Motif IL_13959.3 Version IL_13959.3 of this group appears in releases 1.1 to 1.4

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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		3		4	break		5		6		7		8	1-8	2-7	3-6	4-5
1	IL_3U5H_141	3U5H	0.5328	0		5	LSU rRNA	A	3342	G	3343	A	3344	G	3345	*	C	3360	G	3361	A	3362	U	3363	cWW	ntsS	tHS	cWW
2	IL_3DIR_002	3DIR	0.4335	0		A	Lysine riboswitch	C	70	G	71	A	72	G	73	*	C	19	G	20	A	21	G	22	cWW	tSH	tHS	cWW
3	IL_4A1B_132	4A1B	0.3705	0		1	LSU rRNA	A	3300	G	3301	A	3302	G	3303	*	C	3316	G	3317	A	3318	U	3319	cWW	tSH	tHS	cWW
4	IL_1S72_098	1S72	0.3765	0		0	LSU rRNA	C	2873	G	2874	A	2875	G	2876	*	C	2881	G	2882	A	2883	G	2884	cWW	tSH	tHS	cWW
5	IL_3U5F_085	3U5F	0.3596	0		6	SSU rRNA	A	1744	G	1745	A	1746	G	1747	*	C	1653	G	1654	A	1655	U	1656	cWW	tSH	tHS	cWW
6	IL_2AW7_065	2AW7	0.4639	0		A	SSU rRNA	G	1416	G	1417	A	1418	G	1419	*	U	1481	G	1482	A	1483	C	1484	cWW	tSH	tHS	cWW
7	IL_2XZM_004	2XZM	0.2661	1		A	SSU rRNA	U	37	A	38	A	39	A	40	*	U	458	G	459	C	461	A	462	cWW	tSH	tHS	cWW
8	IL_4A1B_005	4A1B	0.2883	0		1	LSU rRNA	G	125	A	126	A	127	G	128	*	C	138	A	139	A	140	C	141	cWW		tHS	cWW
9	IL_3D0U_002	3D0U	0.1695	0	Double sheared	A	Lysine riboswitch	C	16	G	17	A	18	G	19	*	C	67	G	68	A	69	G	70	cWW	tSH	tHS	cWW
10	IL_1FJG_059	1FJG	0.2804	0	Double sheared (H)	A	SSU rRNA	G	1416	G	1417	A	1418	G	1419	*	U	1481	G	1482	A	1483	C	1484	cWW	tSH	tHS	cWW
11	IL_4A1B_007	4A1B	0.2366	0		1	LSU rRNA	G	254	G	255	A	256	G	257	*	C	162	A	163	A	164	C	165	cWW	ntSH	tHS	cWW
12	IL_3U5H_120	3U5H	0.2586	2		5	LSU rRNA	A	3139	G	3140	A	3141	G	3144	*	C	3004	A	3005	A	3006	U	3007	cWW	tSH	tHS	cWW
13	IL_4A1B_117	4A1B	0.2511	2		1	LSU rRNA	G	3128	G	3129	A	3131	G	3133	*	C	2993	G	2994	A	2995	C	2996	cWW	tSH	tHS	cWW
14	IL_3U5F_013	3U5F	0.2827	0		6	SSU rRNA	G	196	A	197	A	198	G	199	*	C	186	G	187	A	188	C	189	cWW	tSH	tHS	cWW
15	IL_2QBG_017	2QBG	0.2676	0		B	LSU rRNA	G	536	G	537	A	538	G	539	*	U	554	G	555	A	556	C	557	cWW	tSH	tHS	cWW
16	IL_2XZM_089	2XZM	0.1757	0		A	SSU rRNA	U	1682	A	1683	A	1684	A	1685	*	U	1640	G	1641	A	1642	A	1643	cWW	tSH	tHS	cWW
17	IL_3U5F_088	3U5F	0.2129	0		6	SSU rRNA	C	1729	A	1730	A	1731	A	1732	*	U	1669	G	1670	A	1671	G	1672	cWW	tSH	tHS	cWW
18	IL_1SA9_001	1SA9	0.1049	0		A+B	RNA (8-mer)	C	103	G	104	A	105	G	106	*	C	111	G	112	A	113	G	114	cWW	tSH	tHS	cWW
19	IL_1SAQ_002	1SAQ	0.0000	0	Double sheared	A+B	RNA (8-mer)	C	103	G	104	A	105	G	106	*	C	111	G	112	A	113	G	114	cWW	tSH	tHS	cWW
20	IL_2QBG_088	2QBG	0.1321	0		B	LSU rRNA	C	2350	G	2351	A	2352	G	2353	*	C	2364	G	2365	A	2366	G	2367	cWW	tSH	tHS	cWW
21	IL_3V2F_086	3V2F	0.1176	0		A	LSU rRNA	C	2350	G	2351	A	2352	G	2353	*	C	2364	G	2365	A	2366	G	2367	cWW	tSH	tHS	cWW
22	IL_4IOA_083	4IOA	0.1426	0	Double sheared	X	LSU rRNA	C	2329	G	2330	A	2331	G	2332	*	C	2343	G	2344	A	2345	G	2346	cWW	tSH	tHS	cWW
23	IL_4IOA_058	4IOA	0.2635	0	Double sheared	X	LSU rRNA	U	1530	C	1531	A	1532	G	1533	*	C	1491	A	1492	A	1493	G	1494	cWW		tHS	cWW
24	IL_2IL9_002	2IL9	0.6901	0		M	CrPV IRES	A	6058	A	6059	U	6060	A	6061	*	U	6018	A	6019	U	6020	U	6021	cWW		ncWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CGAG*CGAG	8
AGAG*CGAU	3
GGAG*UGAC	3
UAAA*UGACA	1
GAAG*CAAC	1
GGAG*CAAC	1
AGAACG*CAAU	1
GGAAAG*CGAC	1
GAAG*CGAC	1
UAAA*UGAA	1
CAAA*UGAG	1
UCAG*CAAG	1
AAUA*UAUU	1

Non-Watson-Crick part of the motif

Sequence	Counts
GA*GA	14
AA*GA	3
AA*GAC	1
AA*AA	1
GA*AA	1
GAAC*AA	1
GAAA*GA	1
CA*AA	1
AU*AU	1

Release history

Release	1.1	1.2	1.3	1.4
Date	2013-04-08	2013-05-04	2013-06-01	2013-07-01
Status	Updated, 1 parent	Exact match	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in IL_13959.3	Only in the parent motif
IL_13959.2 Compare	IL_3V2F_086, IL_1SAQ_002, IL_2QBG_088, IL_3U5F_085, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_3D0U_002, IL_3U5F_013, IL_4A1B_005, IL_2AW7_065, IL_4A1B_007, IL_1S72_098, IL_3DIR_002, IL_2QBG_017, IL_2XZM_004, IL_2IL9_002, IL_1FJG_059, IL_2XZM_089, IL_1SA9_001	IL_4IOA_083, IL_4IOA_058	IL_2ZJR_057, IL_2ZJR_082

Children motifs

Child motif	Common motif instances	Only in IL_13959.3	Only in the child motif
IL_13959.4 Compare	IL_3V2F_086, IL_4IOA_058, IL_1SAQ_002, IL_2QBG_088, IL_3U5F_085, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_3D0U_002, IL_4IOA_083, IL_4A1B_005, IL_1FJG_059, IL_4A1B_007, IL_1S72_098, IL_3DIR_002, IL_2QBG_017, IL_3U5F_013, IL_2IL9_002, IL_2AW7_065, IL_1SA9_001	IL_2XZM_004, IL_2XZM_089	IL_4BPP_003, IL_2O3V_002, IL_4BPP_087, IL_4BPP_085

Annotations: (19)
Double sheared (4)
Double sheared (H) (1)
Basepair signature: cWW-tSH-tHS-cWW
Heat map statistics: Min 0.07 | Avg 0.36 | Max 0.82

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Coloring options: Nucleotide numbers

Motif IL_13959.3 Version IL_13959.3 of this group appears in releases 1.1 to 1.4 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_13959.3 Version IL_13959.3 of this group appears in releases 1.1 to 1.4

Download

Csv

Json