Motif IL_16396.3 Version IL_16396.3 of this group appears in releases 3.87 to 3.87

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2	break		3		4	1-4	2-3
1	IL_6LTU_001	6LTU	0.6888	2	Multiple bulged bases	B	RNA (56-mer)	A	16	G	19	*	C	11	U	12	cWW	cWW
2	IL_6JXM_001	6JXM	0.4870	2	Multiple bulged bases	B	tRNA	A	34	C	35	*	G	53	U	56	cWW	cWW
3	IL_8VTW_100	8VTW	0.7184	1		1A	LSU rRNA	C	2591	G	2592	*	C	2601	G	2603	cWW	cWW
4	IL_1R3E_001	1R3E	0.3756	3	Multiple bulged bases	E+D	RNA (17-mer)	C	415	C	416	*	G	408	G	412	cWW	cWW
5	IL_1U9S_008	1U9S	0.3279	1	Stack outside cWW	A	RIBONUCLEASE P	G	195	C	196	*	G	217	C	219	cWW	cWW
6	IL_7L0Z_004	7L0Z	0.3050	2	Stack outside cWW	G	RNA (69-MER)	C	23	C	24	*	G	41	G	44	cWW	cWW
7	IL_4KZD_006	4KZD	0.2316	2	Stack outside cWW	R	RNA (84-MER)	C	30	C	31	*	G	49	G	52	cWW	cWW
8	IL_1NTA_001	1NTA	0.3283	1	Stack outside cWW	B+A	RNA (18-mer)	G	114	G	115	*	C	5	C	7	cWW	cWW
9	IL_5LYS_006	5LYS	0.1732	2	Stack outside cWW	B	7SK RNA	C	36	C	37	*	G	70	G	73	cWW	cWW
10	IL_387D_001	387D	0.0000	2	Multiple bulged bases	A	RNA Pseudoknot	U	1	C	2	*	G	15	A	18	cWW	cWW
11	IL_6IV9_001	6IV9	0.2341	2	Multiple bulged bases	B	crRNA (50-MER)	A	-29	C	-28	*	G	-9	U	-6	cWW	cWW
12	IL_6CF2_002	6CF2	0.2142	2	Major groove intercalation	G	RNA (35-MER)	C	10	G	11	*	C	22	G	25	cWW	cWW
13	IL_6XH2_001	6XH2	0.2241	3	Major groove intercalation	D	TRANS-ACTIVATION RESPONSE ELEMENT	C	39	U	40	*	A	22	G	26	cWW	cWW
14	IL_6DLR_004	6DLR	0.2241	2	Multiple bulged bases	A	Guanidine-I riboswitch	G	22	C	23	*	G	36	C	39	cWW	cWW
15	IL_5T83_004	5T83	0.2472	2	Multiple bulged bases	A	Guanidine-I riboswitch	G	22	C	23	*	G	33	C	36	cWW	cWW
16	IL_5LYS_007	5LYS	0.2022	2	Major groove intercalation	B	7SK RNA	C	67	U	68	*	A	39	G	42	cWW	cWW
17	IL_1XOK_002	1XOK	0.2228	2	Major groove intercalation	A+B	alfalfa mosaic virus RNA 3' UTR	C	868	C	869	*	G	877	G	880	cWW	cWW
18	IL_1XOK_001	1XOK	0.2195	2	Major groove intercalation	A	alfalfa mosaic virus RNA 3' UTR	C	846	U	847	*	A	864	G	867	cWW	cWW
19	IL_5WTK_001	5WTK	0.1697	2	Multiple bulged bases	B	RNA (58-MER)	A	3	C	4	*	G	20	U	23	cWW	cWW
20	IL_7OS0_002	7OS0	0.1471	2	Multiple bulged bases	F	crRNA	A	11	C	12	*	G	29	U	32	cWW	cWW
21	IL_7OAX_001	7OAX	0.3303	1	Stack outside cWW	A	Chili RNA Aptamer	C	44	G	45	*	U	8	G	10	cWW	cWW
22	IL_6CZR_119	6CZR	0.2797	2	Multiple bulged bases	1a	SSU rRNA	G	227	G	228	*	U	123	C	126	cWW	cWW
23	IL_4LFB_007	4LFB	0.2562	2	Multiple bulged bases	A	SSU rRNA	G	231	G	232	*	U	129	C	131	cWW	cWW
24	IL_7A0S_067	7A0S	0.4664	2	Major groove intercalation	X	LSU rRNA	U	1833	G	1834	*	U	1881	A	1884	cWW	cWW
25	IL_5J7L_315	5J7L	0.2146	2	Major groove intercalation	DA	LSU rRNA	U	1841	G	1842	*	U	1898	A	1901	cWW	cWW
26	IL_8VTW_071	8VTW	0.2776	2	Stack outside cWW	1A	LSU rRNA	U	1841	G	1842	*	U	1898	A	1901	cWW	cWW
27	IL_4V9F_067	4V9F	0.2326	2	Major groove intercalation	0	LSU rRNA	U	1897	G	1898	*	U	1939	A	1942	cWW	cWW
28	IL_3MXH_004	3MXH	0.1936	2	Multiple bulged bases	R	c-di-GMP riboswitch	G	56	G	57	*	U	81	C	84	cWW	cWW
29	IL_7MLW_005	7MLW	0.1925	1	Stack outside cWW	F	Guanidine-I riboswitch	G	17	G	18	*	U	43	C	45	cWW	cWW
30	IL_1FUF_003	1FUF	0.2029	2	Multiple bulged bases	A+B	RNA (14-mer)	G	9	G	10	*	U	19	C	22	cWW	cWW
31	IL_1FUF_002	1FUF	0.1923	2	Multiple bulged bases	B+A	RNA (14-mer)	G	23	G	24	*	U	5	C	8	cWW	cWW
32	IL_3IWN_004	3IWN	0.1901	2	Multiple bulged bases	A	C-di-GMP riboswitch	G	46	G	47	*	U	76	C	79	cWW	cWW
33	IL_6JQ6_004	6JQ6	0.3471	1	Stack outside cWW	U	Hatchet ribozyme	G	31	G	32	*	U	62	C	64	cWW	cWW
34	IL_8C3A_090	8C3A	0.2525	2	Multiple bulged bases	1	LSU rRNA	U	2178	G	2179	*	U	2219	A	2222	cWW	cWW
35	IL_5TBW_085	5TBW	0.2397	2	Major groove intercalation	1	LSU rRNA	U	2200	G	2201	*	U	2241	A	2244	cWW	cWW
36	IL_4WF9_106	4WF9	0.4034	1	Major groove intercalation	X	LSU rRNA	G	2858	G	2859	*	U	2898	C	2900	cWW	cWW
37	IL_5J7L_352	5J7L	0.4169	1	Major groove intercalation	DA	LSU rRNA	G	2838	G	2839	*	U	2878	C	2880	cWW	cWW
38	IL_5WT1_001	5WT1	0.3273	1	Stack outside cWW	C	tRNA	A	26	C	27	*	G	43	U	45	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
UG*UAAA	3
CC*GUUG	2
AC*GACU	2
GG*UGAC	2
UG*UGAA	2
GG*UAGC	2
GG*UGC	2
GG*UUUC	2
GG*UAC	2
AUUG*CU	1
AC*GAUU	1
CG*CAG	1
CC*GUUCG	1
GC*GGC	1
GG*CGC	1
CC*GCUG	1
UC*GGAA	1
AC*GUCU	1
CG*CUGG	1
CU*AUCUG	1
GC*GGAC	1
GC*GGUC	1
CU*AUUG	1
CC*GAUG	1
CU*AAUG	1
CG*UGG	1
UG*UCAA	1
AC*GGU	1

Non-Watson-Crick part of the motif

Sequence	Counts
*G	6
*GA	6
*UU	5
*AU	3
*A	3
*AA	3
*AC	2
*AG	2
UU*	1
*UUC	1
*CU	1
*UC	1
*UG	1
*UCU	1
*GU	1
*CA	1

Release history

Release	3.87
Date	2024-08-14
Status	Updated, 2 parents

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: Multiple bulged bases (16)
Major groove intercalation (11)
Stack outside cWW (10)
(1)
Basepair signature: cWW-cWW
Heat map statistics: Min 0.04 | Avg 0.30 | Max 0.92

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