH_0951/I/2375:2379,
1/I/2392:2396		Triple sheared
geometric
IL_5J7L_274
IL_17948.2
IL_7UPH_0961/I/2380:2381,
1/I/2389:2391		No text annotation
homologous
IL_5J7L_275
NA
IL_7UPH_0971/I/2488:2490,
1/I/2653:2654		Single bulged C
geometric
IL_4WF9_035
IL_61258.15
IL_7UPH_0981/I/2492:2496,
1/I/2647:2651		UAA/GAN
geometric
IL_7A0S_033
IL_38507.2
IL_7UPH_0991/I/2498:2505,
1/I/2644:2645		SSU/LSU pseudoknot
geometric
IL_7RQB_037
NA
IL_7UPH_1001/I/2505:2507,
1/I/2643:2644		Single bulged U
geometric
IL_5TBW_093
NA
IL_7UPH_1011/I/2512:2518,
1/I/2634:2638		Kink-turn related
geometric
IL_4WF9_039
IL_57188.5
IL_7UPH_1021/I/2518:2524,
1/I/2618:2634		No text annotation
geometric
IL_5J7L_281
IL_50715.3
IL_7UPH_1031/I/2525:2528,
1/I/2615:2617		Isolated non-canonical cWW pair
geometric
IL_4RUM_001
IL_57744.1
IL_7UPH_1041/I/2532:2535,
1/I/2608:2611		Tandem non-canonical cWW pairs
geometric
IL_5J7L_283
IL_85033.2
IL_7UPH_1991/I/2536:2545,
1/I/2602:2607		No text annotation
IL_7UPH_1061/I/2553:2556,
1/I/2570:2573		No text annotation
geometric
IL_1MMS_001
IL_92446.2
IL_7UPH_1071/I/2581:2585,
1/I/2594:2596		Major groove platform with extra cWW
geometric
IL_4V88_397
NA
IL_7UPH_2221/I/2690:2694,
1/I/2739:2744		Partly complementary
geometric
IL_7VYX_008
IL_49751.4
IL_7UPH_1091/I/2696:2701,
1/I/2733:2737		No text annotation
IL_7UPH_1101/I/2702:2709,
1/I/2728:2732		Kink-turn
geometric
IL_5J7L_288
IL_70923.9
IL_7UPH_1111/I/2756:2763,
1/I/3505:3511		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_289
IL_04346.10
IL_7UPH_1121/I/2804:2807,
1/I/3097:3098		Major groove platform; stack outside cWW
geometric
IL_4WF9_049
IL_50694.7
IL_7UPH_1131/I/2813:2817,
1/I/2825:2827		Major groove minor groove platform with tHH
geometric
IL_4WF9_050
IL_83150.2
IL_7UPH_1141/I/2845:2849,
1/I/2870:2874		UAA/GAN
geometric
IL_5TBW_048
NA
IL_7UPH_1151/I/2851:2855,
1/I/2864:2868		tSH-tHW-tHS
geometric
IL_4WF9_052
IL_17136.7
IL_7UPH_2231/I/2909:2910,
1/I/3076:3081		No text annotation
IL_7UPH_1171/I/2911:2915,
1/I/3071:3075		UAA/GAN
geometric
IL_7RQB_055
NA
IL_7UPH_1181/I/2926:2929,
1/I/3051:3055		Tandem non-canonical cWW pairs
geometric
IL_5J7L_296
IL_58112.2
IL_7UPH_1191/I/2929:2934,
1/I/3045:3051		No text annotation
IL_7UPH_1201/I/2944:2945,
1/I/2953:2955		Single bulged U
homologous
IL_5J7L_298
IL_89505.4
IL_7UPH_1211/I/2962:2965,
1/I/3014:3018		No text annotation
geometric
IL_5J7L_299
IL_68574.4
IL_7UPH_2021/I/2968:2973,
1/I/3006:3011		No text annotation
IL_7UPH_1231/I/2974:2976,
1/I/3001:3005		No text annotation
IL_7UPH_1241/I/2983:2985,
1/I/2993:2994		No text annotation
IL_7UPH_1251/I/3020:3023,
1/I/3036:3040		UAA/GAN variation
geometric
IL_5J7L_303
IL_23774.1
IL_7UPH_1261/I/3145:3150,
1/I/3498:3500		No text annotation
geometric
IL_5J7L_304
IL_12566.4
IL_7UPH_1271/I/3157:3159,
1/I/3489:3491		Isolated tWW turn
geometric
IL_5J7L_305
IL_67095.2
IL_7UPH_1281/I/3160:3163,
1/I/3487:3488		Major groove platform; stack outside cWW
geometric
IL_4V9F_008
IL_50694.7
IL_7UPH_1291/I/3180:3185,
1/I/3190:3196		tSH-tSH-tHH-tHS
geometric
IL_5J7L_308
IL_47346.2
IL_7UPH_1301/I/3206:3212,
1/I/3236:3240		6x5 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_309
IL_88269.4
IL_7UPH_2031/I/3213:3218,
1/I/3230:3235		Quadruple sheared
geometric
IL_3FTF_001
IL_06136.2
IL_7UPH_1321/I/3264:3265,
1/I/3474:3476		Single bulged A
geometric
IL_7A0S_064
IL_31462.6
IL_7UPH_1331/I/3292:3298,
1/I/3307:3315		Kink-turn related
geometric
IL_5J7L_313
IL_17069.5
IL_7UPH_1341/I/3331:3334,
1/I/3396:3397		Minor groove platform, major groove intercalation
geometric
IL_1U9S_005
IL_95583.2
IL_7UPH_1351/I/3335:3337,
1/I/3391:3395		Isolated non-canonical cWW with bulges
geometric
IL_7RQB_097
NA
IL_7UPH_1361/I/3340:3343,
1/I/3387:3388		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_316
IL_68140.4
IL_7UPH_2041/I/3345:3354,
1/I/3376:3385		No text annotation
IL_7UPH_2051/I/3358:3361,
1/I/3368:3372		UAA/GAN
homologous
IL_4WF9_075
IL_77691.5
IL_7UPH_1381/I/3427:3428,
1/I/3458:3461		Bulged stacked bases
geometric
IL_7RQB_076
NA
IL_7UPH_1391/I/3428:3439,
1/I/3455:3458		No text annotation
geometric
IL_7A0S_072
IL_04332.3
IL_7UPH_1401/I/3544:3546,
1/I/4111:4112		Major groove platform
geometric
IL_5J7L_320
IL_48076.6
IL_7UPH_1411/I/3548:3550,
1/I/4106:4109		No text annotation
homologous
IL_5J7L_321
IL_83389.2
IL_7UPH_2061/I/3561:3563,
1/I/3936:3937		Single bulged U
geometric
IL_8VTW_079
NA
IL_7UPH_1441/I/3564:3565,
1/I/3932:3935		Minor groove platform
geometric
IL_7RQB_081
NA
IL_7UPH_1451/I/3575:3577,
1/I/3730:3733		Isolated tHS basepair with bulges
geometric
IL_7A0S_077
IL_85599.2
IL_7UPH_2071/I/3579:3581,
1/I/3726:3728		Isolated non-canonical cWW pair
geometric
IL_8C3A_431
NA
IL_7UPH_1471/I/3597:3600,
1/I/3678:3680		No text annotation
IL_7UPH_1481/I/3600:3601,
1/I/3676:3678		Single stack bend
geometric
IL_5J7L_269
IL_26793.1
IL_7UPH_1491/I/3602:3604,
1/I/3673:3675		Isolated non-canonical cWW pair
geometric
IL_1MZP_001
IL_28037.2
IL_7UPH_1501/I/3604:3615,
1/I/3671:3673		Isolated near basepair
geometric
IL_4V88_406
NA
IL_7UPH_1511/I/3618:3621,
1/I/3655:3668		No text annotation
IL_7UPH_2241/I/3623:3630,
1/I/3649:3653		Kink-turn
geometric
IL_5J7L_330
IL_70923.9
IL_7UPH_2101/I/3696:3698,
1/I/3714:3715		Single bulged U
geometric
IL_5J7L_331
IL_89505.4
IL_7UPH_1541/I/3844:3847,
1/I/3858:3861		Double sheared
geometric
IL_7A0S_081
IL_09705.15
IL_7UPH_2251/I/3895:3897,
1/I/3908:3909		No text annotation
IL_7UPH_1561/I/3947:3949,
1/I/3990:3994		No text annotation
IL_7UPH_2261/I/3951:3953,
1/I/3987:3988		Major groove platform
geometric
IL_5J7L_264
IL_48076.6
IL_7UPH_2271/I/3953:3955,
1/I/3983:3987		Major groove minor groove platform with extra cWW
geometric
IL_7A0S_086
IL_51387.2
IL_7UPH_1591/I/3960:3964,
1/I/3974:3978		Triple sheared
geometric
IL_5J7L_338
IL_17948.2
IL_7UPH_2121/I/4001:4002,
1/I/4074:4076		Major groove platform
geometric
IL_5J7L_394
IL_07039.3
IL_7UPH_1611/I/4004:4006,
1/I/4068:4072		Isolated non-canonical cWW with bulges
geometric
IL_7A0S_089
IL_07785.1
IL_7UPH_1621/I/4006:4009,
1/I/4063:4068		No text annotation
IL_7UPH_2131/I/4016:4017,
1/I/4034:4037		Major groove platform with intercalation
geometric
IL_7A0S_091
IL_02555.1
IL_7UPH_1651/I/4085:4086,
1/I/4095:4097		Single bulged A
geometric
IL_1DUQ_002
IL_31462.6
IL_7UPH_1661/I/4129:4134,
1/I/4268:4277		No text annotation
IL_7UPH_1671/I/4146:4152,
1/I/4157:4162		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_5J7L_346
IL_16458.4
IL_7UPH_1681/I/4173:4178,
1/I/4219:4222		No text annotation
IL_7UPH_1691/I/4181:4185,
1/I/4212:4216		No text annotation
geometric
IL_5J7L_348
IL_23774.1
IL_7UPH_2141/I/4189:4190,
1/I/4205:4208		Multiple bulged bases
geometric
IL_5J7L_349
IL_42626.2
IL_7UPH_1711/I/4231:4236,
1/I/4256:4261		UAA/GAN with extra cWW
geometric
IL_5J7L_350
IL_49767.8
IL_7UPH_1721/I/4289:4290,
1/I/4293:4295		Single bulged A
geometric
IL_7A0S_016
IL_31462.6
IL_7UPH_2281/J/16:17,
1/J/64:66		No text annotation
IL_7UPH_2291/J/22:28,
1/J/54:59		No text annotation
IL_7UPH_1751/J/29:32,
1/J/48:53		No text annotation
IL_7UPH_1761/J/32:37,
1/J/43:48		No text annotation
IL_7UPH_1771/J/70:78,
1/J/96:104		No text annotation

Problematic loops

#loop idProblemSequence
IL_7UPH_178No text annotation
IL_7UPH_007No text annotation
IL_7UPH_014No text annotation
IL_7UPH_017No text annotation
IL_7UPH_181No text annotation
IL_7UPH_031No text annotation
IL_7UPH_035Other IL
IL_7UPH_042Decoding loop related
IL_7UPH_045No text annotation
IL_7UPH_185No text annotation
IL_7UPH_050No text annotation
IL_7UPH_057No text annotation
IL_7UPH_190No text annotation
IL_7UPH_191Isolated non-canonical cWW pair
IL_7UPH_064No text annotation
IL_7UPH_193No text annotation
IL_7UPH_066No text annotation
IL_7UPH_194No text annotation
IL_7UPH_078Triple sheared
IL_7UPH_094No text annotation
IL_7UPH_105No text annotation
IL_7UPH_200Isolated non-canonical cWW pair
IL_7UPH_108Tandem non-canonical cWW pairs with near WC pairs
IL_7UPH_116No text annotation
IL_7UPH_201No text annotation
IL_7UPH_122No text annotation
IL_7UPH_131No text annotation
IL_7UPH_137No text annotation
IL_7UPH_142Isolated non-canonical cWW pair
IL_7UPH_143Isolated non-canonical cWW pair
IL_7UPH_146Tandem non-canonical cWW pairs
IL_7UPH_208Tandem non-canonical cWW pairs
IL_7UPH_209No text annotation
IL_7UPH_152No text annotation
IL_7UPH_153No text annotation
IL_7UPH_155Isolated non-canonical cWW with bulges
IL_7UPH_157Major groove platform with extra pair
IL_7UPH_158No text annotation
IL_7UPH_211No text annotation
IL_7UPH_160Decoding loop related
IL_7UPH_163No text annotation
IL_7UPH_164Isolated cWS basepair
IL_7UPH_170No text annotation
IL_7UPH_173Isolated non-canonical cWW pair
IL_7UPH_174No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7UPH_0011/I/45:46,
1/I/360:366,
1/I/392:394		No text annotation
homologous
J3_5J7L_001
J3_67856.4
J3_7UPH_0021/I/585:587,
1/I/650:653,
1/I/753:754		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_7UPH_0251/I/585:587,
1/I/650:654,
1/I/750:754		No text annotation
J3_7UPH_0031/I/670:672,
1/I/716:724,
1/I/731:734		No text annotation
J3_7UPH_0261/I/671:676,
1/I/712:724,
1/I/731:733		No text annotation
J3_7UPH_0041/I/825:828,
1/I/856:860,
1/I/867:873		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_7UPH_0051/I/935:938,
1/I/1343:1349,
1/I/1371:1378		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_7UPH_0061/I/942:946,
1/I/1233:1236,
1/I/1336:1339		No text annotation
J3_7UPH_0071/I/953:961,
1/I/972:983,
1/I/1220:1225		No text annotation
homologous
J3_5J7L_006
J3_83516.4
J3_7UPH_0271/I/989:1005,
1/I/1022:1046,
1/I/1209:1214		No text annotation
J3_7UPH_0081/I/1062:1067,
1/I/1106:1112,
1/I/1186:1192		No text annotation
homologous
J3_5J7L_008
J3_08394.3
J3_7UPH_0091/I/1072:1073,
1/I/1082:1086,
1/I/1097:1101		No text annotation
homologous
J3_5J7L_009
J3_76043.3
J3_7UPH_0101/I/1115:1117,
1/I/1154:1157,
1/I/1180:1183		No text annotation
homologous
J3_5J7L_010
J3_82365.4
J3_7UPH_0281/I/1115:1117,
1/I/1154:1160,
1/I/1174:1183		No text annotation
homologous
J3_6CZR_025
NA
J3_7UPH_0111/I/1236:1240,
1/I/1295:1302,
1/I/1333:1336		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J3_7UPH_0121/I/1478:1484,
1/I/4306:4309,
1/I/4325:4330		No text annotation
J3_7UPH_0131/I/1488:1490,
1/I/4283:4285,
1/I/4299:4300		No text annotation
homologous
J3_5J7L_047
J3_30104.1
J3_7UPH_0141/I/1530:1531,
1/I/1974:1981,
1/I/2009:2010		No text annotation
geometric
J3_4V9F_011
J3_60031.2
J3_7UPH_0291/I/1532:1535,
1/I/1945:1961,
1/I/1968:1973		No text annotation
geometric
J3_5J7L_067
J3_30040.2
J3_7UPH_0151/I/1556:1557,
1/I/1570:1576,
1/I/1610:1614		No text annotation
geometric
J3_8C3A_060
NA
J3_7UPH_0161/I/2183:2189,
1/I/2273:2275,
1/I/2291:2294		No text annotation
geometric
J3_5J7L_038
J3_64189.2
J3_7UPH_0171/I/2198:2200,
1/I/2232:2236,
1/I/2260:2263		No text annotation
geometric
J3_7A0S_005
J3_44724.7
J3_7UPH_0181/I/2549:2551,
1/I/2575:2581,
1/I/2596:2598		No text annotation
geometric
J3_6PRV_001
J3_28621.5
J3_7UPH_0191/I/2792:2797,
1/I/3119:3121,
1/I/3133:3136		No text annotation
geometric
J3_5J7L_041
J3_32852.6
J3_7UPH_0201/I/2800:2803,
1/I/3099:3105,
1/I/3114:3116		No text annotation
geometric
J3_8VTW_005
NA
J3_7UPH_0301/I/2838:2843,
1/I/2876:2881,
1/I/2894:2897		No text annotation
J3_7UPH_0311/I/2918:2923,
1/I/3058:3059,
1/I/3062:3068		No text annotation
geometric
J3_5J7L_069
J3_34864.2
J3_7UPH_0211/I/3585:3587,
1/I/3690:3694,
1/I/3717:3722		No text annotation
homologous
J3_7A0S_009
J3_89368.5
J3_7UPH_0321/I/3776:3779,
1/I/3877:3889,
1/I/3915:3921		No text annotation
geometric
J3_4WF9_019
J3_39320.1
J3_7UPH_0331/I/3787:3793,
1/I/3811:3817,
1/I/3826:3833		No text annotation
J3_7UPH_0221/I/3788:3794,
1/I/3810:3817,
1/I/3826:3832		No text annotation
J3_7UPH_0231/I/4011:4014,
1/I/4039:4041,
1/I/4055:4061		No text annotation
geometric
J3_4WF9_009
J3_32601.5
J3_7UPH_0241/J/9:15,
1/J/67:69,
1/J/105:109		No text annotation
homologous
J3_5J7L_049
J3_89095.1
J4_7UPH_0011/I/114:121,
1/I/238:239,
1/I/285:288,
1/I/310:311		No text annotation
homologous
J4_5J7L_001
J4_35578.3
J4_7UPH_0021/I/141:143,
1/I/177:183,
1/I/192:197,
1/I/218:220		No text annotation
homologous
J4_5J7L_002
J4_01665.1
J4_7UPH_0031/I/574:576,
1/I/763:768,
1/I/809:820,
1/I/878:879		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J4_7UPH_0041/I/1768:1769,
1/I/1870:1875,
1/I/1899:1906,
1/I/1921:1924		No text annotation
homologous
J4_5J7L_018
J4_45801.6
J4_7UPH_0141/I/1797:1801,
1/I/1816:1819,
1/I/1823:1825,
1/I/1837:1841		No text annotation
homologous
J4_9DFE_002
J4_71729.5
J4_7UPH_0061/I/2101:2104,
1/I/2124:2128,
1/I/2135:2138,
1/I/2150:2156		No text annotation
homologous
J4_5J7L_020
J4_60168.1
J4_7UPH_0071/I/2764:2770,
1/I/2788:2789,
1/I/3139:3142,
1/I/3503:3504		No text annotation
homologous
J4_7A0S_004
J4_64571.5
J4_7UPH_0081/I/2807:2808,
1/I/2832:2837,
1/I/2898:2899,
1/I/3091:3097		No text annotation
homologous
J4_5J7L_023
J4_10313.5
J4_7UPH_0091/I/2938:2939,
1/I/2960:2965,
1/I/3014:3020,
1/I/3040:3041		No text annotation
J4_7UPH_0101/I/3266:3270,
1/I/3282:3286,
1/I/3321:3324,
1/I/3469:3473		No text annotation
homologous
J4_5J7L_025
J4_61477.5
J4_7UPH_0111/I/3327:3329,
1/I/3399:3400,
1/I/3418:3427,
1/I/3461:3466		No text annotation
J4_7UPH_0121/I/3779:3783,
1/I/3837:3841,
1/I/3864:3866,
1/I/3875:3877		No text annotation
homologous
J4_9DFE_009
J4_04930.6
J4_7UPH_0151/I/4137:4140,
1/I/4168:4170,
1/I/4225:4229,
1/I/4263:4265		No text annotation
homologous
J4_5J7L_028
J4_77044.4
J5_7UPH_0011/I/35:38,
1/I/402:405,
1/I/435:439,
1/I/496:499,
1/I/544:547		No text annotation
homologous
J5_5J7L_001
J5_92941.1
J5_7UPH_0021/I/35:38,
1/I/402:405,
1/I/435:441,
1/I/491:499,
1/I/544:547		No text annotation
homologous
J5_5J7L_002
J5_67416.1
J5_7UPH_0031/I/57:60,
1/I/105:112,
1/I/313:315,
1/I/336:338,
1/I/349:353		No text annotation
homologous
J5_5J7L_003
J5_59910.6
J5_7UPH_0111/I/1547:1554,
1/I/1616:1621,
1/I/1630:1632,
1/I/1647:1650,
1/I/1676:1678		No text annotation
J5_7UPH_0051/I/2031:2033,
1/I/2060:2064,
1/I/2077:2079,
1/I/2755:2756,
1/I/3511:3512		No text annotation
homologous
J5_4WF9_003
J5_43153.5
J5_7UPH_0061/I/2084:2089,
1/I/2168:2171,
1/I/2309:2312,
1/I/2689:2690,
1/I/2744:2750		No text annotation
homologous
J5_7A0S_004
J5_74302.5
J5_7UPH_0071/I/3160:3176,
1/I/3200:3202,
1/I/3244:3246,
1/I/3250:3258,
1/I/3482:3488		No text annotation
J5_7UPH_0081/I/3163:3176,
1/I/3200:3202,
1/I/3244:3246,
1/I/3250:3258,
1/I/3482:3487		No text annotation
J5_7UPH_0091/I/3551:3558,
1/I/3940:3947,
1/I/3994:4000,
1/I/4077:4082,
1/I/4100:4105		No text annotation
J5_7UPH_0121/I/3568:3571,
1/I/3737:3740,
1/I/3752:3754,
1/I/3774:3776,
1/I/3921:3929		No text annotation
J6_7UPH_0011/I/1545:1546,
1/I/1679:1684,
1/I/1712:1724,
1/I/1731:1735,
1/I/1762:1766,
1/I/1926:1933		No text annotation
J7_7UPH_0011/I/1490:1491,
1/I/1508:1515,
1/I/2025:2031,
1/I/3512:3518,
1/I/3533:3537,
1/I/4119:4124,
1/I/4282:4283		No text annotation
J7_7UPH_0021/I/2317:2322,
1/I/2335:2338,
1/I/2434:2440,
1/I/2465:2470,
1/I/2481:2485,
1/I/2657:2658,
1/I/2679:2684		No text annotation

Problematic loops

#loop idProblemSequence
J4_7UPH_005No text annotation
J4_7UPH_013No text annotation
J5_7UPH_004No text annotation
J5_7UPH_010No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.079 s