Motif IL_55938.2 Version IL_55938.2 of this group appears in releases 0.7 to 1.0

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3	break		4		5		6		7	1-7	2-5	2-6	3-4	5-6
1	IL_2ZJR_039	2ZJR	0.3538	1		X	LSU rRNA	C	1111	U	1112	C	1113	*	G	1098	G	1100	U	1101	G	1102	cWW		cwW	cWW
2	IL_3U5H_061	3U5H	0.3110	1		5	25S rRNA	C	1275	U	1276	C	1277	*	G	1262	G	1264	U	1265	G	1266	cWW		cwW	cWW	cSH
3	IL_2ZJR_018	2ZJR	0.1755	0		X	LSU rRNA	C	769	U	770	C	771	*	G	751	G	752	U	753	G	754	cWW		cwW	cWW	cSH
4	IL_3V2F_022	3V2F	0.1534	0		A	23S Ribosomal RNA	C	756	U	757	C	758	*	G	738	G	739	U	740	G	741	cWW		cwW	cWW	cSH
5	IL_1S72_029	1S72	0.1744	0		0	LSU rRNA	C	849	U	850	C	851	*	G	830	U	831	U	832	G	833	cWW		cwW	cWW	cSH
6	IL_4A1B_038	4A1B	0.0000	0		1	26S RRNA	U	913	U	914	C	915	*	G	894	A	895	U	896	A	897	cWW		cwW	cWW	cSH
7	IL_3U5H_033	3U5H	0.1762	0		5	25S rRNA	A	888	U	889	C	890	*	G	869	G	870	U	871	U	872	cWW		cwW	cWW	cSH
8	IL_3U5F_014	3U5F	0.1919	1		6	18S rRNA	G	204	U	205	A	206	*	U	259	U	261	U	262	C	263	cWW		cwW	cWW	cSH
9	IL_2XZM_014	2XZM	0.2681	1		A	18S RRNA	G	199	U	200	A	201	*	U	256	G	257	U	259	C	260	cWW		cwW	cWW	ncSH
10	IL_1S72_082	1S72	0.2382	1		0	LSU rRNA	G	2494	U	2495	C	2496	*	G	2524	G	2525	U	2527	U	2528	cWW		cwW	cWW	cSH
11	IL_3V2F_091	3V2F	0.2547	1		A	23S Ribosomal RNA	A	2459	U	2460	C	2461	*	G	2489	G	2490	U	2492	U	2493	cWW		cwW	cWW	cSH
12	IL_4A1B_109	4A1B	0.3606	1		1	26S RRNA	G	2816	U	2817	G	2818	*	U	2846	U	2847	U	2849	U	2850	cWW		cwW	cWW
13	IL_3U5H_111	3U5H	0.3840	1		5	25S rRNA	G	2828	U	2829	G	2830	*	U	2858	U	2859	U	2861	U	2862	cWW		cwW	cWW
14	IL_1S72_003	1S72	0.4285	0		0	LSU rRNA	G	39	C	40	G	41	*	C	440	A	441	A	442	C	443	cWW	cWWa	ncWW	cWW	cSH
15	IL_2QBZ_004	2QBZ	0.4374	0		X	M-Box RNA, ykoK riboswitch aptamer	G	149	U	150	G	151	*	C	33	U	34	C	35	C	36	cWW	cWw		cWW	cSH
16	IL_3V2F_003	3V2F	0.5397	0		A	23S Ribosomal RNA	G	42	A	43	G	44	*	C	433	U	434	C	435	C	436	cWW	ncWW		cWW	cSH
17	IL_1XJR_001	1XJR	0.7098	1	Isolated basepair with bulged bases	A	s2m RNA	C	39	A	40	G	41	*	C	9	C	10	A	12	G	13	cWW			cWW
18	IL_3P49_009	3P49	0.6883	1		A	Glycine riboswitch	C	142	A	143	G	144	*	C	109	G	110	A	112	G	113	cWW		ntSH	ncWW
19	IL_3P49_006	3P49	0.6691	1		A	Glycine riboswitch	C	51	A	52	G	53	*	C	34	G	35	A	37	G	38	ncWW		ntSH	ncWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CUC*GAGUG	2
GUG*UUUUU	2
CAG*CGAAG	2
CUC*GGUG	1
GGUG*CUC	1
CUC*GUUG	1
UUC*GAUA	1
AUC*GGUU	1
GUA*UUUUC	1
GUA*UGAUC	1
GUC*GGCUU	1
AUC*GGUUU	1
GCG*CAAC	1
GUG*CUCC	1
GAG*CUCC	1
CAG*CCGAG	1

Non-Watson-Crick part of the motif

Sequence	Counts
U*UUU	3
U*AGU	2
U*GU	2
A*GAA	2
GU*U	1
U*UU	1
U*AU	1
U*GAU	1
U*GCU	1
U*GUU	1
C*AA	1
U*UC	1
A*UC	1
A*CGA	1

Release history

Release	0.7	0.8	0.9	0.10	0.11	0.12	1.0
Date	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-03-04
Status	Updated, 1 parent	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in IL_55938.2	Only in the parent motif
IL_55938.1 Compare	IL_4A1B_038, IL_1XJR_001, IL_2ZJR_018, IL_2ZJR_039, IL_3U5F_014, IL_2QBZ_004, IL_1S72_003, IL_3U5H_061, IL_3U5H_111, IL_1S72_082, IL_4A1B_109, IL_3U5H_033, IL_3P49_006, IL_3P49_009, IL_1S72_029, IL_2XZM_014	IL_3V2F_003, IL_3V2F_091, IL_3V2F_022	IL_1MMS_002, IL_3UXR_092, IL_1MMS_004, IL_3UXR_022

Children motifs

Child motif	Common motif instances	Only in IL_55938.2	Only in the child motif
IL_55938.3 Compare	IL_4A1B_038, IL_1XJR_001, IL_1S72_029, IL_3U5F_014, IL_3V2F_091, IL_1S72_003, IL_2QBZ_004, IL_3U5H_061, IL_3U5H_111, IL_1S72_082, IL_4A1B_109, IL_3U5H_033, IL_3P49_006, IL_3V2F_003, IL_3P49_009, IL_2XZM_014, IL_3V2F_022	IL_2ZJR_018, IL_2ZJR_039	IL_4IOA_018

Annotations: Isolated basepair with bulged bases (1)
Basepair signature: cWW-cWW-cSH-cWW
Heat map statistics: Min 0.11 | Avg 0.45 | Max 0.86

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Coloring options: Nucleotide numbers

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