RNA 3D Hub //

Motif IL_80007.4 Version IL_80007.4 of this group appears in releases 3.19 to 3.19

#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name 1 2break 3 41-42-3
1 IL_5TBW_0585TBW0.54141Single bulged A1 LSU rRNAC1420G1421*C1385G1387cWWcWW
2 IL_5J7L_0495J7L0.31491Single bulged AAA SSU rRNAU1060G1061*C1195A1197cWWcWW
3 IL_1MFQ_0051MFQ0.39971Single bulged AA SRP RNAG175G177*C220C221cWWcWW
4 IL_4R4V_0034R4V0.32511Single bulged AAVS ribozyme RNAC651G653*C766G767cWWcWW
5 IL_4R4V_0094R4V0.32511Single bulged AAVS ribozyme RNAC651||||7_556G653||||7_556*C766||||7_556G767||||7_556cWWcWW
6 IL_4WF9_0064WF90.30021Single bulged AX LSU rRNAC175G177*C152G153cWWcWW
7 IL_4PHY_0044PHY0.28661Single bulged AA+BRNA (26-MER) + RNA (20-mer)C20C22*G30G31ncWWcWW
8 IL_5J7L_3445J7L0.15671Single bulged ADA LSU rRNAC2601G2603*C2591G2592cWWcWW
9 IL_4V9F_0904V9F0.13211Single bulged A0 LSU rRNAC2636G2638*C2626G2627cWWcWW
10 IL_5TBW_1135TBW0.16301Single bulged A1 LSU rRNAC2970G2972*C2960G2961cWWcWW
11 IL_4V88_4524V880.22641Single bulged AA6 SSU rRNAC1426G1428*C1280G1281cWWcWW
12 IL_2QUX_0022QUX0.24381Single bulged AFRNA (25-MER)C5G7*C20G21cWWcWW
13 IL_4V9F_0644V9F0.21071Single bulged A0 LSU rRNAC2021G2023*C1826G1827cWWcWW
14 IL_4R4V_0104R4V0.28041Single bulged AAVS ribozyme RNAU712||||7_556G714||||7_556*C660||||7_556A661||||7_556cWWcWW
15 IL_4R4V_0044R4V0.28041Single bulged AAVS ribozyme RNAU712G714*C660A661cWWcWW
16 IL_6CF2_0026CF20.30892Major groove intercalationGRNA (35-MER)C22G25*C10G11cWWcWW
17 IL_4Y4O_2104Y4O0.32211Single bulged A2A LSU rRNAU895C897*G880G881cWWcWW
18 IL_5TBW_0605TBW0.40001Single bulged A1 LSU rRNAU1398G1400*C1411G1412cWWcWW
19 IL_4IOA_0674IOA0.36222Multiple bulged basesX LSU rRNAU1881A1884*U1833G1834cWWcWW
20 IL_4PHY_0024PHY0.28321Single bulged AB+ARNA (20-mer)G38G40*C12C13cWWcWW
21 IL_6CMN_0016CMN0.26913Multiple bulged basesDTrans-Activation Response RNA ElementA22G26*C39U40cWWcWW
22 IL_5FJC_0015FJC0.22241Single bulged AA SAM-I riboswitchG13G15*C40C41cWWcWW
23 IL_1XOK_0011XOK0.24292Major groove intercalationAalfalfa mosaic virus RNA 3' UTRA864G867*C846U847cWWcWW
24 IL_5LYS_0075LYS0.24552Major groove intercalationB7SK RNAA39G42*C67U68cWWcWW
25 IL_4P43_0024P430.16861Single bulged AB+ARNA (23-mer)A40G42*C7U8cWWcWW
26 IL_4P43_0034P430.17301Single bulged AA+BRNA (23-mer)A17G19*C30U31cWWcWW
27 IL_1XOK_0021XOK0.21242Major groove intercalationB+Aalfalfa mosaic virus RNA 3' UTRG877G880*C868C869cWWcWW
28 IL_5J7L_0025J7L0.16311Single bulged AAA SSU rRNAC396U398*A44G45cWWcWW
29 IL_5TBW_0985TBW0.16011Single bulged A1 LSU rRNAC2625C2627*G2614G2615cWWcWW
30 IL_1JZV_0021JZV0.19301Single bulged AB+ARNA (9-mer)U12C14*G4A5cWWcWW
31 IL_4V9F_0794V9F0.16971Single bulged A0 LSU rRNAU2290C2292*G2279A2280cWWcWW
32 IL_1U63_0041U630.22051Single bulged AD49 NT FRAGMENT OF MRNA FOR L1G28A30*U16C17cWWcWW
33 IL_4AOB_0064AOB0.18721Single bulged AA SAM-I riboswitchG13||||7_555G15||||7_555*C40||||7_555C41||||7_555cWWcWW
34 IL_4AOB_0014AOB0.18721Single bulged AA SAM-I riboswitchG13G15*C40C41cWWcWW
35 IL_5AOX_0025AOX0.11701Single bulged ACALU JO CONSENSUS RNAG56G58*C108C109cWWcWW
36 IL_6CMN_0026CMN0.14451Single bulged ADTrans-Activation Response RNA ElementG34G36*C29C30cWWcWW
37 IL_5LYS_0065LYS0.12972Stack outside cWWB7SK RNAG70G73*C36C37cWWcWW
38 IL_387D_001387D0.20592Multiple bulged basesARNA PseudoknotG15A18*U1C2cWWcWW
39 IL_6RA4_0016RA40.28820M+LRNA (9-mer)C406U407*C401G402cWWcWW
40 IL_1SI3_0021SI30.32500BRNA (9-mer)C406||||4_675U407||||4_675*C401G402cWWcWW
41 IL_1SI2_0011SI20.26120BRNA (9-mer)C406||||4_675U407||||4_675*C401G402cWWncWW
42 IL_6D3P_0026D3P0.20711Single bulged AARNA (45-MER)C12||||12_566C13||||12_566*G27||||12_566G29||||12_566cWWcWW
43 IL_6D3P_0046D3P0.20711Single bulged AARNA (45-MER)C12C13*G27G29cWWcWW
44 IL_2C4Q_0052C4Q0.19221Single bulged ARRNA (19-mer)C14||||P_PC15||||P_P*G5||||P_PG7||||P_P
45 IL_2C4Q_0012C4Q0.19221Single bulged ARRNA (19-mer)C14||||P_1C15||||P_1*G5||||P_1G7||||P_1cWWcWW
46 IL_5TBW_3725TBW0.16981Single bulged AAS 5S rRNAC15U16*A63G65cWWcWW
47 IL_4MCF_0014MCF0.15710D+BGas5 GREM RevU10G11*C9U10ncwWcWW
48 IL_4P3U_0054P3U0.15101Single bulged AB+ARNA (23-mer)C30U31*A17G19cWWcWW
49 IL_4P3U_0084P3U0.15581Single bulged AC+DRNA (23-mer)C7U8*A40G42cWWcWW
50 IL_4P3U_0114P3U0.11711Single bulged AC+DRNA (23-mer)A17G19*C30U31cWWcWW
51 IL_4KZD_0064KZD0.00002Stack outside cWWRRNA (84-MER)G49G52*C30C31cWWcWW
52 IL_5OB3_0045OB30.09032Multiple bulged basesARNA aptamer (69-MER)G41G44*C23C24cWWcWW
53 IL_1I9X_0021I9X0.11681Single bulged AB+ARNA (13-mer)U4A6*U9A10cWWcWW
54 IL_1I9X_0011I9X0.13891Single bulged AA+BRNA (13-mer)U4A6*U9A10cWWcWW
55 IL_3MJA_0013MJA0.24191Single bulged ABDomain 3 of the cricket paralysis virus intergenic region IRES RNAC6194G6195*C6181G6183cWWcWW
56 IL_5TBW_0245TBW0.26811Single bulged A1 LSU rRNAC752C753*G779G781cWWcWW
57 IL_4LGT_0024LGT0.27671Single bulged AEstem-loop of 23S rRNAC2591G2592*C2601G2603cWWcWW
58 IL_6MSF_0016MSF0.26961Single bulged ARRNA (14-mer)G12||||P_1G13||||P_1*C2||||P_1C4||||P_1cWWcWW
59 IL_6MSF_0036MSF0.26961Single bulged ARRNA (14-mer)G12||||P_PG13||||P_P*C2||||P_PC4||||P_P
60 IL_5U30_0015U300.28520BsgRNAG0G1*C11A12cWWcWW
61 IL_4P3U_0024P3U0.27061Single bulged AB+ARNA (23-mer)A40G42*C7U8ncWWcWW
62 IL_3V7E_0013V7E0.35221Single bulged AC SAM-I riboswitchC40C41*G13G15cWWcWW
63 IL_6CZR_1146CZR0.59241Single bulged A1a SSU rRNAG392C394*G45U46cWWcWW
64 IL_5TBW_0825TBW0.36621Single bulged A1 LSU rRNAG2323G2325*C2128U2129cWWcWW
65 IL_4WF9_0024WF90.26541Single bulged AX LSU rRNAG488C490*G36C37cWWcWW
66 IL_5J7L_2465J7L0.24531Single bulged ADA LSU rRNAG442C444*G36C37cWWcWW
67 IL_4Y4O_1804Y4O0.30791Single bulged A2A LSU rRNAG442C444*G36C37cWWcWW
68 IL_4IOA_0024IOA0.31611Single bulged AX LSU rRNAG454C456*G36C37cWWcWW
69 IL_1NBS_0051NBS0.28621Single bulged AB RNase P class BG129C131*G113C114cWWcWW
70 IL_2VPL_0022VPL0.21621Single bulged ABFRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITEG28A30*U16C17cWWcWW
71 IL_2YGH_0052YGH0.20761Single bulged AA SAM-I riboswitchG13||||8_554G15||||8_554*C40||||8_554C41||||8_554cWWcWW
72 IL_2YGH_0012YGH0.20761Single bulged AA SAM-I riboswitchG13G15*C40C41cWWcWW
73 IL_4JGN_0064JGN0.31820ERNA (20-mer)U503G504*C520||||4_555U521||||4_555cWwcWW
74 IL_3OXE_0013OXE0.42161Single bulged AAdomain II of glycine riboswitchU27C28*G12A14cWWcWW
75 IL_4Y4O_1964Y4O0.33961Single bulged A2A LSU rRNAC697C698*G763G765cWWcWW
76 IL_4IOA_0154IOA0.33201Single bulged AX LSU rRNAC710C711*G776G778cWWcWW
77 IL_4Y4O_2354Y4O0.37911Single bulged A2A LSU rRNAC1450|||AC1451*G1459G1461cWWcWW
78 IL_4WF9_0224WF90.41931Single bulged AX LSU rRNAU742C743*G808A810cWWcWW
79 IL_5TBW_0015TBW0.443901+4 LSU rRNA + 5.8S rRNAU3U4*A155U156cWwcWW
80 IL_5J7L_2615J7L0.58171Single bulged ADA LSU rRNAG697C698*G763C765cWWcWW
81 IL_4IOA_0644IOA0.54771Single bulged AX LSU rRNAG1963U1965*G1761C1762cWWcWW
82 IL_5J7L_3125J7L0.51591Single bulged ADA LSU rRNAG1980U1982*G1770C1771cWWcWW
83 IL_4WF9_0684WF90.50331Single bulged AX LSU rRNAG2007U2009*G1797C1798cWWcWW
84 IL_4IOA_0114IOA0.43581Single bulged AX LSU rRNAG600C602*G678C679cWWcWW
85 IL_1DUQ_0021DUQ0.37511Single bulged AB+ATHE REV BINDING ELEMENTG120C122*G108C109cWWcWW
86 IL_1CSL_0021CSL0.40031Single bulged AB+ARNA (15-mer)G67C69*G50C51cWWcWW
87 IL_1U9S_0011U9S0.40051Single bulged AARIBONUCLEASE PG107C109*G95C96cWWcWW
88 IL_1U9S_0081U9S0.35231Stack outside cWWARIBONUCLEASE PG217C219*G195C196cWWcWW
89 IL_5TBW_0135TBW0.47461Single bulged A1+4 LSU rRNA + 5.8S rRNAG337C339*G25U26cWWcWW
90 IL_4LFB_0024LFB0.47871Single bulged AA SSU rRNAG396C398*G44U45cWWcWW
91 IL_4Y4O_2424Y4O0.46821Single bulged A2A LSU rRNAG1980C1982*G1770C1771cWWcWW
92 IL_4V88_4094V880.38591Single bulged AA6 SSU rRNAA505U507*A481U482cWWcWW
93 IL_4V9F_0024V9F0.37441Single bulged A0 LSU rRNAG448C450*G33C34cWWcWW
94 IL_5T83_0045T830.33402Multiple bulged basesAGuanidine-I riboswitchG33C36*G22C23cWWcWW
95 IL_5TBW_1235TBW0.33241Single bulged A1 LSU rRNAG3177U3179*A3210C3211cWWcWW
96 IL_4Y4O_2244Y4O0.43621Single bulged A2A LSU rRNAG1219C1221*G1229C1230cWWcWW
97 IL_6DLR_0046DLR0.37302Multiple bulged basesAGuanidine-I riboswitchG36C39*G22C23cWWcWW
98 IL_4V88_3994V880.35641Single bulged AA6 SSU rRNAA265U267*A288U289cWWcWW
99 IL_5WWT_0015WWT0.36251Single bulged AC tRNAG37U39*A31C32cWWcWW
100 IL_6CZR_1476CZR0.43991Single bulged A1a SSU rRNAU1376C1378*G900A901cWWcWW
101 IL_5J7L_0395J7L0.39281Single bulged AAA SSU rRNAU1393C1395*G922A923cWWcWW
102 IL_4LFB_0354LFB0.41351Single bulged AA SSU rRNAU1393C1395*G922A923cWWcWW
103 IL_4V88_4414V880.40681Single bulged AA6 SSU rRNAU1630C1632*G1146A1147cWWcWW
104 IL_5TBW_0455TBW0.40331Single bulged A1 LSU rRNAU1074C1076*G1083A1084cWWcWW
105 IL_4V9F_0984V9F0.38471Single bulged A0 LSU rRNAC2895C2897*G2860G2861cWWcWW
106 IL_5FDV_1115FDV0.58351Single bulged A1B 5S rRNAC65G67*C17G18cWWcWW
107 IL_4V9F_1014V9F0.57621Major groove intercalation9 5S rRNAC64G66*C15G16cWWcWW
108 IL_5J7L_3025J7L0.51301Single bulged ADA LSU rRNAC1489G1491*C1499G1500cWWcWW
109 IL_4IOA_0844IOA0.45321Major groove platformX LSU rRNAU2380C2382*G2393G2394cWWcWW
110 IL_5J7L_3525J7L0.47011Major groove intercalationDA LSU rRNAU2878C2880*G2838G2839cWWcWW

3D structures

Complete motif including flanking bases
SequenceCounts
CAG*CG12
GAC*GC12
GAG*CC9
CC*GAG9
UAC*GA7
AAG*CU4
CG*CAG3
CAC*GG3
UAC*GG3
CU*CG3
CU*AAG3
GAC*GU3
GAU*GC3
UAG*CA2
GAA*UC2
UG*CU2
GUUG*CC2
UAA*UA2
GG*CAC2
UC*GAA2
AAU*AU2
GAU*AC2
UG*CAA1
CUGG*CG1
UAG*CG1
UGAA*UG1
AUCUG*CU1
AAUG*CU1
AUUG*CU1
GAUG*CC1
CAU*AG1
GCUG*CC1
GGAA*UC1
GG*CA1
GAG*CU1
UU*AU1
GC*GAC1
GGC*GC1
GGUC*GC1
GGAC*GC1
Non-Watson-Crick part of the motif
SequenceCounts
A*69
*A21
*7
GA*3
UU*3
AU*2
UG*1
UCU*1
CU*1
G*1
GU*1

Release history

Release3.19
Date2019-05-31
StatusUpdated, 1 parent

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.
Annotations
  • Single bulged A (87)
  • (7)
  • Major groove intercalation (6)
  • Multiple bulged bases (6)
  • Stack outside cWW (3)
  • Major groove platform (1)
    • Basepair signature
    cWW-cWW
    Heat map statistics
    Min 0.04 | Avg 0.40 | Max 0.98
    Help

    Coloring options:

    Copyright 2025 BGSU RNA group. Page generated in 1.4104 s