#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name for chain 1 2 3 4 5 6 7 8 91-92-6
1 HL_4V9K_0354V9K0.37940T-loop with 2 stacked bulged basesAW tRNAG53U54U55C56G57A58A59U60C61cWWntWH
2 HL_2ZNI_0032ZNI0.36350T-loop with 2 stacked bulged basesCbacterial tRNAG53U54G55A56A57A58C59U60C61cWWtWH
3 HL_4WSM_2544WSM0.36430T-loop with 2 stacked bulged bases3L tRNAG64U65U66C67A68A69G70U71C72ncWWntWH
4 HL_1J2B_0021J2B0.26150T-loop with 2 stacked bulged basesCtRNA(Val)G954U955U956C957A958A959G960U961C962cWWtWH
5 HL_1H4S_0031H4S0.29500T-loop with 2 stacked bulged basesT tRNAG535MU54PSU55C56A57G58A59U60C61cWWtWH
6 HL_5J8B_1135J8B0.28630T-loop with 2 stacked bulged bases (H)y tRNAG535MU54PSU55C56G57A58U59U60C61cWWtWH
7 HL_1B23_0031B230.28710T-loop with 2 stacked bulged basesR tRNAG535MU54PSU55C56G57A58C59U60C61cWWtWH
8 HL_6CFJ_1086CFJ0.27310T-loop with 2 stacked bulged bases1x tRNAG535MU54PSU55C56A57A58A59U60C61cWWtWH
9 HL_5J8B_1105J8B0.25030T-loop with 2 stacked bulged bases (H)x tRNAG535MU54PSU55C56A57A58A59U60C61cWWtWH
10 HL_1F7U_0031F7U0.24190T-loop with 2 stacked bulged basesBTRNA(ARG)G9535MU954PSU955C956A9571MA958G959U960C961cWWtWH
11 HL_7VNV_0037VNV0.24890T-loop with 2 stacked bulged basesA tRNAG53SUR54PSU55OMC567S3571MA58G59U60C61cWWtWH
12 HL_1IL2_0031IL20.27790T-loop with 2 stacked bulged basesC tRNAG9535MU954PSU955C956A957A958U959U960C961cWWtWH
13 HL_3KFU_0063KFU0.24850T-loop with 2 stacked bulged basesL tRNAG535MU54PSU55C56G57A58G59U60C61cWWtWH
14 HL_5E81_2075E810.25720T-loop with 2 stacked bulged bases1K tRNAG535MU54PSU55C56G57A58A59U60C61cWWtWH
15 HL_7U2J_1057U2J0.283101w tRNAG535MU54PSU55C56G57A58U59U60C61cWWtWH
16 HL_5E6M_0035E6M0.21820T-loop with 2 stacked bulged basesC tRNAG53U54U55C56G57A58U59U60C61cWW
17 HL_2DVI_0012DVI0.18850BtRNA (34-MER)G12U13U14C15G16A17U18U19C20cWWtWH
18 HL_5UD5_0035UD50.16560T-loop with 2 stacked bulged basesC tRNAG53U54U55A56G57A58U59U60C61cWWtWH
19 HL_2D6F_0062D6F0.17180T-loop with 2 stacked bulged basesFtRNAG953U954U955C956G957A958C959U960C961cWWtWH
20 HL_3OVB_0013OVB0.19790T-loop with 2 stacked bulged basesCRNA (35-MER)G12U13U14C15A16A17G18U19C20cWWtWH
21 HL_3AMU_0033AMU0.16090T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58A59U60C61cWWtWH
22 HL_3WFS_0033WFS0.18090T-loop with 2 stacked bulged basesA tRNAG53U54U55C56G57A58U59U60C61cWWtWH
23 HL_4TUE_1434TUE0.17290XV tRNAG53U54U55C56A57A58A59U60C61ncWWtWH
24 HL_4GCW_0024GCW0.13770T-loop with 2 stacked bulged basesBTRNA(THR)G53U54U55C56G57A58G59C60C61cWWtWH
25 HL_7K98_0037K980.13310T-loop with 2 stacked bulged basesC tRNAG54U55U56C57G58A59U60C61C62cWWtWH
26 HL_4YCP_0034YCP0.12360T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58G59U60C61cWWtWH
27 HL_5WT1_0035WT10.11860T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
28 HL_6MJ0_0046MJ00.12920T-loop with 2 stacked bulged bases (H)AtRNA-like 3' UTR elementG66U67G68C69A70A71C72U73C74cWWtWH
29 HL_1QU2_0031QU20.10740T-loop with 2 stacked bulged basesT tRNAG53U54U55C56A57A58G59U60C61cWWtWH
30 HL_4YCO_0034YCO0.08520T-loop with 2 stacked bulged basesD tRNAG53U54U55C56G57A58U59U60C61cWWtWH
31 HL_5AXM_0035AXM0.08750T-loop with 2 stacked bulged basesP tRNAG53U54U55C56G57A58U59C60C61cWWtWH
32 HL_7EQJ_0067EQJ0.12410T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58U59C60C61cWWtWH
33 HL_7YSE_0037YSE0.12570T-loop with 2 stacked bulged basesE tRNAG53U54U55C56G57A58G59U60C61cWWtWH
34 HL_8B0X_0328B0X0.10960T-loop with 2 stacked bulged bases (H)Z tRNAG53U54U55C56A57A58A59U60C61cWWtWH
35 HL_7KJT_0037KJT0.11080T-loop with 2 stacked bulged basesA tRNAG53U54U55C56A57A58A59U60C61cWWtWH
36 HL_2ZUE_0032ZUE0.11040T-loop with 2 stacked bulged basesBtRNA-ArgG953U954U955C956A957A958A959U960C961cWWtWH
37 HL_5AH5_0085AH50.08720T-loop with 2 stacked bulged basesD tRNAG53U54U55C56A57A58G59U60C61cWWtWH
38 HL_9MTS_1039MTS0.08350T-loop with 2 stacked bulged bases1x tRNAG535MU54PSU55C56G57A58C59U60C61cWWtWH
39 HL_3WQY_0033WQY0.10010T-loop with 2 stacked bulged basesC tRNAG1653U1654U1655C1656A1657A1658A1659U1660C1661cWWtWH
40 HL_2ZZN_0062ZZN0.10950T-loop with 2 stacked bulged basesDRNA (71-MER)G53U54U55C56A57A58A59U60C61cWWtWH
41 HL_1QTQ_0031QTQ0.07860T-loop with 2 stacked bulged basesB tRNAG953U954U955C956G957A958A959U960C961cWWtWH
42 HL_5HR6_0035HR60.07300T-loop with 2 stacked bulged basesC tRNAG52U53U54C55G56A57A58U59C60cWWtWH
43 HL_6UGG_0066UGG0.07150T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58G59U60C61cWWtWH
44 HL_8VU0_0038VU00.07270T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58G59U60C61cWWtWH
45 HL_5HR7_0065HR70.06440T-loop with 2 stacked bulged basesD tRNAG52U53U54C55G56A57A58U59C60cWWtWH
46 HL_4YYE_0034YYE0.00000T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
47 HL_4JXZ_0034JXZ0.08620T-loop with 2 stacked bulged basesB tRNAG953U954U955C956G957A958A959U960C961cWWtWH
48 HL_8K0Y_0028K0Y0.13230T-loop with 2 stacked bulged basesAMALAT1-associated small cytoplasmic RNA/MEN beta RNAG37U38U39C40A41A42U43U44C45cWWtWH
49 HL_2BTE_0082BTE0.11630T-loop with 2 stacked bulged bases (H)E tRNAG53U54U55C56A57A58G59U60C61cWWtWH
50 HL_1WZ2_0081WZ20.14890T-loop with 2 stacked bulged basesDtRNAG965U966U967C968G969A970A971U972C973cWWtWH
51 HL_4V9Q_2154V9Q0.12560T-loop with 2 stacked bulged basesDV tRNAG53U54U55C56A57A58A59U60C61cWWtWH
52 HL_8WND_0058WND0.13320T-loop with 2 stacked bulged basesT tRNAG53U54U55C56A57A58G59U60C61cWWtWH
53 HL_8G9Z_0048G9Z0.11000T-loop with 2 stacked bulged basesESelenocysteine transfer RNAG53||AU54||AU55||AC56||AA57||AA58||AU59||AU60||AC61||AcWWtWH
54 HL_3RG5_0083RG50.12850T-loop with 2 stacked bulged basesBSelenocysteine transfer RNAG53U54U55C56A57A58U59U60C61cWWtWH
55 HL_3ZGZ_0033ZGZ0.11200T-loop with 2 stacked bulged basesB tRNAG53U54U55C56A57A58G59U60C61cWWtWH
56 HL_4LCK_0034LCK0.13440T-loop with 2 stacked bulged basesB tRNAG52U53U54C55G56A57A58U59C60cWWtWH
57 HL_4MGN_0044MGN0.18060T-loop with 2 stacked bulged basesBtRNA-glycineG52U53U54C55G56A57G58U59C60cWWtWH
58 HL_5WWT_0025WWT0.18690T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
59 HL_3ADD_0043ADD0.18130T-loop with 2 stacked bulged basesCSelenocysteine transfer RNAG53U54U55C56A57A58U59U60C61cWWtWH
60 HL_3IGI_0013IGI0.19190T-loop with 2 stacked bulged basesAGroup IIC intronG30U31G32A33G34A35G36U37C38cWWtWH
61 HL_2DU3_0032DU30.13670T-loop with 2 stacked bulged basesDtRNAG952U953U954C955G956A957A958U959C960cWWtWH
62 HL_4X4V_0014X4V0.16360T-loop with 2 stacked bulged basesBHuman MenBeta minihelix ending in CCACCG12U13U14C15G16A17G18U19C20cWWtWH
63 HL_3FOZ_0063FOZ0.19490T-loop with 2 stacked bulged basesDtRNA(Phe)G53U54U55C56G57A58U59U60C61cWWtWH
64 HL_2DER_0062DER0.18820T-loop with 2 stacked bulged basesDtRNAG53U54U55C56G57A58A59U60C61cWWtWH
65 HL_3TUP_0033TUP0.17690T-loop with 2 stacked bulged basesT tRNAG53U54U55C56G57A58U59U60C61cWWntWH
66 HL_1N78_0031N780.15910T-loop with 2 stacked bulged basesCtRNA(Glu)G553U554U555C556G557A558U559U560C561cWWtWH
67 HL_3EPH_0033EPH0.16940T-loop with 2 stacked bulged basesEtRNAG53U54U55C56G57A58U59C60C61cWWtWH
68 HL_1U0B_0031U0B0.16450T-loop with 2 stacked bulged basesA tRNAG53U54U55C56G57A58C59U60C61cWWtWH
69 HL_5B63_0045B630.14990T-loop with 2 stacked bulged basesD tRNAG954U955U956C957G958A959A960U961C962cWWtWH
70 HL_3AKZ_0123AKZ0.18450T-loop with 2 stacked bulged basesEtRNAGlnG53U54U55C56G57A58G59U60C61cWWtWH
71 HL_3ICQ_0053ICQ0.21900T-loop with 2 stacked bulged basesERNA (62-MER)G53U54U55C56G57A58U59C60C61cWWtWH
72 HL_2CSX_0032CSX0.20010T-loop with 2 stacked bulged basesCRNA (75-MER)G53U54U55C56G57A58G59U60C61cWWtWH
73 HL_5Y85_0035Y850.22550T-loop with 2 stacked bulged basesDDNA/RNA (50-MER)G11U12G13C14A15A16G17U18C19cWWtWH
74 HL_5T5A_0015T5A0.28150T-loop with 2 stacked bulged basesADNA/RNA (71-MER)G21U22G23C24A25A26G27C28C29cWWtWH
75 HL_8B0X_0488B0X0.30731a LSU rRNAU568U569U570U571G572U573A574U575A577cWW
76 HL_4WF9_0184WF90.30731T-loop with 2 stacked bulged basesX LSU rRNAU609U610U611U612G613U614A615G616A618cWW
77 HL_9DFE_0169DFE0.34841T-loop with 2 stacked bulged bases1A LSU rRNAU566A567U568U569G570A571A572G573A575cWW
78 HL_7A0S_0187A0S0.33411T-loop with 2 stacked bulged basesX LSU rRNAU575A576U577U578G579A580A581G582A584cWW
79 HL_8P9A_1268P9A0.35071T-loop with 2 stacked bulged basesAR LSU rRNAU640C641U642U643G644A645A646A647A649cWW
80 HL_8GLP_1198GLP0.31131T-loop with 2 stacked bulged bases (H)L5 LSU rRNAU1317C1318U1319U1320G13211MA1322A1323A1324A2M1326cWW
81 HL_9AXU_0139AXU0.31681T-loop with 2 stacked bulged bases (H)2 LSU rRNAU665C666U667U668G669A670A671A672A674cWW
82 HL_8OI5_0138OI50.32681T-loop with 2 stacked bulged bases (H)1 LSU rRNAU638C639U640U641G642A643A644A645A647cWW
83 HL_9E6Q_0189E6Q0.31391T-loop with 2 stacked bulged bases (H)1 LSU rRNAU647C648U649A650G651A652A653A654A656cWW
84 HL_4V9F_0184V9F0.27091T-loop with 2 stacked bulged bases0 LSU rRNAU623U624U625U626G6271MA628A629A630A632cWWntWH
85 HL_4WSM_2114WSM0.35370T-loop with 2 stacked bulged bases1K tRNAG645MU65PSU66C67A68A69G70U71C72cWW
86 HL_8P9A_1438P9A0.29380T-loop with 2 stacked bulged basesAR LSU rRNAA1462U1463G1464A1465G1466A1467A1468C1469U1470cWWtWH
87 HL_8OI5_0278OI50.31700T-loop with 2 stacked bulged bases (H)1 LSU rRNAA1458U1459G1460A1461G1462A1463A1464C1465U1466cWWtWH
88 HL_9AXU_0289AXU0.32840T-loop with 2 stacked bulged bases (H)2 LSU rRNAA1496U1497G1498A1499G1500A1501A1502C1503U1504cWWtWH
89 HL_8GLP_0338GLP0.34070T-loop with 2 stacked bulged bases (H)L5 LSU rRNAA2376C2377G2378A2379G2380A2381A2382C2383U2384cWWtWH
90 HL_8B0X_0608B0X0.31980T-loop with 2 stacked bulged bases (H)a LSU rRNAG1283U1284G1285A1286A1287A1288A1289G1290C1291cWWtWH
91 HL_4V9F_0344V9F0.36540T-loop with 2 stacked bulged bases0 LSU rRNAG1387U1388G1389A1390G1391A1392A1393C1394C1395cWWtWH
92 HL_9E6Q_0319E6Q0.27050T-loop with 2 stacked bulged bases (H)1 LSU rRNAG1409U1410G1411A1412G1413A1414A1415G1416C1417cWWtWH
93 HL_9DFE_0319DFE0.27030T-loop with 2 stacked bulged bases1A LSU rRNAG1281U1282G1283A1284G1285A1286A1287U1288C1289cWWtWH
94 HL_4WF9_0324WF90.30830T-loop with 2 stacked bulged basesX LSU rRNAG1318U1319G1320A1321G1322A1323A1324U1325C1326cWWtWH
95 HL_7A0S_0327A0S0.29030T-loop with 2 stacked bulged basesX LSU rRNAG1294U1295G1296A1297G1298A1299A1300U1301C1302cWWtWH
96 HL_8V1I_0068V1I0.36610T-loop with 2 stacked bulged basesBMALAT1-associated small cytoplasmic RNA/MEN beta RNAG38U39U40C41A42A43A44U45C46cWWtWH

3D structures

Complete motif including flanking bases
SequenceCounts
GUUCGAAUC11
GUUCAAAUC11
GUUCAAGUC9
GUUCGAUUC7
GUUCGAGUC7
GUUCGAUCC5
GUUCAAUUC4
UCUUGAAACA3
AUGAGAACU3
GUGAGAAUC3
G(5MU)(PSU)CAAAUC2
GUUCGACUC2
UAUUGAAGCA2
GUGAAACUC1
GCAGAUC1
G(5MU)(PSU)CGAUUC1
GCGACUC1
GCAGUC1
G(SUR)(PSU)(OMC)(7S3)(1MA)GUC1
G(5MU)(PSU)CAAUUC1
GCGAGUC1
G(5MU)(PSU)CGAAUC1
GCGAUUC1
GUUAGAUUC1
GUUCGAGCC1
GUGCAACUC1
G(5MU)(PSU)CGACUC1
GUGAGAGUC1
GUGCAAGUC1
GUGCAAGCC1
UUUUGUAUAA1
UUUUGUAGAA1
UCUUG(1MA)AAC(A2M)1
UCUAGAAACA1
UUUUG(1MA)AAAA1
G(5MU)(PSU)CAAGUC1
ACGAGAACU1
GUGAAAAGC1
GUGAGAACC1
GUGAGAAGC1
Non-Watson-Crick part of the motif
SequenceCounts
UUCGAAU11
UUCAAAU11
UUCAAGU9
UUCGAUU7
UUCGAGU7
UUCGAUC5
UUCAAUU4
UGAGAAC4
CUUGAAAC3
UGAGAAU3
(5MU)(PSU)CGAUU2
(5MU)(PSU)CGACU2
(5MU)(PSU)CAAAU2
UUCGACU2
AUUGAAGC2
UGAAACU1
(5MU)(PSU)CAGAU1
(5MU)(PSU)CA(1MA)GU1
(SUR)(PSU)(OMC)(7S3)(1MA)GU1
(5MU)(PSU)CAAUU1
(5MU)(PSU)CGAGU1
(5MU)(PSU)CGAAU1
UUAGAUU1
UUCGAGC1
UGCAACU1
UGAGAGU1
UGCAAGU1
UGCAAGC1
UUUGUAUA1
UUUGUAGA1
CUUG(1MA)AAC1
CUAGAAAC1
UUUG(1MA)AAA1
(5MU)(PSU)CAAGU1
CGAGAAC1
UGAAAAG1
UGAGAAG1

Release history

Release4.0
Date2025-08-13
StatusNew id, 1 parent

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.
Annotations
  • T-loop with 2 stacked bulged bases (78)
  • T-loop with 2 stacked bulged bases (H) (14)
  • (4)
  • Basepair signature
    cWW-tWH-F-F-F-F-F
    Heat map statistics
    Min 0.06 | Avg 0.28 | Max 0.63
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