#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name 1 2 3break 4 51-53-4
1 IL_4V9F_0794V9F1.19970Single bulged A0 LSU rRNAU2290A2291C2292*G2279A2280cWWcWW
2 IL_5TBW_0985TBW1.21030Single bulged A1 LSU rRNAC2625A2626C2627*G2614G2615cWWcWW
3 IL_8C3A_1078C3A1.18020Single bulged A1 LSU rRNAC2597A2598C2599*G2586G2587cWWcWW
4 IL_7KGA_0057KGA1.03130Single bulged ABFlavivirus DB elementU39A40G41*C14A15cWWcWW
5 IL_4V9F_0324V9F1.30480Single bulged A0 LSU rRNAU942A943G944*C1023G1024cWWcWW
6 IL_3G9C_0053G9C1.09810Single bulged AF+QRNA (11-mer) + GLMS RIBOZYMEC5A6G7*C52G53cWWcWW
7 IL_5J7L_3025J7L0.77680Single bulged ADA LSU rRNAC1489A1490G1491*C1499G1500cWWcWW
8 IL_8VMA_0038VMA0.68070Single bulged ACRNA (88-MER)U46A47G48*C78G79cWWcWW
9 IL_5FJC_0015FJC0.60260Single bulged AA SAM-I riboswitchG13A14||AG15*C40C41cWWcWW
10 IL_2OZB_0012OZB0.84220Single bulged ACRNA comprising the 5' Stem-Loop RNA of U4snRNAU24A25G26*C47G48cWWcWW
11 IL_8VTW_0618VTW0.79900Single bulged A1A LSU rRNAU1489A1490G1491*C1499G1500cWWcWW
12 IL_4V9F_0984V9F0.58440Single bulged A0 LSU rRNAC2895A2896C2897*G2860G2861cWWcWW
13 IL_8VTW_0478VTW0.45360Single bulged A1A LSU rRNAG1219A1220C1221*G1229C1230cWWcWW
14 IL_5TBW_0455TBW0.55570Single bulged A1 LSU rRNAU1074A1075C1076*G1083A1084cWWcWW
15 IL_4V88_4414V880.59840Single bulged AA6 SSU rRNAU1630A1631C1632*G1146A1147cWWcWW
16 IL_8C3A_4478C3A0.58110Single bulged ACM SSU rRNAU1617A1618C1619*G1131A1132cWWcWW
17 IL_5J7L_0395J7L0.55510Single bulged AAA SSU rRNAU1393A1394C1395*G922A923cWWcWW
18 IL_4LFB_0354LFB0.56540Single bulged AA SSU rRNAU1393A1394C1395*G922A923cWWcWW
19 IL_6CZR_1476CZR0.56650Single bulged A1a SSU rRNAU1376A1377C1378*G900A901cWWcWW
20 IL_8C3A_1228C3A0.60630Single bulged A1 LSU rRNAC2942A2943G2944*C2932G2933cWWcWW
21 IL_5TBW_1135TBW0.57800Single bulged A1 LSU rRNAC2970A2971G2972*C2960G2961cWWcWW
22 IL_5J7L_3445J7L0.44260Single bulged ADA LSU rRNAC2601A2602G2603*C2591G2592cWWcWW
23 IL_4AOB_0014AOB0.42550Single bulged AA SAM-I riboswitchG13A14G15*C40C41cWWcWW
24 IL_4P3U_0024P3U0.38790Single bulged AB+ARNA (23-mer)A40A41G42*C7U8ncWWcWW
25 IL_3V7E_0013V7E0.37360Single bulged AC SAM-I riboswitchG13A14G15*C40C41cWWcWW
26 IL_8C3A_0148C3A0.00000Single bulged A1+4 LSU rRNA + 5.8S rRNAG337A338C339*G25U26cWWcWW
27 IL_5TBW_0135TBW0.10730Single bulged A1+4 LSU rRNA + 5.8S rRNAG337A338C339*G25U26cWWcWW
28 IL_5J7L_2465J7L0.23900Single bulged ADA LSU rRNAG442A443C444*G36C37cWWcWW
29 IL_4WF9_0024WF90.23270Single bulged AX LSU rRNAG488A489C490*G36C37cWWcWW
30 IL_7A0S_0027A0S0.28840Single bulged AX LSU rRNAG454A455C456*G36C37cWWcWW
31 IL_1NBS_0051NBS0.28150Single bulged AB RNase P class BG129A130C131*G113C114cWWcWW
32 IL_1I9X_0011I9X0.27140Single bulged AA+BRNA (13-mer)U4A5A6*U9A10cWWcWW
33 IL_1U9S_0011U9S0.28490Single bulged AARIBONUCLEASE PG107A108C109*G95C96cWWcWW
34 IL_4V88_4094V880.22350Single bulged AA6 SSU rRNAA505A506U507*A481U482cWWcWW
35 IL_6MSF_0016MSF0.47210Single bulged ARRNA (14-mer)C2||||P_1A3||||P_1C4||||P_1*G12||||P_1G13||||P_1cWWcWW
36 IL_2C4Q_0012C4Q0.49500Single bulged ARRNA (19-mer)G5||||P_1A6||||P_1G7||||P_1*C14||||P_1C15||||P_1cWWcWW
37 IL_1GID_0091GID0.31690Single bulged ABP4-P6 RNA RIBOZYME DOMAINC209A210C211*G110G111cWWcWW
38 IL_2VPL_0022VPL0.42920Single bulged ABFRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITEG28A29A30*U16C17cWWcWW
39 IL_4R4V_0034R4V0.36730Single bulged AAVS ribozyme RNAC651A652G653*C766G767cWWcWW
40 IL_4P3U_0054P3U0.46710Single bulged AA+BRNA (23-mer)A17A18G19*C30U31cWWcWW
41 IL_4P3U_0084P3U0.48370Single bulged AD+CRNA (23-mer)A40A41G42*C7U8cWWcWW
42 IL_4P3U_0114P3U0.51700Single bulged AC+DRNA (23-mer)A17A18G19*C30U31cWWcWW
43 IL_5TBW_0185TBW0.47510Single bulged A1 LSU rRNAC577A578G579*U512G513cWWcWW
44 IL_8C3A_0208C3A0.39390Single bulged A1 LSU rRNAC575A576G577*C508G509cWWcWW
45 IL_1I9X_0021I9X0.35160Single bulged AB+ARNA (13-mer)U4A5A6*U9A10cWWcWW
46 IL_1CSL_0021CSL0.36360Single bulged AB+ARNA (15-mer)G67A68C69*G50C51cWWcWW
47 IL_1DUQ_0021DUQ0.38400Single bulged AB+ATHE REV BINDING ELEMENTG120A121C122*G108C109cWWcWW
48 IL_5AOX_0025AOX0.47440Single bulged ACALU JO CONSENSUS RNAG56A57G58*C108C109cWWcWW
49 IL_4P43_0024P430.40360Single bulged AB+ARNA (23-mer)A40A41G42*C7U8cWWcWW
50 IL_4P43_0034P430.38330Single bulged AA+BRNA (23-mer)A17A18G19*C30U31cWWcWW
51 IL_3CGP_0023CGP0.48310Single bulged AB+ARNA (13-mer)U19A20A21*PSU6A7cWWcWW
52 IL_5TBW_0245TBW0.43080Single bulged A1 LSU rRNAG779A780G781*C752C753cWWcWW
53 IL_8C3A_0268C3A0.42090Single bulged A1 LSU rRNAG775A776G777*C748C749cWWcWW
54 IL_1JZV_0021JZV0.45590Single bulged AB+ARNA (9-mer)U12A13C14*G4A5cWWcWW
55 IL_4L8H_0014L8H0.56270Single bulged ARRNA operator hairpinC4A5U6*A16G17cWWcWW
56 IL_8VM9_0038VM90.40720Single bulged ARRNA (85-MER)U43A44G45*C75G76cWWcWW
57 IL_8UO6_0018UO60.56320Single bulged AAHIV-1 Rev Response Element Stem-Loop II with tRNA scaffoldG60A61C62*G42C43cWWcWW
58 IL_4PHY_0044PHY0.58920Single bulged AA+BRNA (26-MER) + RNA (20-mer)C20A21C22*G30G31ncWWcWW
59 IL_7VTI_0017VTI0.62240Single bulged ABcrRNAU31A32C33*G4G5cWWcWW
60 IL_8VTW_0328VTW0.29200Single bulged A1A LSU rRNAU895A896C897*G880G881cWWcWW
61 IL_6XH2_0026XH20.24430Single bulged ADTRANS-ACTIVATION RESPONSE ELEMENTG34A35G36*C29C30cWWcWW
62 IL_7MKY_0017MKY0.34920Single bulged AARNA (66-MER)G49A50U51*A35C36cWWcWW
63 IL_5WWT_0015WWT0.33630Single bulged AC tRNAG37A38U39*A31C32cWWcWW
64 IL_7DLZ_0017DLZ0.42930Single bulged AXRNA (45-MER)U6A7C8*G39G40cWWcWW
65 IL_8VMB_0028VMB0.44460Single bulged ARRNA (83-MER)U46A47G48*C75G76cWWcWW
66 IL_4V9F_0024V9F0.33410Single bulged A0 LSU rRNAG448A449C450*G33C34cWWcWW
67 IL_4V88_3994V880.30500Single bulged AA6 SSU rRNAA265A266U267*A288U289cWWcWW
68 IL_4V9F_0644V9F0.41830Single bulged A0 LSU rRNAC2021A2022G2023*C1826G1827cWWcWW
69 IL_8VTW_0688VTW0.39180Single bulged A1A LSU rRNAG1980A1981C1982*G1770C1771cWWcWW
70 IL_8C3A_0878C3A0.40480Single bulged A1 LSU rRNAG2301A2302G2303*C2106U2107cWWcWW
71 IL_5TBW_0825TBW0.41230Single bulged A1 LSU rRNAG2323A2324G2325*C2128U2129cWWcWW
72 IL_5J7L_3125J7L0.43480Single bulged ADA LSU rRNAG1980A1981U1982*G1770C1771cWWcWW
73 IL_7A0S_0647A0S0.43480Single bulged AX LSU rRNAG1963A1964U1965*G1761C1762cWWcWW
74 IL_4WF9_0684WF90.44330Single bulged AX LSU rRNAG2007A2008U2009*G1797C1798cWWcWW
75 IL_8C3A_1438C3A0.59770Single bulged A3 5S rRNAA63A64G65*C15U16cWWcWW
76 IL_5TBW_3725TBW0.58850Single bulged AAS 5S rRNAA63A64G65*C15U16cWWcWW
77 IL_7A0S_0127A0S0.50530Single bulged AX LSU rRNAG600A601C602*G678C679cWWcWW
78 IL_3MJA_0013MJA0.41340Single bulged ABDomain 3 of the cricket paralysis virus intergenic region IRES RNAC6181A6182G6183*C6194G6195cWWcWW
79 IL_5TBW_0605TBW0.53330Single bulged A1 LSU rRNAU1398A1399G1400*C1411G1412cWWcWW
80 IL_3CGS_0023CGS0.45780Single bulged AB+ARNA (13-mer)G20A21C22*G5PSU6cWWcWW
81 IL_3CGR_0023CGR0.56140Single bulged AB+ARNA (13-mer)A19A20C21*G6PSU7cWWcWW
82 IL_8VTW_0588VTW0.74740Single bulged A1A LSU rRNAG1459A1460G1461*C1450|||AC1451cWWcWW
83 IL_4V9F_0254V9F0.54620Single bulged A0 LSU rRNAG856A857U858*A788C789cWWcWW
84 IL_5J7L_2615J7L0.56110Single bulged ADA LSU rRNAG763A764C765*G697C698cWWcWW
85 IL_4WF9_0224WF90.55370Single bulged AX LSU rRNAG808A809A810*U742C743cWWcWW
86 IL_8VTW_0188VTW0.54760Single bulged A1A LSU rRNAG763A764G765*C697C698cWWcWW
87 IL_7A0S_0167A0S0.55860Single bulged AX LSU rRNAG776A777G778*C710C711cWWcWW
88 IL_8C3A_0318C3A0.50830Single bulged A1 LSU rRNAA891A892U893*A824U825cWWcWW
89 IL_8C3A_0198C3A0.62580Single bulged A1 LSU rRNAG505A506G507*C578C579cWWcWW
90 IL_4LGT_0024LGT0.68040Single bulged AEstem-loop of 23S rRNAC2601A2602G2603*C2591G2592cWWcWW
91 IL_8X5V_0028X5V0.79420Single bulged ABRNA (110-mer)G61A62C63*G55C56cWWcWW
92 IL_1MFQ_0051MFQ0.72270Single bulged AA SRP RNAG175A176G177*C220C221cWWcWW
93 IL_8UIW_0018UIW0.61230Single bulged ANyjdF RNA (R. gauvreauii)G44A45U46*A63C64cWWcWW
94 IL_6D3P_0046D3P0.77600Single bulged AARNA (45-MER)G27A28G29*C12C13cWWcWW
95 IL_7JJU_0027JJU0.79650Single bulged AA PLRV_xrRNAC31A32U33*A12G13cWWcWW
96 IL_7JJU_0047JJU0.79680Single bulged AB PLRV_xrRNAC31A32U33*A12G13cWWcWW
97 IL_6CYT_0016CYT0.89570Single bulged ANRNA (17-mer)G34A35G36*C29C30cWWcWW
98 IL_7KGA_0027KGA0.85780Single bulged AAFlavivirus DB elementU39A40G41*C14A15cWWcWW
99 IL_8XZL_0038XZL1.20180Single bulged AARNA (53-MER)G32A33C34*G27C28cWWcWW
100 IL_5TBW_0585TBW1.08020Single bulged A1 LSU rRNAC1385A1386G1387*C1420G1421cWWcWW
101 IL_8C3A_0628C3A1.00930Single bulged A1 LSU rRNAC1381A1382G1383*C1416G1417cWWcWW
102 IL_3OXE_0013OXE0.82090Single bulged AAdomain II of glycine riboswitchG12A13A14*U27C28cWWcWW
103 IL_5J7L_0495J7L1.01520Single bulged AAA SSU rRNAC1195A1196A1197*U1060G1061cWWcWW
104 IL_8C3A_4188C3A0.86020Single bulged ACM SSU rRNAA503A504U505*A479U480cWWcWW
105 IL_8C3A_4588C3A0.77440Single bulged ACM SSU rRNAC1412A1413G1414*C1265G1266cWWcWW
106 IL_4V88_4524V880.81780Single bulged AA6 SSU rRNAC1426A1427G1428*C1280G1281cWWcWW
107 IL_4WF9_0064WF90.57300Single bulged AX LSU rRNAC175A176G177*C152G153cWWcWW
108 IL_2QUX_0022QUX0.65410Single bulged AFRNA (25-MER)C5A6G7*C20G21cWWcWW
109 IL_6WPI_0016WPI0.51900Single bulged ABRNA (47-MER)G11A12A13*U41C42cWWcWW
110 IL_1U63_0041U630.50750Single bulged AD49 NT FRAGMENT OF MRNA FOR L1G28A29A30*U16C17cWWcWW
111 IL_5TBW_1235TBW0.68490Single bulged A1 LSU rRNAG3177A3178U3179*A3210C3211cWWcWW
112 IL_8C3A_1318C3A0.59570Single bulged A1 LSU rRNAG3147A3148U3149*A3175C3176cWWcWW
113 IL_4R4V_0044R4V0.58530Single bulged AAVS ribozyme RNAU712A713G714*C660A661cWWcWW
114 IL_6CZR_1146CZR1.20060Single bulged A1a SSU rRNAG392A393C394*G45U46cWWcWW
115 IL_4LFB_0024LFB1.24720Single bulged AA SSU rRNAG396A397C398*G44U45cWWcWW
116 IL_5J7L_0025J7L1.21060Single bulged AAA SSU rRNAC396A397U398*A44G45cWWcWW
117 IL_4P97_0024P971.19730Single bulged AB+ARNA (11-mer)G38A39G40*C12C13cWWcWW
118 IL_5CNR_0025CNR1.16250Single bulged AB+ARNA (11-mer)G38A39G40*C12C13cWWcWW
119 IL_4PHY_0024PHY1.17060Single bulged AB+ARNA (20-mer)G38A39G40*C12C13cWWcWW
120 IL_5J7L_3555J7L1.55210Major groove intercalationDB 5S rRNAU65A66G67*C17G18cWWcWW
121 IL_7JNH_0037JNH1.59730Major groove intercalationBCore double ENE RNA (Xtal construct) from Oryza sativa transposonU55A56C57*G35G36cWWcWW
122 IL_4WF9_1124WF91.64160Major groove intercalationY 5S rRNAU63A64G65*C15A16cWWcWW
123 IL_8VTW_1108VTW1.65140Major groove intercalation1B 5S rRNAC65A66G67*C17G18cWWcWW
124 IL_4V9F_1014V9F1.67740Major groove intercalation9 5S rRNAC64A65G66*C15G16cWWcWW
125 IL_7DLZ_0027DLZ1.83520Major groove intercalationXRNA (45-MER)U9A10C11*G37G38cWWcWW

3D structures

Complete motif including flanking bases
SequenceCounts
CAG*CG18
GAG*CC18
GAC*GC15
UAC*GA8
UAG*CG8
AAG*CU8
CAC*GG6
GAU*AC6
GAA*UC5
UAC*GG5
UAG*CA4
GAC*GU4
AAU*AU4
CAU*AG4
GAU*GC3
UAA*UA2
GAG*CU2
CAG*UG1
UAA*(PSU)A1
GAC*G(PSU)1
AAC*G(PSU)1
CAA*UG1
Non-Watson-Crick part of the motif
SequenceCounts
A*125

Release history

Release3.88
Date2024-09-11
StatusUpdated, 2 parents

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.
Annotations
  • Single bulged A (119)
  • Major groove intercalation (6)
  • Basepair signature
    cWW-L-cWW
    Heat map statistics
    Min 0.03 | Avg 0.84 | Max 2.16
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