IL_13959.7

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3		4	break		5		6		7		8	1-8	2-7	3-6	4-5
1	IL_2IL9_002	2IL9	0.7139	0		M	Ribosomal Binding Domain of the IRES RNA	A	6058	A	6059	U	6060	A	6061	*	U	6018	A	6019	U	6020	U	6021	cWW		ncWW	cWW
2	IL_1VWW_125	1VWW	0.4528	1		5	28S ribosomal RNA	C	3926	U	3927	A	3928	G	3929	*	U	4181	G	4182	G	4184	G	4185	cWW	ncWW	tHS	ncWW
3	IL_3D0U_002	3D0U	0.2075	0	Double sheared	A	Lysine Riboswitch RNA	C	16	G	17	A	18	G	19	*	C	67	G	68	A	69	G	70	cWW	tSH	tHS	cWW
4	IL_2QBG_088	2QBG	0.1990	0		B	23S rRNA	C	2350	G	2351	A	2352	G	2353	*	C	2364	G	2365	A	2366	G	2367	cWW	tSH	tHS	cWW
5	IL_1VWW_055	1VWW	0.1834	59		5	28S ribosomal RNA	C	1431	G	1432	A	1433	G	1434	*	C	1450	G	1451	A	1452	G	1453	cWW	tSH	ntHS	cWW
6	IL_4IOA_058	4IOA	0.2882	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
7	IL_4A1B_007	4A1B	0.2366	0		1	26S RRNA	C	162	A	163	A	164	C	165	*	G	254	G	255	A	256	G	257	cWW	tSH	ntHS	cWW
8	IL_1FJG_059	1FJG	0.2804	0	Double sheared (H)	A	SSU rRNA	U	1481	G	1482	A	1483	C	1484	*	G	1416	G	1417	A	1418	G	1419	cWW	tSH	tHS	cWW
9	IL_4BPP_085	4BPP	0.2264	0		A	18S RRNA	U	1625	A	1626	A	1627	C	1628	*	G	1697	G	1698	A	1699	A	1700	cWW	tSH	tHS	cWW
10	IL_4KZD_002	4KZD	0.2343	0	Double sheared	R	RNA (84-MER)	U	71	A	72	A	73	C	74	*	G	11	A	12	A	13	A	14	cWW	tSH	tHS	cWW
11	IL_4A1B_005	4A1B	0.2883	0		1	26S RRNA	C	138	A	139	A	140	C	141	*	G	125	A	126	A	127	G	128	cWW	tSH		cWW
12	IL_3U5F_013	3U5F	0.2827	0		6	18S rRNA	C	186	G	187	A	188	C	189	*	G	196	A	197	A	198	G	199	cWW	tSH	tHS	cWW
13	IL_2QBG_017	2QBG	0.2676	0		B	23S rRNA	U	554	G	555	A	556	C	557	*	G	536	G	537	A	538	G	539	cWW	tSH	tHS	cWW
14	IL_1VWW_142	1VWW	0.2943	1		5	28S ribosomal RNA	C	4582	C	4583	A	4584	U	4585	*	A	4717	G	4718	G	4719	G	4721	cWW		tHS	cWW
15	IL_3U5H_120	3U5H	0.2586	2		5	25S rRNA	C	3004	A	3005	A	3006	U	3007	*	A	3139	G	3140	A	3141	G	3144	cWW	tSH	tHS	cWW
16	IL_4CUV_124	4CUV	0.2823	2		1	25S RRNA	C	3004	A	3005	A	3006	U	3007	*	A	3139	G	3140	A	3141	G	3144	cWW	ntSH	tHS	cWW
17	IL_4A1B_117	4A1B	0.2511	2		1	26S RRNA	C	2993	G	2994	A	2995	C	2996	*	G	3128	G	3129	A	3131	G	3133	cWW	tSH	tHS	cWW
18	IL_1VX6_121	1VX6	0.3024	3		A	28S ribosomal RNA	U	3390	G	3391	A	3392	C	3393	*	G	3524	A	3525	A	3528	A	3530	cWW	tSH	tHS	cWW
19	IL_4CUX_090	4CUX	0.2639	0		2	18S RRNA	C	1729	A	1730	A	1731	A	1732	*	U	1669	G	1670	A	1671	G	1672	cWW		ntHS	cWW
20	IL_3U5F_088	3U5F	0.2281	0		6	18S rRNA	C	1729	A	1730	A	1731	A	1732	*	U	1669	G	1670	A	1671	G	1672	cWW	tSH	tHS	cWW
21	IL_4BPP_087	4BPP	0.1762	0		A	18S RRNA	U	1682	A	1683	A	1684	A	1685	*	U	1640	G	1641	A	1642	A	1643	cWW	tSH	tHS	cWW
22	IL_3J7A_078	3J7A	0.1610	0	Double sheared (H)	A	SSU rRNA	U	2021	A	2022	A	2023	A	2024	*	U	1966	G	1967	A	1968	A	1969	cWW	tSH	tHS	cWW
23	IL_1VW3_072	1VW3	0.2688	0		A	21S ribosomal RNA	G	2631	A	2632	A	2633	A	2634	*	U	2617	A	2618	A	2619	C	2620	cWW	tSH	tHS	cWW
24	IL_1SA9_001	1SA9	0.1049	0		B+A	RNA (8-mer)	C	111	G	112	A	113	G	114	*	C	103	G	104	A	105	G	106	cWW	tSH	tHS	cWW
25	IL_1SAQ_002	1SAQ	0.0000	0	Double sheared	B+A	RNA (8-mer)	C	111	G	112	A	113	G	114	*	C	103	G	104	A	105	G	106	cWW	tSH	tHS	cWW
26	IL_4QCN_086	4QCN	0.1064	0		A	23S Ribosomal RNA	C	2376	G	2377	A	2378	G	2379	*	C	2362	G	2363	A	2364	G	2365	cWW	tSH	tHS	cWW
27	IL_4IOA_083	4IOA	0.1426	0	Double sheared	X	LSU rRNA	C	2343	G	2344	A	2345	G	2346	*	C	2329	G	2330	A	2331	G	2332	cWW	tSH	tHS	cWW
28	IL_4BPP_003	4BPP	0.2419	1		A	18S RRNA	U	37	A	38	A	39	A	40	*	U	458	G	459	C	461	A	462	cWW	tSH	tHS	cWW
29	IL_1VX2_003	1VX2	0.2708	1		2	18S ribosomal RNA	C	37	A	38	A	39	A	40	*	U	514	G	515	C	517	G	518	cWW	ntSH	tHS	cWW
30	IL_2AW7_065	2AW7	0.4639	0		A	16S ribosomal RNA	U	1481	G	1482	A	1483	C	1484	*	G	1416	G	1417	A	1418	G	1419	cWW	tSH	tHS	cWW
31	IL_4CUX_086	4CUX	0.3951	0		2	18S RRNA	C	1653	G	1654	A	1655	U	1656	*	A	1744	G	1745	A	1746	G	1747	cWW		ntHS	cWW
32	IL_3DIR_002	3DIR	0.4369	0		A	RNA (174-MER)	C	70	G	71	A	72	G	73	*	C	19	G	20	A	21	G	22	cWW	tSH	tHS	cWW
33	IL_3J7A_075	3J7A	0.3878	0	Double sheared (H)	A	SSU rRNA	C	1950	G	1951	A	1952	U	1953	*	A	2036	A	2037	A	2038	G	2039	cWW	tSH	ntHS	cWW
34	IL_3U5F_085	3U5F	0.3596	0		6	18S rRNA	C	1653	G	1654	A	1655	U	1656	*	A	1744	G	1745	A	1746	G	1747	cWW	tSH	tHS	cWW
35	IL_4A1B_132	4A1B	0.3705	0		1	26S RRNA	C	3316	G	3317	A	3318	U	3319	*	A	3300	G	3301	A	3302	G	3303	cWW	tSH	tHS	cWW
36	IL_1S72_098	1S72	0.3625	0		0	LSU rRNA	C	2873	G	2874	A	2875	G	2876	*	C	2881	G	2882	A	2883	G	2884	cWW	tSH	tHS	cWW
37	IL_3U5H_141	3U5H	0.5328	0		5	25S rRNA	C	3360	G	3361	A	3362	U	3363	*	A	3342	G	3343	A	3344	G	3345	cWW	tSH	ntSs	cWW
38	IL_4CUV_147	4CUV	0.6545	0		1	25S RRNA	C	3360	G	3361	A	3362	U	3363	*	A	3342	G	3343	A	3344	G	3345	cWW		ntSs	cWW
39	IL_1VWW_157	1VWW	0.6695	0		5	28S ribosomal RNA	C	5032	G	5033	A	5034	U	5035	*	A	5014	G	5015	A	5016	G	5017	cWW			ncWW
40	IL_1VX6_139	1VX6	0.6174	0		A	28S ribosomal RNA	A	3734	A	3735	A	3736	G	3737	*	C	3752	G	3753	A	3754	U	3755	cWW		ntWS	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CGAG*CGAG	8
CGAU*AGAG	5
UGAC*GGAG	3
CAAU*AGAACG	2
CAAA*UGAG	2
UAAA*UGAA	2
AAUA*UAUU	1
CUAG*UGGGG	1
CAGUCGAGAGUGGACGGGAGCGGCGGGGGCGGCGCGCGCGCG*CCCCCGGAGCCCCGCGGACGCUACG	1
UCAG*CAAG	1
CAAC*GGAG	1
UAAC*GGAA	1
UAAC*GAAA	1
CAAC*GAAG	1
CGAC*GAAG	1
CCAU*AGGCG	1
CGAC*GGAAAG	1
UGAC*GAUUAAA	1
GAAA*UAAC	1
UAAA*UGACA	1
CAAA*UGACG	1
CGAU*AAAG	1
AGAG*CGAU	1
AAAG*CGAU	1

Non-Watson-Crick part of the motif

Sequence	Counts
GA*GA	17
AA*GA	7
AA*AA	3
GA*AA	2
AA*GAAC	2
AA*GAC	2
AU*AU	1
UA*GGG	1
AGUCGAGAGUGGACGGGAGCGGCGGGGGCGGCGCGCGCGC*CCCCGGAGCCCCGCGGACGCUAC	1
CA*AA	1
CA*GGC	1
GA*GAAA	1
GA*AUUAA	1

Release history

Release	1.17
Date	2014-09-04
Status	Updated, 1 parent

Parent motifs

Parent motif	Common motif instances	Only in IL_13959.7	Only in the parent motif
IL_13959.6 Compare	IL_4BPP_003, IL_4IOA_058, IL_4CUX_090, IL_4CUV_147, IL_2QBG_088, IL_3U5F_085, IL_1VW3_072, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_3D0U_002, IL_4CUX_086, IL_4IOA_083, IL_1SAQ_002, 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_4BPP_087, IL_4BPP_085, IL_1SA9_001, IL_2AW7_065, IL_4CUV_124	IL_1VX6_121, IL_3J7A_078, IL_4KZD_002, IL_4QCN_086, IL_1VX6_139, IL_1VWW_142, IL_1VWW_157, IL_3J7A_075, IL_1VWW_055, IL_1VX2_003, IL_1VWW_125	IL_2O3V_002, IL_4NVV_085

Children motifs

Child motif	Common motif instances	Only in IL_13959.7	Only in the child motif
IL_13959.8 Compare	IL_4BPP_003, IL_4IOA_058, IL_4CUX_090, IL_1VX6_139, IL_1SAQ_002, IL_2QBG_088, IL_3U5F_085, IL_1VW3_072, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_3D0U_002, IL_4BPP_085, IL_1VX6_121, IL_4CUX_086, IL_4KZD_002, IL_4QCN_086, IL_4IOA_083, IL_4CUV_147, IL_4A1B_005, IL_1FJG_059, IL_4A1B_007, IL_1S72_098, IL_3DIR_002, IL_2QBG_017, IL_3U5F_013, IL_3J7A_078, IL_4BPP_087, IL_3J7A_075, IL_1SA9_001, IL_2AW7_065, IL_4CUV_124	IL_1VX2_003, IL_1VWW_142, IL_1VWW_157, IL_1VWW_055, IL_2IL9_002, IL_1VWW_125	IL_4W21_167, IL_4W23_077, IL_4W21_148, IL_4W21_051, IL_4W23_003
IL_99561.1 Compare	IL_2IL9_002	IL_4BPP_003, IL_4IOA_058, IL_4CUX_090, IL_1VX6_139, IL_3J7A_075, IL_4CUV_147, IL_2QBG_088, IL_3U5F_085, IL_1VW3_072, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_1VWW_142, IL_3D0U_002, IL_1VWW_125, IL_1VX6_121, IL_4CUX_086, IL_4KZD_002, IL_4QCN_086, IL_4IOA_083, IL_1SAQ_002, IL_4A1B_005, IL_1FJG_059, IL_4A1B_007, IL_1S72_098, IL_3DIR_002, IL_2QBG_017, IL_3U5F_013, IL_3J7A_078, IL_1VX2_003, IL_4BPP_087, IL_1VWW_157, IL_4BPP_085, IL_1VWW_055, IL_1SA9_001, IL_2AW7_065, IL_4CUV_124	IL_1VW3_042, IL_4QCN_053, IL_4IOA_055, IL_1LNG_002, IL_4QCN_010

Motif IL_13959.7 Version IL_13959.7 of this group appears in releases 1.17 to 1.17 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_13959.7 Version IL_13959.7 of this group appears in releases 1.17 to 1.17

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