Motif IL_06429.2 Version IL_06429.2 of this group appears in releases 0.10 to 0.12

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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_1XOK_001	1XOK	0.8159	2	Major groove intercalation	A	alfalfa mosaic virus RNA 3' UTR	C	846	U	847	*	A	864	G	867	cWW	cWW
2	IL_1XOK_002	1XOK	0.7398	2	Major groove intercalation	A+B	alfalfa mosaic virus RNA 3' UTR	C	868	C	869	*	G	877	G	880	cWW	cWW
3	IL_387D_001	387D	0.6775	2	Multiple bulged bases	A	RNA Pseudoknot	U	1	C	2	*	G	15	A	18	cWW	cWW
4	IL_1U9S_008	1U9S	0.5344	1	Stack outside cWW	A	RIBONUCLEASE P	G	195	C	196	*	G	217	C	219	cWW	cWW
5	IL_3U5H_031	3U5H	0.5003	1		5	25S rRNA	G	833	U	834	*	G	859	C	861	cWW	cWW
6	IL_3V2F_008	3V2F	0.5267	1		A	23S Ribosomal RNA	G	271\|\|\|I	C	271\|\|\|J	*	G	271\|\|\|M	C	271\|\|\|O	cWW	cWW
7	IL_3SNP_002	3SNP	0.5107	1		C	ferritin H IRE RNA	A	13	C	14	*	G	18	U	20	cWW	cWW
8	IL_2QBG_022	2QBG	0.4818	1		B	23S rRNA	G	697	C	698	*	G	763	C	765	cWW	cWW
9	IL_3SN2_002	3SN2	0.5124	1	Single bulged C	B	transferrin receptor iron regulatory element B RNA	G	13	C	14	*	G	18	C	20	cWW	cWW
10	IL_4A1B_113	4A1B	0.1350	2		1	26S RRNA	C	2869	U	2870	*	A	2928	G	2931	cWW	cWW
11	IL_3U5H_115	3U5H	0.1014	2		5	25S rRNA	C	2881	U	2882	*	A	2940	G	2943	cWW	cWW
12	IL_1S72_086	1S72	0.0000	2		0	LSU rRNA	C	2547	C	2548	*	G	2606	G	2609	cWW	cWW
13	IL_4FAW_014	4FAW	0.5007	2		A	Group II catalytic intron D1-D4-1	U	365	A	366	*	U	375	G	378	cWW	cWW
14	IL_3V2F_095	3V2F	0.3645	2		A	23S Ribosomal RNA	C	2512	G	2513	*	C	2571	G	2574	cWW	cWW
15	IL_2ZJR_091	2ZJR	0.4039	2		X	LSU rRNA	C	2491	G	2492	*	C	2550	G	2553	cWW	cWW
16	IL_2QBG_097	2QBG	0.5363	2		B	23S rRNA	C	2512	A	2513	*	U	2571	G	2574	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CU*AACG	2
CG*CACG	2
CU*AAUG	1
CC*GAUG	1
UC*GGAA	1
GC*GGC	1
GU*GGC	1
GC*GUC	1
AC*GUU	1
GC*GAC	1
GC*GCC	1
CC*GUCG	1
UA*UACG	1
CA*UACG	1

Non-Watson-Crick part of the motif

Sequence	Counts
*AC	6
*AU	2
*G	2
*U	2
*GA	1
*A	1
*C	1
*UC	1

Release history

Release	0.10	0.11	0.12
Date	2013-02-17	2013-02-17	2013-02-17
Status	Updated, 1 parent	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in IL_06429.2	Only in the parent motif
IL_06429.1 Compare	IL_387D_001, IL_3V2F_095, IL_2QBG_097, IL_3SN2_002, IL_2QBG_022, IL_1U9S_008, IL_1XOK_001, IL_4A1B_113, IL_2ZJR_091, IL_1XOK_002, IL_3U5H_115, IL_1S72_086, IL_3SNP_002, IL_3U5H_031, IL_3V2F_008	IL_4FAW_014	IL_3G78_015

Children motifs

Child motif	Common motif instances	Only in IL_06429.2	Only in the child motif
IL_06429.3 Compare	IL_387D_001, IL_3V2F_095, IL_2QBG_097, IL_3SN2_002, IL_2QBG_022, IL_1U9S_008, IL_1XOK_001, IL_4A1B_113, IL_2ZJR_091, IL_1XOK_002, IL_3U5H_115, IL_1S72_086, IL_3SNP_002, IL_3U5H_031, IL_3V2F_008	IL_4FAW_014
IL_91487.1 Compare	IL_4FAW_014	IL_387D_001, IL_3V2F_095, IL_2QBG_097, IL_3SN2_002, IL_2QBG_022, IL_1U9S_008, IL_1XOK_001, IL_4A1B_113, IL_2ZJR_091, IL_1XOK_002, IL_3U5H_115, IL_1S72_086, IL_3SNP_002, IL_3U5H_031, IL_3V2F_008	IL_2QBG_086, IL_2NZ4_007, IL_1S72_045, IL_2XZM_033, IL_1S72_042, IL_3U5H_063, IL_1FJG_005, IL_2QBG_060, IL_3U5F_033, IL_1FJG_022, IL_1S72_022, IL_2ZJR_024, IL_4A1B_063, IL_2AW7_029, IL_3V2F_107, IL_3U5H_137, IL_1S72_099, IL_2AW7_005, IL_3V2F_059, IL_3U5H_019

Annotations: (11)
Major groove intercalation (2)
Stack outside cWW (1)
Multiple bulged bases (1)
Single bulged C (1)
Basepair signature: cWW-cWW
Heat map statistics: Min 0.08 | Avg 0.55 | Max 0.96

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