RNA 3D Hub //

Motif HL_33239.4 Version HL_33239.4 of this group appears in releases 3.11 to 3.11

#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name 1 2 3 4 5 6 7 8 91-92-62-93-53-6
1 HL_3OVB_0013OVB0.43960T-loop with 2 stacked bulged basesCRNA (35-MER)G12U13U14C15A16A17G18U19C20cWWtWH
2 HL_2DRA_0012DRA0.37940T-loop with 2 stacked bulged basesBtRNA (34-MER)G12U13U14C15G16A17U18U19C20cWWtWH
3 HL_1GAX_0061GAX0.40090T-loop with 2 stacked bulged basesDTRNA(VAL)G952U953U954C955A956A957G958U959C960cWWtWH
4 HL_2CSX_0032CSX0.33150T-loop with 2 stacked bulged basesCRNA (75-MER)G53U54U55C56G57A58G59U60C61cWWtWH
5 HL_1J2B_0021J2B0.40650Other HLCtRNA(Val)G954U955U956C957A958A959G960U961C962cWWtWH
6 HL_5E6M_0035E6M0.41340T-loop with 2 stacked bulged basesC tRNAG53U54U55C56G57A58U59U60C61cWWntWW
7 HL_4QEI_0064QEI0.41020T-loop with 2 stacked bulged basesC tRNAG53||||2_555U54||||2_555U55||||2_555C56||||2_555G57||||2_555A58||||2_555U59||||2_555U60||||2_555C61||||2_555cWWntWW
8 HL_4QEI_0034QEI0.41020T-loop with 2 stacked bulged basesC tRNAG53U54U55C56G57A58U59U60C61cWWntWW
9 HL_4V9K_0354V9K0.37940T-loop with 2 stacked bulged basesAW tRNAG53U54U55C56G57A58A59U60C61cWWntWH
10 HL_3Q1Q_0113Q1Q0.39010 CTRNA (PHE)G63U64U65C66G67A68U69U70C71cWWtWHncWW
11 HL_4V90_0344V900.36230T-loop with 2 stacked bulged basesAV tRNAG53U54U55C56G57A58U59U60C61cWWtWH
12 HL_2ZNI_0032ZNI0.44130T-loop with 2 stacked bulged basesCbacterial tRNAG53U54G55A56A57A58C59U60C61cWWntWH
13 HL_4GMA_0024GMA0.41710 ZAdenosylcobalamin riboswitchG58U59G60A61G62A63A64U65C66cWWntWH
14 HL_4GXY_0024GXY0.39200T-loop with 2 stacked bulged basesAAdenosylcobalamin riboswitchG49U50G51C52A53A54G55U56C57cWWtWH
15 HL_4R0D_0014R0D0.38960 AGroup II catalytic intronG31U32G33A34A35A36G37U38C39cWWtWH
16 HL_3IGI_0013IGI0.27050T-loop with 2 stacked bulged basesAGroup IIC intronG30U31G32A33G34A35G36U37C38cWWtWH
17 HL_3AM1_0043AM10.25500T-loop with 2 stacked bulged basesBASL-truncated tRNAG59U60U61C62G63A64U65U66C67cWWtWH
18 HL_3AM1_0083AM10.25500T-loop with 2 stacked bulged basesBASL-truncated tRNAG59||||5_555U60||||5_555U61||||5_555C62||||5_555G63||||5_555A64||||5_555U65||||5_555U66||||5_555C67||||5_555cWWtWH
19 HL_3ADD_0043ADD0.21170T-loop with 2 stacked bulged basesCSelenocysteine transfer RNAG53U54U55C56A57A58U59U60C61cWWtWH
20 HL_3W3S_0083W3S0.17810T-loop with 2 stacked bulged basesBSelenocysteine transfer RNAG53||||43_455U54||||43_455U55||||43_455C56||||43_455G57||||43_455A58||||43_455U59||||43_455U60||||43_455C61||||43_455cWWtWH
21 HL_3W3S_0043W3S0.17810T-loop with 2 stacked bulged basesBSelenocysteine transfer RNAG53U54U55C56G57A58U59U60C61cWWtWH
22 HL_3RG5_0123RG50.15280T-loop with 2 stacked bulged basesBSelenocysteine transfer RNAG53||||1_556U54||||1_556U55||||1_556C56||||1_556A57||||1_556A58||||1_556U59||||1_556U60||||1_556C61||||1_556cWWtWH
23 HL_3RG5_0083RG50.15280T-loop with 2 stacked bulged basesBSelenocysteine transfer RNAG53U54U55C56A57A58U59U60C61cWWtWH
24 HL_5WWT_0025WWT0.20890T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
25 HL_4MGN_0044MGN0.18110T-loop with 2 stacked bulged basesBtRNA-glycineG52U53U54C55G56A57G58U59C60cWWtWH
26 HL_4LCK_0034LCK0.14390T-loop with 2 stacked bulged basesB tRNAG52U53U54C55G56A57A58U59C60cWWtWH
27 HL_2DU3_0062DU30.16600T-loop with 2 stacked bulged basesDtRNAG952||||4_555U953||||4_555U954||||4_555C955||||4_555G956||||4_555A957||||4_555A958||||4_555U959||||4_555C960||||4_555cWWtWH
28 HL_2DU3_0032DU30.16600T-loop with 2 stacked bulged basesDtRNAG952U953U954C955G956A957A958U959C960cWWtWH
29 HL_4X4V_0014X4V0.17500T-loop with 2 stacked bulged basesBHuman MenBeta minihelix ending in CCACCG12U13U14C15G16A17G18U19C20cWWtWH
30 HL_1N78_0031N780.17100T-loop with 2 stacked bulged basesCtRNA(Glu)G553U554U555C556G557A558U559U560C561cWWtWH
31 HL_3EPH_0033EPH0.19740T-loop with 2 stacked bulged basesEtRNAG53U54U55C56G57A58U59C60C61cWWtWH
32 HL_3TUP_0033TUP0.21820T-loop with 2 stacked bulged basesT tRNAG53U54U55C56G57A58U59U60C61cWWtWH
33 HL_2DER_0062DER0.22270T-loop with 2 stacked bulged basesDtRNAG53U54U55C56G57A58A59U60C61cWWtWH
34 HL_3WFS_0033WFS0.16760T-loop with 2 stacked bulged basesA tRNAG53U54U55C56G57A58U59U60C61cWWtWH
35 HL_3A2K_0033A2K0.17610 Cbacterial tRNAG54U55U56C57G58A59G60U61C62cWWtWH
36 HL_3AMU_0033AMU0.17020T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58A59U60C61cWWtWHntWH
37 HL_1U0B_0031U0B0.16060T-loop with 2 stacked bulged basesA tRNAG53U54U55C56G57A58C59U60C61cWWtWH
38 HL_4GCW_0024GCW0.14570T-loop with 2 stacked bulged basesBTRNA(THR)G53U54U55C56G57A58G59C60C61cWWtWH
39 HL_4GCW_0044GCW0.14570T-loop with 2 stacked bulged basesBTRNA(THR)G53||||2_556U54||||2_556U55||||2_556C56||||2_556G57||||2_556A58||||2_556G59||||2_556C60||||2_556C61||||2_556cWWtWH
40 HL_5B63_0045B630.14920T-loop with 2 stacked bulged basesD tRNAG954U955U956C957G958A959A960U961C962cWWtWH
41 HL_4WT8_2174WT80.15190T-loop with 2 stacked bulged basesD4 tRNAG54U55U56C57A58A59A60U61C62cWWtWH
42 HL_2AZX_0062AZX0.15330T-loop with 2 stacked bulged basesD72-MERG553U554U555C556G557A558A559U560C561cWWtWH
43 HL_2AZX_0092AZX0.15330T-loop with 2 stacked bulged basesD72-MERG553||||6_555U554||||6_555U555||||6_555C556||||6_555G557||||6_555A558||||6_555A559||||6_555U560||||6_555C561||||6_555cWWtWH
44 HL_4WJ4_0064WJ40.13530T-loop with 2 stacked bulged basesB tRNAG53||||5_455U54||||5_455U55||||5_455C56||||5_455G57||||5_455A58||||5_455G59||||5_455U60||||5_455C61||||5_455cWWtWH
45 HL_4WJ4_0034WJ40.13530T-loop with 2 stacked bulged basesB tRNAG53U54U55C56G57A58G59U60C61cWWtWH
46 HL_3AL0_0033AL00.13940T-loop with 2 stacked bulged basesEtRNAGlnG53U54U55C56G57A58G59U60C61cWWtWH
47 HL_4JXZ_0034JXZ0.11130T-loop with 2 stacked bulged basesBRNA (71-MER)G953U954U955C956G957A958A959U960C961cWWtWH
48 HL_5HR7_0065HR70.11490T-loop with 2 stacked bulged basesD tRNAG52U53U54C55G56A57A58U59C60cWWtWH
49 HL_5HR6_0035HR60.10030T-loop with 2 stacked bulged basesC tRNAG52U53U54C55G56A57A58U59C60cWWtWH
50 HL_1QTQ_0031QTQ0.11550T-loop with 2 stacked bulged basesB tRNAG953U954U955C956G957A958A959U960C961cWWtWH
51 HL_5AXM_0035AXM0.07700T-loop with 2 stacked bulged basesP tRNAG53U54U55C56G57A58U59C60C61cWWtWH
52 HL_5AXM_0065AXM0.07700T-loop with 2 stacked bulged basesP tRNAG53||||2_555U54||||2_555U55||||2_555C56||||2_555G57||||2_555A58||||2_555U59||||2_555C60||||2_555C61||||2_555cWWtWH
53 HL_4YCO_0034YCO0.00000T-loop with 2 stacked bulged basesD tRNAG53U54U55C56G57A58U59U60C61cWWtWH
54 HL_3ZGZ_0033ZGZ0.07730T-loop with 2 stacked bulged basesB tRNAG53U54U55C56A57A58G59U60C61cWWtWH
55 HL_4YYE_0034YYE0.08350T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
56 HL_4RDX_0064RDX0.11450T-loop with 2 stacked bulged basesC tRNAG53||||4_577U54||||4_577U55||||4_577C56||||4_577A57||||4_577A58||||4_577G59||||4_577U60||||4_577C61||||4_577cWWtWH
57 HL_4RDX_0034RDX0.11450T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58G59U60C61cWWtWH
58 HL_2ZUE_0032ZUE0.10580T-loop with 2 stacked bulged basesBtRNA-ArgG953U954U955C956A957A958A959U960C961cWWtWH
59 HL_1J1U_0061J1U0.08280T-loop with 2 stacked bulged basesBtRNA(Tyr)G554||||4_556U555||||4_556U556||||4_556C557||||4_556A558||||4_556A559||||4_556A560||||4_556U561||||4_556C562||||4_556cWWtWH
60 HL_1J1U_0031J1U0.08280T-loop with 2 stacked bulged basesBtRNA(Tyr)G554U555U556C557A558A559A560U561C562cWWtWH
61 HL_2ZZN_0062ZZN0.11990T-loop with 2 stacked bulged basesDRNA (71-MER)G53U54U55C56A57A58A59U60C61cWWtWH
62 HL_3WQY_0033WQY0.12120T-loop with 2 stacked bulged basesC tRNAG1653U1654U1655C1656A1657A1658A1659U1660C1661cWWtWH
63 HL_5X6B_0035X6B0.11270T-loop with 2 stacked bulged basesP tRNAG52U53U54C55A56A57A58U59C60cWWtWH
64 HL_2ZZM_0042ZZM0.11990T-loop with 2 stacked bulged basesBRNA (84-MER)G53U54U55C56A57A58A59U60C61cWWtWH
65 HL_1QU2_0031QU20.10210T-loop with 2 stacked bulged basesT tRNAG53U54U55C56A57A58G59U60C61cWWtWH
66 HL_5WT1_0035WT10.13040T-loop with 2 stacked bulged basesC tRNAG53U54U55C56A57A58A59U60C61cWWtWH
67 HL_4TUE_0354TUE0.14230T-loop with 2 stacked bulged basesQV tRNAG53U54U55C56A57A58A59U60C61ncWWtWH
68 HL_4V9Q_2154V9Q0.16040T-loop with 2 stacked bulged basesDV tRNAG53U54U55C56A57A58A59U60C61cWWtWHtSH
69 HL_5AH5_0085AH50.13470T-loop with 2 stacked bulged basesD tRNAG53U54U55C56A57A58G59U60C61cWWtWH
70 HL_2BTE_0042BTE0.17000T-loop with 2 stacked bulged basesB tRNAG53U54U55C56A57A58G59U60C61cWWtWH
71 HL_1WZ2_0081WZ20.17300T-loop with 2 stacked bulged basesDtRNAG965U966U967C968G969A970A971U972C973cWWtWH
72 HL_4ZDO_0044ZDO0.14350T-loop with 2 stacked bulged basesESelenocysteine transfer RNAG53||AU54||AU55||AC56||AA57||AA58||AU59||AU60||AC61||AcWWtWH
73 HL_4P5J_0034P5J0.14070T-loop with 2 stacked bulged basesAtRNA-like 3' UTR elementG46U47G48C49A50A51C52U53C54cWWtWH
74 HL_5UD5_0035UD50.21080T-loop with 2 stacked bulged basesC tRNAG53U54U55A56G57A58U59U60C61cWWtWH
75 HL_2D6F_0062D6F0.18060T-loop with 2 stacked bulged basesFtRNAG953U954U955C956G957A958C959U960C961cWWtWH
76 HL_4WJ3_0094WJ30.20550 S tRNAG53U54U55C56G57A58G59U60C61cWWtWH
77 HL_5VPP_0345VPP0.21430 QV tRNAG55U56U57C58G59A60A61U62C63cWWtWH
78 HL_5VPP_1405VPP0.21430 XV tRNAG55U56U57C58G59A60A61U62C63cWWtWH
79 HL_3ICQ_0053ICQ0.25070T-loop with 2 stacked bulged basesERNA (62-MER)G53U54U55C56G57A58U59C60C61cWWtWH
80 HL_4V8Q_1104V8Q0.22420T-loop with 2 stacked bulged basesBY SsrAG66U67U68C69G70A71C72U73C74cWWtWH
81 HL_2NR0_0042NR00.24050 Eleucyl tRNAG53U54U55C56A57A58G59U60C61cWWtWHntWH
82 HL_4V8N_1454V8N0.24890T-loop with 2 stacked bulged basesCV tRNAG55U56U57C58G59A60A61U62C63cWWtWH
83 HL_4V8P_0984V8P0.30681 D1 LSU rRNAU664C665U666U667G668A669A670A671A673cWWntWH
84 HL_5TBW_0145TBW0.31941T-loop with 2 stacked bulged bases1 LSU rRNAU640C641U642U643G644A645A646A647A649cWWntWH
85 HL_4IOA_0174IOA0.36551T-loop with 2 stacked bulged basesX LSU rRNAU575A576U577U578G579A580A581G582A584cWW
86 HL_4Y4O_1204Y4O0.35211T-loop with 2 stacked bulged bases2A LSU rRNAU566A567U568U569G570A571A572G573A575cWW
87 HL_5J7L_1505J7L0.28131T-loop with 2 stacked bulged basesDA LSU rRNAU566U567U568U569G570U571A572U573A575cWW
88 HL_4WF9_0184WF90.29511T-loop with 2 stacked bulged basesX LSU rRNAU609U610U611U612G613U614A615G616A618cWW
89 HL_5J7L_1655J7L0.42390T-loop with 2 stacked bulged basesDA LSU rRNAG1281U1282G1283A1284A1285A1286A1287G1288C1289cWWtWH
90 HL_4V8P_1134V8P0.41780 D1 LSU rRNAA1488U1489G1490A1491G1492A1493A1494C1495U1496cWWtWH
91 HL_5TBW_0315TBW0.42790T-loop with 2 stacked bulged bases1 LSU rRNAA1462U1463G1464A1465G1466A1467A1468C1469U1470cWWtWH
92 HL_4V9F_0344V9F0.45200T-loop with 2 stacked bulged bases0 LSU rRNAG1387U1388G1389A1390G1391A1392A1393C1394C1395cWWtWH
93 HL_4WF9_0324WF90.43260T-loop with 2 stacked bulged basesX LSU rRNAG1318U1319G1320A1321G1322A1323A1324U1325C1326cWWtWH
94 HL_4IOA_0314IOA0.39570T-loop with 2 stacked bulged basesX LSU rRNAG1294U1295G1296A1297G1298A1299A1300U1301C1302cWWtWH
95 HL_4Y4O_1344Y4O0.39630T-loop with 2 stacked bulged bases2A LSU rRNAG1281U1282G1283A1284G1285A1286A1287U1288C1289cWWtWH
96 HL_5Y85_0035Y850.28150T-loop with 2 stacked bulged basesDDNA/RNA (50-MER)G11U12G13C14A15A16G17U18C19cWWtWH
97 HL_5T5A_0015T5A0.43000T-loop with 2 stacked bulged basesADNA/RNA (71-MER)G21U22G23C24A25A26G27C28C29cWWtWH
98 HL_3VJR_0013VJR0.58160Other HLBtRNA CCA-acceptorG13U14U15C16G17A18U19C20C21cWWtWH
99 HL_3F2X_0043F2X0.76250T-loop with 2 bulged bases not stackedXFMN riboswitchG68U69G70A71A72A73U74U75C76cWWtWH
100 HL_3F2X_0013F2X0.73690T-loop with 2 bulged bases not stackedXFMN riboswitchG17U18G19A20A21A22U23U24C25cWWtWH
101 HL_5C45_0015C450.75340T-loop with 2 bulged bases not stackedXFMN RiboswitchG17U18G19A20A21A22U23U24C25cWWtWH
102 HL_6DN2_0016DN20.76650T-loop with 2 bulged bases not stackedXRNA RIBOSWITCHG17U18G19A20A21A22U23U24C25cWWtWH
103 HL_5C45_0035C450.78640T-loop with 2 bulged bases not stackedYFMN RiboswitchG68U69G70A71A72A73U74U75C76cWWtWH
104 HL_6DN2_0036DN20.76960T-loop with 2 bulged bases not stackedYRNA (56-MER)G68U69G70A71A72A73U74U75C76cWWtWH
105 HL_4FRG_0014FRG0.75630T-loop with 2 bulged bases not stackedBcobalamin riboswitch aptamer domainG28U29G30A31A32A33U34U35C36cWWntWH
106 HL_4FRN_0054FRN0.77910T-loop with 2 bulged bases not stackedBCobalamin riboswitch aptamer domainG28U29G30U31A32A33U34U35C36cWWtWH

3D structures

Complete motif including flanking bases
SequenceCounts
GUUCGAAUC17
GUUCGAUUC14
GUUCAAAUC13
GUUCAAGUC10
GUUCGAGUC8
GUGAAAUUC7
GUUCGAUCC5
GUGAGAAUC4
GUUCAAUUC4
GUUCGACUC3
GUGCAAGUC2
GUUCGAGCC2
UCUUGAAACA2
UAUUGAAGCA2
AUGAGAACU2
GUGAAACUC1
GUGAAAGUC1
GUGAGAGUC1
GUGCAACUC1
GUUAGAUUC1
UUUUGUAUAA1
UUUUGUAGAA1
GUGAAAAGC1
GUGAGAACC1
GUGCAAGCC1
GUGUAAUUC1
Non-Watson-Crick part of the motif
SequenceCounts
UUCGAAU17
UUCGAUU14
UUCAAAU13
UUCAAGU10
UUCGAGU8
UGAAAUU7
UUCGAUC5
UGAGAAU4
UUCAAUU4
UUCGACU3
UGAGAAC3
UGCAAGU2
UUCGAGC2
CUUGAAAC2
AUUGAAGC2
UGAAACU1
UGAAAGU1
UGAGAGU1
UGCAACU1
UUAGAUU1
UUUGUAUA1
UUUGUAGA1
UGAAAAG1
UGCAAGC1
UGUAAUU1

Release history

Release3.11
Date2018-10-19
StatusUpdated, 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 (86)
  • T-loop with 2 bulged bases not stacked (8)
  • Other HL (2)
    • Basepair signature
    cWW-R-R-tWH-R-R-R
    Heat map statistics
    Min 0.00 | Avg 0.38 | Max 0.98
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