RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8JSH_0241/g/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_8JSH_0021/g/80:89No text annotation
homologous
HL_6CZR_073
NA
HL_8JSH_0031/g/158:163GNRA
geometric
HL_5J7L_016
HL_37824.8
HL_8JSH_0041/g/186:191GNRA
homologous
HL_5J7L_004
HL_37824.8
HL_8JSH_0051/g/207:212UNCG
geometric
HL_6CK5_001
HL_34617.5
HL_8JSH_0061/g/259:267GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_8JSH_0071/g/296:301GNRA
homologous
HL_5J7L_007
HL_37824.8
HL_8JSH_0081/g/320:333No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_8JSH_0251/g/342:347UNCG
homologous
HL_6CZR_080
NA
HL_8JSH_0101/g/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_8JSH_0111/g/419:424UNCG
homologous
HL_4LFB_011
HL_34617.5
HL_8JSH_0121/g/462:470GNRA wlth extra near cWW
homologous
HL_5J7L_012
HL_81538.2
HL_8JSH_0131/g/522:527No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_8JSH_0141/g/616:624tRNA anticodon loop
geometric
HL_8H1B_001
HL_10453.3
HL_8JSH_0151/g/689:698No text annotation
HL_8JSH_0161/g/726:731GNRA
homologous
HL_4LFB_016
HL_37824.8
HL_8JSH_0171/g/786:796No text annotation
geometric
HL_8KAL_003
HL_75660.5
HL_8JSH_0181/g/840:846No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_8JSH_0191/g/862:867GNRA
homologous
HL_5J7L_019
HL_37824.8
HL_8JSH_0201/g/897:902GNRA
homologous
HL_4LFB_020
HL_37824.8
HL_8JSH_0221/g/1449:1454UNCG
homologous
HL_5J7L_030
HL_34617.5
HL_8JSH_0231/g/1515:1520GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_8JSH_001No text annotation
HL_8JSH_009No text annotation
HL_8JSH_021No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8JSH_0021/g/30:32,
1/g/552:553		Single bulged G
homologous
IL_5J7L_001
IL_00225.14
IL_8JSH_0031/g/44:45,
1/g/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_8JSH_0041/g/47:52,
1/g/359:361		No text annotation
geometric
IL_5J7L_003
IL_14177.2
IL_8JSH_0051/g/52:56,
1/g/356:359		No text annotation
IL_8JSH_0061/g/63:66,
1/g/103:104		Multiple bulged bases
homologous
IL_5J7L_005
IL_82107.5
IL_8JSH_0071/g/67:69,
1/g/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_8JSH_0081/g/70:77,
1/g/92:98		No text annotation
IL_8JSH_0571/g/70:80,
1/g/89:98		No text annotation
IL_8JSH_0101/g/128:132,
1/g/230:233		No text annotation
IL_8JSH_0111/g/132:136,
1/g/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_8JSH_0121/g/144:146,
1/g/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_8JSH_0131/g/147:153,
1/g/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_8JSH_0581/g/147:156,
1/g/165:175		No text annotation
IL_8JSH_0171/g/203:206,
1/g/213:214		Minor groove platform
geometric
IL_6CZR_155
NA
IL_8JSH_0181/g/242:247,
1/g/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_8JSH_0191/g/249:252,
1/g/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_8JSH_0201/g/292:293,
1/g/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_8JSH_0211/g/367:369,
1/g/392:393		Single bulged U
homologous
IL_5J7L_017
IL_89505.4
IL_8JSH_0221/g/371:375,
1/g/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_8JSH_0591/g/371:376,
1/g/387:390		C-loop with extra cWW pair
geometric
IL_4V88_408
NA
IL_8JSH_0231/g/375:376,
1/g/387:389		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_8JSH_0601/g/409:416,
1/g/427:433		No text annotation
homologous
IL_5J7L_020
IL_28026.3
IL_8JSH_0251/g/440:442,
1/g/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_8JSH_0261/g/446:450,
1/g/483:488		No text annotation
IL_8JSH_0271/g/450:454,
1/g/479:483		No text annotation
IL_8JSH_0611/g/450:455,
1/g/477:483		No text annotation
homologous
IL_6CZR_406
NA
IL_8JSH_0281/g/454:455,
1/g/477:479		No text annotation
IL_8JSH_0311/g/504:511,
1/g/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_8JSH_0321/g/515:521,
1/g/528:536		Kink-turn related
geometric
IL_4V88_415
NA
IL_8JSH_0631/g/569:575,
1/g/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_8JSH_0711/g/580:584,
1/g/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_8JSH_0721/g/594:596,
1/g/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_8JSH_0731/g/597:598,
1/g/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_68140.4
IL_8JSH_0361/g/602:612,
1/g/628:636		No text annotation
IL_8JSH_0371/g/654:655,
1/g/751:754		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_50694.7
IL_8JSH_0391/g/658:659,
1/g/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_8JSH_0641/g/659:660,
1/g/745:747		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_8JSH_0741/g/662:666,
1/g/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_8JSH_0411/g/682:688,
1/g/699:708		No text annotation
IL_8JSH_0421/g/774:779,
1/g/803:805		No text annotation
IL_8JSH_0431/g/779:783,
1/g/799:803		tSH-tHW-tHS
geometric
IL_7A0S_049
IL_17136.7
IL_8JSH_0461/g/887:894,
1/g/905:910		No text annotation
IL_8JSH_0481/g/1399:1401,
1/g/1501:1504		No text annotation
homologous
IL_4LFB_056
IL_61438.4
IL_8JSH_0491/g/1401:1404,
1/g/1497:1501		No text annotation
homologous
IL_5J7L_059
IL_65718.4
IL_8JSH_0751/g/1405:1409,
1/g/1491:1496		No text annotation
IL_8JSH_0511/g/1412:1416,
1/g/1484:1488		No text annotation
IL_8JSH_0761/g/1412:1423,
1/g/1477:1488		No text annotation
IL_8JSH_0521/g/1430:1435,
1/g/1466:1470		No text annotation
IL_8JSH_0541/g/1440:1442,
1/g/1460:1461		Single stack bend
geometric
IL_5TBW_035
NA
IL_8JSH_0551/g/1445:1448,
1/g/1455:1457		No text annotation
homologous
IL_5J7L_065
IL_31531.3

Problematic loops

#loop idProblemSequence
IL_8JSH_001Isolated non-canonical cWW pair
IL_8JSH_009No text annotation
IL_8JSH_014Tandem non-canonical cWW pairs
IL_8JSH_015Isolated non-canonical cWW pair
IL_8JSH_016Tandem non-canonical cWW pairs
IL_8JSH_024No text annotation
IL_8JSH_029Isolated non-canonical cWW pair
IL_8JSH_062No text annotation
IL_8JSH_030Tandem non-canonical cWW pairs
IL_8JSH_070No text annotation
IL_8JSH_033No text annotation
IL_8JSH_034Major groove platform with extra pair
IL_8JSH_035No text annotation
IL_8JSH_038Isolated non-canonical cWW pair
IL_8JSH_040No text annotation
IL_8JSH_065No text annotation
IL_8JSH_044Isolated non-canonical cWW pair
IL_8JSH_045No text annotation
IL_8JSH_047Isolated non-canonical cWW pair
IL_8JSH_050No text annotation
IL_8JSH_066No text annotation
IL_8JSH_067No text annotation
IL_8JSH_053Isolated non-canonical cWW pair
IL_8JSH_068Multiple bulged bases with non-canonical cWW
IL_8JSH_056No text annotation
IL_8JSH_069No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8JSH_0021/g/46:47,
1/g/361:369,
1/g/392:395		No text annotation
J3_8JSH_0031/g/46:52,
1/g/359:369,
1/g/392:395		No text annotation
J3_8JSH_0041/g/46:56,
1/g/356:369,
1/g/392:395		No text annotation
J3_8JSH_0051/g/586:588,
1/g/651:654,
1/g/754:755		No text annotation
geometric
J3_4LFB_011
J3_56052.5
J3_8JSH_0061/g/586:588,
1/g/651:655,
1/g/751:755		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_8JSH_0081/g/672:678,
1/g/712:725,
1/g/732:734		No text annotation
J3_8JSH_0011/g/826:829,
1/g/857:861,
1/g/868:874		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J4_8JSH_0011/g/115:122,
1/g/239:240,
1/g/286:289,
1/g/311:312		No text annotation
homologous
J4_5J7L_001
J4_35578.3
J4_8JSH_0021/g/141:144,
1/g/178:184,
1/g/193:198,
1/g/219:222		No text annotation
J4_8JSH_0031/g/575:577,
1/g/764:769,
1/g/810:821,
1/g/879:880		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J5_8JSH_0011/g/36:39,
1/g/403:408,
1/g/434:440,
1/g/497:500,
1/g/545:548		No text annotation
J5_8JSH_0021/g/36:39,
1/g/403:408,
1/g/434:442,
1/g/492:500,
1/g/545:548		No text annotation
J5_8JSH_0031/g/58:61,
1/g/106:113,
1/g/314:316,
1/g/337:340,
1/g/349:354		No text annotation

Problematic loops

#loop idProblemSequence
J3_8JSH_007No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1133 s