IL_56465.3

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name for chain		1		2		3	break		4		5	1-5	2-4	3-4
1	IL_1FJG_046	1FJG	0.4097	0		A	SSU rRNA	G	1143	G	1144	C	1145	*	G	1127	C	1128	cWW		ncWW
2	IL_2AW7_024	2AW7	0.4171	0		A	SSU rRNA	C	477	A	478	U	479	*	G	454	G	455	cWW		cWW
3	IL_2QBG_029	2QBG	0.4041	0		B	LSU rRNA	G	926	A	927	A	928	*	U	850	C	851	cWW		cWW
4	IL_2AW7_047	2AW7	0.2828	0		A	SSU rRNA	G	1041	A	1042	G	1043	*	C	998	C	999	cWW		cWW
5	IL_1S72_079	1S72	0.2361	0	Single stack bend (H)	0	LSU rRNA	U	2436	A	2437	G	2438	*	C	2454	A	2455	cWW		cWW
6	IL_4IOA_056	4IOA	0.2810	0	Single stack bend (H)	X	LSU rRNA	A	1463	A	1464	G	1465	*	C	1477	U	1478	cWW	ncWW	cWW
7	IL_3V2F_005	3V2F	0.1538	0		A	LSU rRNA	G	212	A	213	G	214	*	C	183	C	184	cWW		cWW
8	IL_2QBG_010	2QBG	0.1951	0		B	LSU rRNA	G	212	A	213	G	214	*	C	183	C	184	cWW		cWW
9	IL_1S72_005	1S72	0.2038	0	Single stack bend (H)	0	LSU rRNA	G	182	A	183	G	184	*	C	153	C	154	cWW		cWW
10	IL_3U5H_004	3U5H	0.1817	0		5	LSU rRNA	G	56	A	57	G	58	*	C	27	C	28	cWW		cWW
11	IL_4A1B_001	4A1B	0.1373	0		1	LSU rRNA	G	54	A	55	G	56	*	C	25	C	26	cWW		cWW
12	IL_4IOA_005	4IOA	0.0000	0	Single stack bend (H)	X	LSU rRNA	A	189	A	190	G	191	*	C	160	U	161	cWW		cWW
13	IL_3V2F_024	3V2F	0.1713	0		A	LSU rRNA	G	940	A	941	G	942	*	C	837	C	838	cWW		cWW
14	IL_4IOA_021	4IOA	0.1947	0	Single stack bend (H)	X	LSU rRNA	G	951	A	952	G	953	*	C	850	C	851	cWW		cWW
15	IL_2QBG_027	2QBG	0.2326	0		B	LSU rRNA	G	940	A	941	G	942	*	C	837	C	838	cWW		cWW
16	IL_2QBG_090	2QBG	0.2618	0		B	LSU rRNA	C	2498	C	2499	U	2500	*	A	2453	G	2454	cWW		cWW
17	IL_4IOA_085	4IOA	0.4161	0		X	LSU rRNA	C	2477	C	2478	U	2479	*	A	2432	G	2433	cWW		cWW
18	IL_3V2F_088	3V2F	0.4402	0		A	LSU rRNA	C	2498	C	2499	U	2500	*	A	2453	G	2454	cWW		cWW
19	IL_4A1B_042	4A1B	0.4042	0		1	LSU rRNA	U	1138	A	1139	G	1140	*	C	994	A	995	cWW		cWW
20	IL_3U5H_037	3U5H	0.4172	0		5	LSU rRNA	U	1111	A	1112	G	1113	*	C	969	A	970	cWW		cWW
21	IL_4A1B_018	4A1B	0.5416	0		1	LSU rRNA	U	466	A	467	A	468	*	U	511	G	512	cWW		cWW
22	IL_2AW7_025	2AW7	0.5884	0		A	SSU rRNA	U	472	U	473	G	474	*	U	458	A	459	cWW		cWW
23	IL_4A1B_073	4A1B	0.3900	0		1	LSU rRNA	U	1802	U	1803	G	1804	*	C	1694	A	1695	cWW		cWW
24	IL_3U5H_146	3U5H	0.3208	0		7	5S rRNA	C	47	U	48	G	49	*	C	29	G	30	cWW		cWW
25	IL_3U5H_009	3U5H	0.3116	0		5	LSU rRNA	C	163	A	164	A	165	*	U	257	G	258	cWW		cWW
26	IL_1O9M_001	1O9M	0.3799	1		B+A	EUBACTERIAL A-SITE	G	1494	U	1495	C	1496	*	G	1405	C	1407	cWW		cWW
27	IL_2O3X_001	2O3X	0.3613	1	Stack and bulge	B+A	RNA (23-mer)	G	42	U	43	C	44	*	G	5	C	7	cWW		cWW
28	IL_2QBG_084	2QBG	0.5966	1		B	LSU rRNA	A	2184	U	2185	G	2186	*	C	2103	U	2105	cWW		cWW
29	IL_4IOA_046	4IOA	0.4993	1	Intercalated cWW (H)	X	LSU rRNA	G	1241	A	1242	G	1243	*	U	1232	C	1234	cWW		cWW
30	IL_4IOA_102	4IOA	0.7491	2	Decoding loop related (H)	X	LSU rRNA	G	2818	G	2819	C	2820	*	G	2846	C	2849	cWW		cWW
31	IL_1ZX7_001	1ZX7	0.4895	2		B+A	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
32	IL_1ZX7_007	1ZX7	0.5542	2		H+G	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
33	IL_2O3X_003	2O3X	0.5754	2	Decoding loop related	B+A	RNA (23-mer)	C	30	A	31	C	32	*	G	16	G	19	cWW		cWW
34	IL_1DUH_005	1DUH	0.7500	4		A	4.5S RNA DOMAIN IV	C	66	A	67	A	68	*	U	38\|\|\|\|4_555	G	43\|\|\|\|4_555	cWW		cWW
35	IL_1DUH_001	1DUH	0.7500	4		A	4.5S RNA DOMAIN IV	C	66\|\|\|\|4_555	A	67\|\|\|\|4_555	A	68\|\|\|\|4_555	*	U	38	G	43	cWW		cWW
36	IL_1T0E_001	1T0E	0.6309	2	Decoding loop related	C+A	RNA (17-mer)	C	16	A	17	C	18	*	G	7	G	10\|\|A	cWW		cWW
37	IL_1O9M_002	1O9M	0.7424	2		A+B	EUBACTERIAL A-SITE	C	1407	A	1408	C	1409	*	G	1491	G	1494	cWW		cWW
38	IL_2O3X_002	2O3X	0.7253	2	Decoding loop related	A+B	RNA (23-mer)	C	7	A	8	C	9	*	G	39	G	42	cWW		cWW
39	IL_1MWL_003	1MWL	0.7170	2		B+A	RNA (22-mer)	C	28	A	29	C	30	*	G	15	G	18\|\|A	cWW		cWW
40	IL_1MWL_002	1MWL	0.7243	2		A+B	RNA (22-mer)	C	6	A	7	C	8	*	G	37	G	40	cWW		cWW
41	IL_3TD1_005	3TD1	0.8060	2		B+A	RNA (23-mer)	C	30	G	31	C	32	*	G	16	G	19	cWW		cWW
42	IL_3TD1_002	3TD1	0.7777	2		A+B	RNA (23-mer)	C	7	G	8	C	9	*	G	39	G	42	cWW		cWW
43	IL_3T4B_001	3T4B	0.5196	1		A	HCV IRES pseudoknot domain plus crystallization module	U	287	A	288	C	289	*	G	135	G	137	cWW		cWW
44	IL_4A1B_009	4A1B	0.5238	0		1	LSU rRNA	U	173	A	174	A	175	*	U	245	G	246	cWW		ncWW
45	IL_3MOJ_004	3MOJ	0.5173	0	Single stack bend	A	LSU rRNA	C	2540	A	2541	A	2542	*	U	2522	G	2523	cWW		cWW
46	IL_2QWY_002	2QWY	0.5972	0		A	SAM-II riboswitch	C	43	U	44	A	45	*	U	21	G	22	cWW		cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GAG*CC	9
CAC*GAAG	6
UAG*CA	3
CCU*AG	3
AAG*CU	2
UAA*UG	2
CAA*UG	2
GUC*GUC	2
GAAG*CAC	2
CGC*GAAG	2
GGC*GC	1
CAU*GG	1
GAA*UC	1
UUG*UA	1
UUG*CA	1
CUG*CG	1
AUG*CCU	1
GAG*UAC	1
GGC*GGAC	1
CAA*UACCAG	1
UACCAG*CAA	1
UAC*GAG	1
CUA*UG	1

Non-Watson-Crick part of the motif

Sequence	Counts
A*	20
A*AA	6
U*	4
C*	3
U*U	2
A*A	2
AA*A	2
G*AA	2
G*	1
U*C	1
G*GA	1
A*ACCA	1
ACCA*A	1

Release history

Release	1.1	1.2	1.3	1.4	1.5	1.6	1.7	1.8	1.9
Date	2013-04-08	2013-05-04	2013-06-01	2013-07-01	2013-08-03	2013-08-31	2013-09-28	2013-11-05	2013-12-07
Status	Updated, 1 parent	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in IL_56465.3	Only in the parent motif
IL_56465.2 Compare	IL_2QBG_084, IL_3U5H_009, IL_3V2F_088, IL_1DUH_005, IL_3TD1_005, IL_3TD1_002, IL_3V2F_024, IL_3U5H_004, IL_3U5H_146, IL_2QWY_002, IL_4A1B_073, IL_1O9M_001, IL_2QBG_027, IL_1DUH_001, IL_2AW7_025, IL_2QBG_029, IL_1S72_005, IL_4A1B_009, IL_3V2F_005, IL_4A1B_018, IL_2QBG_090, IL_1MWL_003, IL_1MWL_002, IL_1ZX7_007, IL_2AW7_024, IL_1O9M_002, IL_1ZX7_001, IL_3U5H_037, IL_3MOJ_004, IL_2AW7_047, IL_1S72_079, IL_2QBG_010, IL_4A1B_042, IL_1T0E_001, IL_2O3X_001, IL_2O3X_002, IL_2O3X_003, IL_1FJG_046, IL_3T4B_001, IL_4A1B_001	IL_4IOA_085, IL_4IOA_056, IL_4IOA_046, IL_4IOA_102, IL_4IOA_005, IL_4IOA_021	IL_2ZJR_044, IL_2ZJR_055, IL_2ZJR_021, IL_2ZJR_084, IL_2ZJR_005

Children motifs

Child motif	Common motif instances	Only in IL_56465.3	Only in the child motif
IL_56465.4 Compare	IL_2QBG_084, IL_3TD1_002, IL_4IOA_056, IL_3V2F_088, IL_2QBG_029, IL_3TD1_005, IL_3U5H_009, IL_3V2F_024, IL_3U5H_004, IL_1O9M_002, IL_2QWY_002, IL_1FJG_046, IL_4A1B_018, IL_2QBG_027, IL_3U5H_146, IL_2AW7_025, IL_1DUH_005, IL_1S72_005, IL_2O3X_001, IL_4A1B_042, IL_4A1B_073, IL_1O9M_001, IL_4IOA_085, IL_2QBG_090, IL_1MWL_003, IL_1MWL_002, IL_1ZX7_007, IL_2AW7_047, IL_1ZX7_001, IL_3U5H_037, IL_3V2F_005, IL_3MOJ_004, IL_4A1B_001, IL_4IOA_102, IL_1S72_079, IL_4IOA_005, IL_2QBG_010, IL_4IOA_021, IL_4IOA_046, IL_4A1B_009, IL_2O3X_002, IL_2AW7_024, IL_2O3X_003, IL_1T0E_001, IL_1DUH_001, IL_3T4B_001		IL_4M30_001

Motif IL_56465.3 Version IL_56465.3 of this group appears in releases 1.1 to 1.9 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_56465.3 Version IL_56465.3 of this group appears in releases 1.1 to 1.9

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