Motif IL_13730.4 Version IL_13730.4 of this group appears in releases 3.20 to 3.21

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name for chain		1		2	break		3		4	1-2	1-4	2-3
1	IL_4WF9_071	4WF9	0.2981	2	Major groove intercalation	X	LSU rRNA	U	1925	A	1928	*	U	1868	G	1869		cWW	cWW
2	IL_5J7L_315	5J7L	0.1620	2	Major groove intercalation	DA	LSU rRNA	U	1898	A	1901	*	U	1841	G	1842		cWW	cWW
3	IL_4V9F_067	4V9F	0.1717	2	Major groove intercalation	0	LSU rRNA	U	1939	A	1942	*	U	1897	G	1898		cWW	cWW
4	IL_5TBW_085	5TBW	0.1274	2	Major groove intercalation	1	LSU rRNA	U	2241	A	2244	*	U	2200	G	2201		cWW	cWW
5	IL_3MXH_004	3MXH	0.0000	2	Multiple bulged bases	R	Cyclic di-GMP-I riboswitch	U	81	C	84	*	G	56	G	57		cWW	cWW
6	IL_1FUF_003	1FUF	0.0811	2	Multiple bulged bases	B+A	RNA (14-mer)	U	19	C	22	*	G	9	G	10		cWW	cWW
7	IL_1FUF_002	1FUF	0.0846	2	Multiple bulged bases	A+B	RNA (14-mer)	U	5	C	8	*	G	23	G	24		cWW	cWW
8	IL_3IWN_004	3IWN	0.1229	2	Multiple bulged bases	A	Cyclic di-GMP-I riboswitch	U	76	C	79	*	G	46	G	47		cWW	cWW
9	IL_6CZR_119	6CZR	0.2639	2	Multiple bulged bases	1a	SSU rRNA	U	123	C	126	*	G	227	G	228		cWW	cWW
10	IL_4LFB_007	4LFB	0.1761	2	Multiple bulged bases	A	SSU rRNA	U	129	C	131	*	G	231	G	232		cWW	cWW
11	IL_4IOA_033	4IOA	0.4050	6	SSU/LSU pseudoknot	X	LSU rRNA	U	1015	A	1022	*	U	1161	A	1162		cWW	cWW
12	IL_5TBW_049	5TBW	0.2930	6	SSU/LSU pseudoknot	1	LSU rRNA	U	1173	A	1180	*	U	1325	A	1326		cWW	cWW
13	IL_1U9S_003	1U9S	0.2303	2	Major groove intercalation	A	RNase P class A	C	224	A	227	*	U	116	G	117		cWW	cWW
14	IL_1NBS_009	1NBS	0.2416	2	Major groove intercalation	B	RNase P class B	U	228	A	231	*	U	181	G	182		cWW	cWW
15	IL_6CZR_117	6CZR	0.3281	2	Multiple bulged bases	1a	SSU rRNA	C	64	G	67	*	C	97	G	98		cWW	cWW
16	IL_5J7L_005	5J7L	0.3151	2	Multiple bulged bases	AA	SSU rRNA	C	63	A	66	*	U	103	G	104		cWW	cWW
17	IL_4LFB_005	4LFB	0.3614	2	Multiple bulged bases	A	SSU rRNA	C	63	G	66	*	C	103	G	104		cWW	cWW
18	IL_4V9F_021	4V9F	0.3247	2	Multiple bulged bases	0	LSU rRNA	C	699	G	702	*	C	726	G	727		cWW	cWW
19	IL_4YAZ_008	4YAZ	0.4195	2	Multiple bulged bases	R	Cyclic di-GMP-I riboswitch	C	64	C	67	*	G	51	G	52		cWW	cWW
20	IL_6CZR_132	6CZR	0.3218	6	SSU/LSU pseudoknot	1a	SSU rRNA	C	488	C	495	*	G	524	G	525	ncSH	cWW	cWW
21	IL_5W1H_001	5W1H	0.3041	2	Multiple bulged bases	B	mature crRNA	C	-7	U	-4	*	A	-23	G	-22		cWW	cWW
22	IL_5WLH_001	5WLH	0.3068	2	Multiple bulged bases	B	pre-crRNA	C	-7	U	-4	*	A	-23	G	-22		cWW	cWW
23	IL_4V88_392	4V88	0.3981	2	Multiple bulged bases	A6	SSU rRNA	U	113	U	116	*	A	300	A	301		cWW	cWW
24	IL_5WTK_001	5WTK	0.4367	2	Multiple bulged bases	B	RNA (58-MER)	G	20	U	23	*	A	3	C	4		cWW	cWW
25	IL_5XWP_001	5XWP	0.5219	2	Multiple bulged bases	C	RNA (59-MER)	G	22	U	25	*	A	5	C	6		cWW	cWW
26	IL_6IV9_001	6IV9	0.3447	2	Multiple bulged bases	B	crRNA (50-MER)	G	-9	U	-6	*	A	-29	C	-28		cWW	cWW
27	IL_1R3E_002	1R3E	0.4692	3	Multiple bulged bases	E+D	RNA (17-mer)	G	408	G	412	*	C	415	C	416		cWW	cWW
28	IL_1R3E_001	1R3E	0.4404	3	Multiple bulged bases	E+D	RNA (17-mer)	C	415	C	416	*	G	408	G	412		cWW	cWW
29	IL_6JOO_001	6JOO	0.5883	3		B	Guide RNA	G	57	C	58	*	G	61	C	65		cWW	cWW
30	IL_5TBW_136	5TBW	0.7747	2	Multiple bulged bases	1	LSU rRNA	C	3349	C	3350	*	G	3353	G	3356		ncWW	cWW
31	IL_4V9F_088	4V9F	0.6914	2	Multiple bulged bases	0	LSU rRNA	C	2547	C	2548	*	G	2606	G	2609		cWW	cWW
32	IL_5TBW_109	5TBW	0.6785	2	Multiple bulged bases	1	LSU rRNA	C	2881	U	2882	*	A	2940	G	2943		cWW	cWW
33	IL_5TBW_119	5TBW	0.5455	2	Multiple bulged bases	1	LSU rRNA	C	3063	U	3064	*	A	3077	G	3080		cWW	cWW
34	IL_5J7L_349	5J7L	0.3920	2	Multiple bulged bases	DA	LSU rRNA	U	2695	U	2696	*	A	2711	G	2714		cWW	cWW
35	IL_4WF9_103	4WF9	0.3920	2	Multiple bulged bases	X	LSU rRNA	U	2722	U	2723	*	A	2738	G	2741		cWW	cWW
36	IL_1KXK_003	1KXK	0.4647	2	Multiple bulged bases	A	Group II catalytic intron	U	28	G	29	*	C	42	G	45		cWW	cWW
37	IL_3IGI_013	3IGI	0.5631	2	Multiple bulged bases	A	Group II catalytic intron D1-D4-3	U	365	A	366	*	U	375	G	378		cWW	cWW
38	IL_4IOA_092	4IOA	0.7110	2	Multiple bulged bases	X	LSU rRNA	C	2491	G	2492	*	C	2550	G	2553		cWW	cWW
39	IL_4Y4O_273	4Y4O	0.7278	2	Multiple bulged bases	2A	LSU rRNA	C	2512	G	2513	*	C	2571	G	2574		cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
UAAA*UG	4
UAGC*GG	2
UUUC*GG	2
UGAC*GG	2
CGUG*CG	2
CAAU*AG	2
GACU*AC	2
CG*CACG	2
UCAA*UG	1
UCCCUAAA*UA	1
UGCCGGAA*UA	1
CAAA*UG	1
CGAA*UG	1
CAUG*CG	1
CAGC*GG	1
CGGCCAAC*GG	1
UCGU*AA	1
GUCU*AC	1
GUUCG*CC	1
CC*GUUCG	1
GC*GUUUC	1
CC*GUUG	1
CC*GUCG	1
CU*AACG	1
CU*AUUG	1
UU*ACUG	1
UU*AUAG	1
UG*CACG	1
UA*UACG	1

Non-Watson-Crick part of the motif

Sequence	Counts
AA*	7
*AC	5
AG*	3
GA*	3
UU*	2
GU*	2
AC*	2
*UU	2
CA*	1
CCCUAA*	1
GCCGGA*	1
AU*	1
GGCCAA*	1
CG*	1
UC*	1
UUC*	1
*UUC	1
*UUU	1
*UC	1
*CU	1
*UA	1

Release history

Release	3.20	3.21
Date	2019-06-28	2019-07-26
Status	Updated, 2 parents	Exact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: Multiple bulged bases (29)
Major groove intercalation (6)
SSU/LSU pseudoknot (3)
(1)
Basepair signature: cWW-cWW
Heat map statistics: Min 0.02 | Avg 0.47 | Max 0.99

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Coloring options: Nucleotide numbers

Motif IL_13730.4 Version IL_13730.4 of this group appears in releases 3.20 to 3.21 Download Csv Json

3D structures

Complete motif including flanking bases

Non-Watson-Crick part of the motif

Release history

Parent motifs

Children motifs

Motif IL_13730.4 Version IL_13730.4 of this group appears in releases 3.20 to 3.21

Download

Csv

Json