IL_40289.1

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2	break		3		4	1-4	2-3
1	IL_1S72_099	1S72	0.0000	1	Major groove intercalation (H)	9	5S rRNA	C	15	G	16	*	C	64	G	66	cWW	cWW
2	IL_2ZJR_068	2ZJR	0.3182	2	Major groove outside cWW, minor groove, intercalation pocket (H)	X	LSU rRNA	U	1833	G	1834	*	U	1881	A	1884	cWW	cWW
3	IL_3F1H_105	3F1H	0.3841	1		A	23S RRNA	G	2838	G	2839	*	U	2878	C	2880	cWW	cWW
4	IL_3F1H_018	3F1H	0.7025	1		A	23S RRNA	G	763	G	765	*	C	697	C	698	cWW	cWW
5	IL_2ZJR_011	2ZJR	0.5550	1	Single bulged A (H)	X	LSU rRNA	G	678	C	679	*	G	600	C	602	cWW	cWW
6	IL_3F1H_037	3F1H	0.6051	1		A	23S RRNA	G	1011	C	1013	*	G	1149	C	1150	cWW	cWW
7	IL_2ZJR_034	2ZJR	0.6087	1		X	LSU rRNA	A	1022	G	1024	*	C	1160	U	1161	cWW	cWW
8	IL_2ZJR_056	2ZJR	0.7115	1	Single bulged C (H)	X	LSU rRNA	A	1534	C	1535	*	G	1488	U	1490	cWW	cWW
9	IL_1GID_009	1GID	0.7246	1	Single bulged A	B	P4-P6 RNA RIBOZYME DOMAIN	G	110	G	111	*	C	209	C	211	cWW	cWW
10	IL_2ZJR_015	2ZJR	0.7148	1		X	LSU rRNA	G	776	G	778	*	C	710	C	711	cWW	cWW
11	IL_1U9S_001	1U9S	0.7506	1	Single bulged A	A	RIBONUCLEASE P	G	95	C	96	*	G	107	C	109	cWW	cWW
12	IL_2ZJR_024	2ZJR	0.7286	1		X	LSU rRNA	C	863	C	864	*	G	938	G	940	cWW	cWW
13	IL_1S72_086	1S72	0.7446	2		0	LSU rRNA	G	2606	G	2609	*	C	2547	C	2548	cWW	cWW
14	IL_1S72_070	1S72	0.7382	2		0	LSU rRNA	G	1974	C	1975	*	G	2005	U	2008	cWW	cWW
15	IL_1DUQ_002	1DUQ	0.7869	1	Single bulged A	A+B	THE REV BINDING ELEMENT	G	108	C	109	*	G	120	C	122	cWW	cWW
16	IL_2IPY_002	2IPY	0.7877	1		C	ferritin IRE RNA	A	24	C	25	*	G	7	U	9	cWW	cWW
17	IL_1DUQ_006	1DUQ	0.8036	1		E+F	THE REV BINDING ELEMENT	G	308	C	309	*	G	320	C	322	cWW	cWW
18	IL_1CSL_002	1CSL	0.8045	1	Single bulged A	A+B	RNA (13-mer) + RNA (15-mer)	G	50	C	51	*	G	67	C	69	cWW	cWW
19	IL_2ZJR_065	2ZJR	0.8221	1	Single bulged A (H)	X	LSU rRNA	G	1761	C	1762	*	G	1963	U	1965	cWW	cWW
20	IL_3D2V_004	3D2V	0.8985	1	Single bulged U (H)	B	TPP riboswitch (THI element)	C	5	C	6	*	G	73	G	75	cWW	cWW
21	IL_3D2V_001	3D2V	0.9054	1	Single bulged U	A	TPP riboswitch (THI element)	C	5	C	6	*	G	73	G	75	cWW	cWW
22	IL_1FJG_040	1FJG	0.9122	1	Single bulged U (H)	A	SSU rRNA	C	1208	C	1209	*	G	1048	G	1050	cWW	cWW
23	IL_3F1H_095	3F1H	0.9094	2		A	23S RRNA	C	2571	G	2574	*	C	2512	G	2513	cWW	cWW
24	IL_3HHN_003	3HHN	0.9288	1	Single bulged C	E	Class I ligase ribozyme, self-ligation product	A	112	C	113	*	G	46	U	48	cWW	cWW
25	IL_2BQ5_002	2BQ5	0.9691	1		S	RNA (19-mer)	G	5\|\|\|\|P_1	G	7\|\|\|\|P_1	*	C	14\|\|\|\|P_1	C	15\|\|\|\|P_1	cWW	ncWW
26	IL_2ZJR_072	2ZJR	0.8909	2	Bulged stacked bases (H)	X	LSU rRNA	G	1916	C	1917	*	G	1947	C	1950	cWW	cWW
27	IL_3F1H_046	3F1H	0.8943	1		A	23S RRNA	G	1229	C	1230	*	G	1219	C	1221	cWW	cWW
28	IL_2IPY_005	2IPY	0.8321	1		D	ferritin IRE RNA	A	24	C	25	*	G	7	U	9	cWW	cWW
29	IL_3F1H_073	3F1H	0.7458	2		A	23S RRNA	G	1933	C	1934	*	G	1964	C	1967	cWW	cWW
30	IL_1S72_030	1S72	0.7008	1	Single bulged U (H)	0	LSU rRNA	G	834	G	836	*	C	847	C	848	cWW	cWW
31	IL_1FJG_002	1FJG	0.7301	1	Single bulged A (H)	A	SSU rRNA	G	44	U	45	*	G	396	C	398	cWW	cWW
32	IL_1S72_014	1S72	0.6899	1	Single bulged U (H)	0	LSU rRNA	G	322	C	323	*	G	307	C	309	cWW	cWW
33	IL_2VPL_002	2VPL	0.7264	1	Single bulged A	B	FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE	U	16	C	17	*	G	28	A	30	cWW	cWW
34	IL_1S72_026	1S72	0.8017	1		0	LSU rRNA	G	856	U	858	*	A	788	C	789	cWW	cWW
35	IL_2PJP_001	2PJP	0.7620	1	Single bulged U	B	SECIS RNA	A	29	C	30	*	G	16	U	18	cWW	cWW
36	IL_1DUQ_004	1DUQ	0.7844	1		C+D	THE REV BINDING ELEMENT	G	208	C	209	*	G	220	C	222	cWW	cWW
37	IL_1S72_027	1S72	0.7761	1	Single bulged G (H)	0	LSU rRNA	A	819	U	821	*	A	793	U	794	cWW	cWW
38	IL_1GID_012	1GID	0.8395	1	Single bulged U	B	P4-P6 RNA RIBOZYME DOMAIN	A	192	C	193	*	G	129	U	131	cWW	cWW
39	IL_2ZJR_002	2ZJR	0.6983	1	Single bulged A (H)	X	LSU rRNA	G	36	C	37	*	G	454	C	456	cWW	cWW
40	IL_1FJG_014	1FJG	0.7491	1	Single bulged U (H)	A	SSU rRNA	G	392	A	393	*	U	367	C	369	cWW	cWW
41	IL_3F1H_019	3F1H	0.7746	1		A	23S RRNA	G	702	U	703	*	G	728	C	730	cWW	cWW
42	IL_2OIU_001	2OIU	0.6801	1		P	L1 Ribozyme RNA Ligase	A	41	C	42	*	G	18	U	20	cWW	cWW
43	IL_3F1H_002	3F1H	0.6829	1		A	23S RRNA	G	36	C	37	*	G	442	C	444	cWW	cWW
44	IL_1S72_002	1S72	0.6861	1	Single bulged A (H)	0	LSU rRNA	G	33	C	34	*	G	448	C	450	cWW	cWW
45	IL_2ZJR_016	2ZJR	0.7432	1	Single bulged G (H)	X	LSU rRNA	G	741	A	743	*	U	715	U	716	cWW	cWW
46	IL_3F1H_066	3F1H	0.6658	1		A	23S RRNA	G	1770	C	1771	*	G	1980	C	1982	cWW	cWW
47	IL_3OWZ_005	3OWZ	0.6490	1		B	Domain II of glycine riboswitch	U	27	C	28	*	G	12	A	14	cWW	cWW
48	IL_2OIU_003	2OIU	0.5594	1	Single bulged U	Q	L1 Ribozyme RNA Ligase	A	41	C	42	*	G	18	U	20	cWW	cWW
49	IL_1DUQ_008	1DUQ	0.7703	1		G+H	THE REV BINDING ELEMENT	G	408	C	409	*	G	420	C	422	cWW	cWW
50	IL_2GIS_001	2GIS	0.7807	1		A	SAM-I riboswitch	C	40	C	41	*	G	13	G	15	cWW	cWW
51	IL_3OWZ_001	3OWZ	0.8977	1		A	Domain II of glycine riboswitch	G	12	A	14	*	U	27	C	28	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GC*GAC	11
AC*GCU	4
AC*GUU	4
CC*GUG	3
CC*GAG	2
GAG*CC	2
GC*GCAC	2
UC*GAA	2
CG*CAG	1
UG*UGAA	1
GG*UCC	1
GUC*GC	1
AUG*CU	1
GG*CAC	1
CC*GCG	1
GUCG*CC	1
GC*GCAU	1
GC*GAU	1
CG*CACG	1
GAC*GC	1
GUG*CC	1
GU*GAC	1
GC*GUC	1
GAU*AC	1
AGU*AU	1
GA*UUC	1
GU*GGC	1
GGA*UU	1
GAA*UC	1

Non-Watson-Crick part of the motif

Sequence	Counts
*A	19
*U	9
*C	6
A*	5
U*	3
*CA	3
G*	2
*GA	1
UC*	1
*AC	1
*G	1

Release history

Release	0.3
Date	2011-12-08
Status	New id, 2 parents

Parent motifs

Parent motif	Common motif instances	Only in IL_40289.1	Only in the parent motif
IL_63653.1 Compare	IL_2BQ5_002, IL_2ZJR_056, IL_2ZJR_034, IL_2ZJR_011, IL_2ZJR_016, IL_2ZJR_015, IL_3F1H_066, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1FJG_040, IL_1DUQ_008, IL_1GID_012, IL_3D2V_004, IL_3D2V_001, IL_3F1H_037, IL_3F1H_018, IL_2GIS_001, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_2VPL_002, IL_1U9S_001, IL_2OIU_003, IL_3F1H_073, IL_2ZJR_065, IL_2IPY_002, IL_2OIU_001, IL_2ZJR_024, IL_1CSL_002, IL_2ZJR_002, IL_1FJG_014, IL_1GID_009, IL_2PJP_001, IL_2IPY_005, IL_1S72_070, IL_1S72_030, IL_3F1H_019, IL_1S72_014, IL_3F1H_002, IL_3OWZ_005, IL_3OWZ_001, IL_3F1H_046, IL_2ZJR_072, IL_3HHN_003, IL_1S72_086	IL_3F1H_105, IL_1S72_099, IL_3F1H_095, IL_2ZJR_068	IL_2PN4_008, IL_2PN4_003, IL_2C50_002, IL_1ET4_004, IL_2C50_001, IL_1S72_042, IL_1S72_040, IL_3F1H_077, IL_2IPY_003, IL_2IPY_001, IL_2IPY_006, IL_2IPY_004, IL_3F1H_098, IL_1ET4_008, IL_1GID_005, IL_1ET4_002, IL_1GID_002, IL_2ZJR_093, IL_2ZJR_091, IL_3B31_001, IL_2ZJR_098, IL_2NOK_006, IL_3F1H_087, IL_1I9X_001, IL_2NOK_003, IL_1I9X_002, IL_2OZB_001, IL_2ZJR_031, IL_1FJG_043, IL_1S72_064, IL_1S72_067, IL_2PLY_002, IL_1S72_104, IL_1U9S_006, IL_6MSF_001, IL_1U9S_003, IL_2C4Z_002, IL_2C4Z_001, IL_1S72_077, IL_1S72_074, IL_2BQ5_001, IL_2BU1_002, IL_2BU1_001, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_088, IL_3F1H_032, IL_3F1H_034, IL_3D0U_005, IL_3D0U_001, IL_2IZN_002, IL_2IZN_001, IL_2NZ4_007, IL_2IZM_002, IL_1KXK_003, IL_1FJG_016, IL_1S72_093, IL_3G78_015, IL_1S72_096, IL_3DIR_001, IL_3DIR_005, IL_1S03_002, IL_1S03_001, IL_1S03_006, IL_1S03_005, IL_1S72_010, IL_3MUR_003, IL_1R3E_001, IL_3MUR_004, IL_1R3E_002, IL_3F1H_103, IL_2IZ9_001, IL_2IZ9_002, IL_2ZY6_002, IL_2IZM_001, IL_2NZ4_004, IL_1FJG_005, IL_1FJG_007, IL_1FJG_001, IL_397D_001, IL_3MEI_001, IL_2VPL_005, IL_3F1H_059, IL_1DQH_001, IL_1FJG_035, IL_1FJG_036, IL_2QUX_004, IL_2QUX_005, IL_2QUX_006, IL_1JZV_002, IL_1JZV_005, IL_2QUX_001, IL_2QUX_002, IL_2QUX_003, IL_1FUF_002, IL_1FUF_003, IL_2PLY_001, IL_1F7Y_002, IL_3HHN_001, IL_2ZJR_076
IL_23027.1 Compare	IL_3F1H_105, IL_1S72_099, IL_3F1H_095, IL_2ZJR_068	IL_2BQ5_002, IL_2ZJR_056, IL_2ZJR_034, IL_2ZJR_011, IL_2ZJR_016, IL_2ZJR_015, IL_3F1H_066, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1FJG_040, IL_1DUQ_008, IL_1GID_012, IL_3D2V_004, IL_3D2V_001, IL_3F1H_037, IL_3F1H_018, IL_2GIS_001, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_2VPL_002, IL_1U9S_001, IL_2OIU_003, IL_3F1H_073, IL_2ZJR_065, IL_2IPY_002, IL_2OIU_001, IL_2ZJR_024, IL_1CSL_002, IL_2ZJR_002, IL_1FJG_014, IL_1GID_009, IL_2PJP_001, IL_2IPY_005, IL_1S72_070, IL_1S72_030, IL_3F1H_019, IL_1S72_014, IL_3F1H_002, IL_3OWZ_005, IL_3OWZ_001, IL_3F1H_046, IL_2ZJR_072, IL_3HHN_003, IL_1S72_086	IL_1S72_022

Children motifs

Child motif	Common motif instances	Only in IL_40289.1	Only in the child motif
IL_40289.2 Compare	IL_2ZJR_056, IL_1S72_014, IL_2ZJR_011, IL_2ZJR_016, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1DUQ_008, IL_1GID_012, IL_3OWZ_005, IL_3F1H_037, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_1U9S_001, IL_2OIU_003, IL_3F1H_073, IL_2ZJR_065, IL_2IPY_002, IL_2OIU_001, IL_2ZJR_068, IL_2ZJR_024, IL_2IPY_005, IL_2ZJR_002, IL_2PJP_001, IL_1S72_099, IL_1S72_070, IL_3F1H_019, IL_3F1H_066, IL_3F1H_002, IL_3F1H_105, IL_3F1H_046, IL_1CSL_002, IL_2ZJR_072, IL_3HHN_003	IL_2BQ5_002, IL_3D2V_004, IL_3F1H_095, IL_3D2V_001, IL_3F1H_018, IL_2GIS_001, IL_2ZJR_034, IL_1S72_030, IL_2ZJR_015, IL_1FJG_014, IL_3OWZ_001, IL_2VPL_002, IL_1GID_009, IL_1FJG_040, IL_1S72_086	IL_1FJG_035, IL_3HHN_001
IL_89429.1 Compare	IL_2BQ5_002, IL_3F1H_095, IL_3F1H_018, IL_2ZJR_034, IL_1S72_030, IL_2ZJR_015, IL_1FJG_014, IL_3OWZ_001, IL_1S72_086	IL_2ZJR_056, IL_2IPY_002, IL_1S72_014, IL_2ZJR_011, IL_2ZJR_016, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1FJG_040, IL_1DUQ_008, IL_1GID_012, IL_3D2V_004, IL_3D2V_001, IL_3F1H_019, IL_2GIS_001, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_2VPL_002, IL_1U9S_001, IL_2ZJR_068, IL_2ZJR_065, IL_1S72_099, IL_2OIU_003, IL_3F1H_105, IL_2OIU_001, IL_3F1H_073, IL_2ZJR_024, IL_1CSL_002, IL_2ZJR_002, IL_1GID_009, IL_2PJP_001, IL_2IPY_005, IL_1S72_070, IL_3F1H_037, IL_3F1H_066, IL_3F1H_002, IL_3OWZ_005, IL_3F1H_046, IL_2ZJR_072, IL_3HHN_003	IL_2NOK_006, IL_2BQ5_001, IL_1I9X_001, IL_2NOK_003, IL_2IZM_001, IL_2BU1_002, IL_397D_001, IL_1FJG_043, IL_1S72_040, IL_2VPL_005, IL_3D0U_001, IL_3F1H_077, IL_2IZN_002, IL_2IZN_001, IL_2IPY_003, IL_2IZM_002, IL_2IPY_006, IL_1S72_093, IL_3G78_015, IL_2C4Z_001, IL_3DIR_001, IL_1S72_074, IL_1S03_001, IL_1S03_005, IL_1R3E_001, IL_1R3E_002, IL_2ZJR_091, IL_6MSF_001, IL_2IZ9_001, IL_2IZ9_002, IL_2ZJR_076
IL_96481.1 Compare	IL_3D2V_004, IL_3D2V_001, IL_2GIS_001, IL_2VPL_002, IL_1GID_009, IL_1FJG_040	IL_2BQ5_002, IL_2ZJR_056, IL_2IPY_002, IL_2ZJR_034, IL_2ZJR_011, IL_2ZJR_016, IL_2ZJR_015, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1DUQ_008, IL_1GID_012, IL_3F1H_105, IL_3F1H_019, IL_3F1H_018, IL_2OIU_001, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_1U9S_001, IL_2ZJR_068, IL_2ZJR_065, IL_1S72_099, IL_2OIU_003, IL_3F1H_095, IL_3F1H_073, IL_2ZJR_024, IL_1CSL_002, IL_2ZJR_002, IL_1FJG_014, IL_2PJP_001, IL_2IPY_005, IL_1S72_070, IL_1S72_030, IL_3F1H_037, IL_1S72_014, IL_3F1H_066, IL_3F1H_002, IL_3OWZ_005, IL_3OWZ_001, IL_3F1H_046, IL_2ZJR_072, IL_3HHN_003, IL_1S72_086	IL_2PN4_008, IL_1I9X_002, IL_2BU1_001, IL_2ZJR_031, IL_1FJG_001, IL_1S72_088, IL_2C50_002, IL_1ET4_004, IL_2C50_001, IL_1S72_045, IL_3F1H_034, IL_2PLY_001, IL_3MEI_001, IL_2PN4_003, IL_1DQH_001, IL_1S03_006, IL_1KXK_001, IL_3F1H_098, IL_1JZV_002, IL_1JZV_005, IL_2C4Z_002, IL_1ET4_008, IL_1S72_077, IL_1GID_005, IL_1FJG_036, IL_1ET4_002, IL_1GID_002, IL_2PLY_002, IL_1S03_002, IL_1S72_104, IL_2ZJR_093, IL_1F7Y_002, IL_2ZY6_002

Motif IL_40289.1 Version IL_40289.1 of this group appears in releases 0.3 to 0.3 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_40289.1 Version IL_40289.1 of this group appears in releases 0.3 to 0.3

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Csv

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