Motif IL_65553.4 Version IL_65553.4 of this group appears in releases 0.10 to 1.0

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3		4		5	break		6		7		8		9		10		11		12	1-12	2-10	2-11	3-4	3-10	3-11	4-7	4-9	5-6	5-10	6-10	7-8
1	IL_3NPB_003	3NPB	0.4019	1		A	TL5 RNA	C	17	A	18	G	19	A	20	G	21	*	C	31	G	32	A	33	G	35	A	36	A	37	G	38	cWW			ncSH			tSs		cWW
2	IL_4A1B_062	4A1B	0.3345	1		1	26S RRNA	U	1441	G	1442	G	1443	A	1444	G	1445	*	C	1414	C	1415	U	1416	G	1418	A	1419	A	1420	G	1421	cWW		tSH		ntSH		ntSs	tHS	cWW
3	IL_1S72_048	1S72	0.3039	1	Kink-turn (H)	0	LSU rRNA	U	1338	G	1339	G	1340	A	1341	C	1342	*	G	1312	A	1313	U	1314	G	1316	A	1317	A	1318	G	1319	cWW		tSH		tSH		ntSs	tHS	cWW
4	IL_2ZJR_043	2ZJR	0.3133	1	Kink-turn (H)	X	LSU rRNA	U	1247	G	1248	G	1249	A	1250	G	1251	*	C	1221	G	1222	G	1223	G	1225	A	1226	A	1227	G	1228	cWW		tSH		tSH			tHS	cWW
5	IL_2QBG_047	2QBG	0.3196	1		B	23S rRNA	U	1234	G	1235	G	1236	A	1237	G	1238	*	C	1208	U	1209	G	1210	G	1212	A	1213	A	1214	G	1215	cWW		tSH		ntSH			ntHS	cWW
6	IL_3U5H_064	3U5H	0.2195	1		5	25S rRNA	U	1415	C	1416	G	1417	A	1418	A	1419	*	U	1388	G	1389	A	1390	G	1392	A	1393	A	1394	G	1395	cWW		tSH		tSH		tSs	tHS	cWW
7	IL_3V2F_044	3V2F	0.1550	1		A	23S Ribosomal RNA	U	1234	G	1235	G	1236	A	1237	G	1238	*	C	1208	G	1209	A	1210	G	1212	A	1213	A	1214	G	1215	cWW		tSH		tSH			tHS	cWW
8	IL_3GX5_002	3GX5	0.0000	1		A	RNA (94-MER)	U	17	G	18	G	19	A	20	G	21	*	C	31	G	32	A	33	G	35	A	36	A	37	A	38	cWW		tSH		tSH		tSs	tHS	cWW
9	IL_3V7E_006	3V7E	0.1496	1	Kink-turn (H)	D	SAM-I riboswitch	U	217	G	218	G	219	A	220	G	221	*	C	231	G	232	A	233	G	235	A	236	A	237	A	238	cWW		tSH				ntSs	tHS	cWW
10	IL_4AOB_002	4AOB	0.3364	1	Kink-turn	A	SAM-I riboswitch	G	17	C	18	A	19	A	20	G	21	*	U	31	G	32	A	33	G	35	A	36	C	37	C	38	cWW		cWB				tSs	tHS	cWW
11	IL_1S72_004	1S72	0.3515	1	Kink-turn (H)	0	LSU rRNA	G	77	G	78	G	79	A	80	G	81	*	C	93	G	94	A	95	G	97	A	98	A	99	C	100	cWW		tSH		ntSH		ntSs	tHS	cWW	ntsS
12	IL_3V2F_004	3V2F	0.3883	1		A	23S Ribosomal RNA	G	81	G	82	G	83	A	84	G	85	*	C	97	G	98	U	99	G	102	A	103	U	104	C	105	cWW		tSH				ntSs	tHS	cWW	ntsS
13	IL_4GXY_005	4GXY	0.3524	1	Kink-turn	A	Adenosylcobalamin riboswitch	G	82	G	83	G	84	A	85	G	86	*	C	139	G	140	A	141	G	143	A	144	U	145	C	146	cWW		tSH				ntSs	tHS	cWW		ncsS
14	IL_1T0K_001	1T0K	0.3471	1	Kink-turn	C+D	RNA (13-mer) + RNA (16-mer)	C	9	G	10	G	11	A	12	G	13	*	C	54	A	55	G	56	G	58	A	59	U	60	G	61	cWW		ntSH				tSs	ntHS	cWW
15	IL_4GMA_003	4GMA	0.4696	1	Kink-turn	Z	Adenosylcobalamin riboswitch	A	93	G	94	G	95	A	96	C	97	*	G	143	G	144	A	145	G	147	A	148	G	149	U	150	ncWW		tSH				ntSs	tHS	cWW	ntsS	ncsS
16	IL_3U5F_051	3U5F	0.4959	1		6	18S rRNA	G	895	U	896	C	897	A	898	G	899	*	C	910	U	911	U	912	G	914	A	915	U	916	U	917	ncWW						ntSs	tHS	cWW	tsS	ncsS
17	IL_2ZJR_004	2ZJR	0.4942	1	Kink-turn (H)	X	LSU rRNA	A	80	C	81	G	82	A	83	G	84	*	C	96	U	97	U	98	G	100	A	101	C	102	U	103	cWW		ncWB				tSs	ntHS	cWW	ntsS
18	IL_1S72_032	1S72	0.5483	2	Kink-turn (H)	0	LSU rRNA	C	936	C	937	G	938	A	939	G	940	*	C	1026	G	1027	U	1028	G	1031	A	1032	C	1033	G	1034	cWW		cWB				ntSs	tHS	ncWW
19	IL_2AW7_014	2AW7	0.6943	2		A	16S ribosomal RNA	G	242	A	243	U	245	A	246	G	247	*	C	277	G	278	A	279	G	281	A	282	U	283	C	284	cWW	tWH				cwW		tHS	cWW		ncsS	ncSH
20	IL_2XZM_017	2XZM	0.7245	2		A	18S RRNA	U	302	A	303	C	305	A	306	G	307	*	C	339	A	340	G	341	C	343	A	344	C	345	G	346	ncWW	ncWB				cWw	ntSs		cWW
21	IL_3U5F_019	3U5F	0.7169	2		6	18S rRNA	U	311	A	312	C	314	A	315	A	316	*	U	348	U	349	U	350	A	352	A	353	C	354	G	355	cWW	tWH				cWw	tSs	ntHS	cWW		ncsS
22	IL_3RW6_002	3RW6	0.6179	4	Kink-turn with non-sequential stacking	H	constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA	U	11	A	12	C	16	A	17	G	18	*	C	43	A	44	A	45	G	47	A	48	C	49	G	50	cWW	tWH				cWw	tSs	tHS	cWW		ncsS

3D structures

Complete motif including flanking bases

Sequence	Counts
CAGAG*CGACGAAG	1
UGGAG*CCUAGAAG	1
UGGAC*GAUGGAAG	1
UGGAG*CGGAGAAG	1
UGGAG*CUGCGAAG	1
UCGAA*UGACGAAG	1
UGGAG*CGAUGAAG	1
UGGAG*CGACGAAA	1
UGGAG*CGAUGAAA	1
GCAAG*UGAUGACC	1
GGGAG*CGAAGAAC	1
GGGAG*CGUGGAUC	1
GGGAG*CGAGGAUC	1
CGGAG*CAGAGAUG	1
AGGAC*GGAUGAGU	1
GUCAG*CUUGGAUU	1
ACGAG*CUUUGACU	1
CCGAG*CGUUUGACG	1
GAUUAG*CGACGAUC	1
UAUCAG*CAGUCACG	1
UAUCAA*UUUCAACG	1
UAAGACAG*CAAUGACG	1

Non-Watson-Crick part of the motif

Sequence	Counts
GGA*GAUGAA	2
AGA*GACGAA	1
GGA*CUAGAA	1
GGA*AUGGAA	1
GGA*GGAGAA	1
GGA*UGCGAA	1
CGA*GACGAA	1
GGA*GACGAA	1
CAA*GAUGAC	1
GGA*GAAGAA	1
GGA*GUGGAU	1
GGA*GAGGAU	1
GGA*AGAGAU	1
GGA*GAUGAG	1
UCA*UUGGAU	1
CGA*UUUGAC	1
CGA*GUUUGAC	1
AUUA*GACGAU	1
AUCA*AGUCAC	1
AUCA*UUCAAC	1
AAGACA*AAUGAC	1

Release history

Release	0.10	0.11	0.12	1.0
Date	2013-02-17	2013-02-17	2013-02-17	2013-03-04
Status	Updated, 1 parent	Exact match	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in IL_65553.4	Only in the parent motif
IL_65553.3 Compare	IL_4GXY_005, IL_3V2F_044, IL_2AW7_014, IL_1S72_048, IL_2XZM_017, IL_3V2F_004, IL_3U5H_064, IL_2QBG_047, IL_1S72_004, IL_3GX5_002, IL_2ZJR_043, IL_3V7E_006, IL_2ZJR_004, IL_4A1B_062, IL_3RW6_002, IL_3U5F_051, IL_1S72_032, IL_1T0K_001, IL_4GMA_003, IL_3U5F_019, IL_4AOB_002, IL_3NPB_003		IL_3U4M_004

Children motifs

Child motif	Common motif instances	Only in IL_65553.4	Only in the child motif
IL_65553.5 Compare	IL_1S72_032, IL_3V7E_006, IL_3U5F_019, IL_2QBG_047, IL_1T0K_001, IL_3U5F_051, IL_4GXY_005, IL_1S72_048, IL_4A1B_062, IL_3GX5_002, IL_3V2F_044, IL_3U5H_064, IL_2AW7_014, IL_4AOB_002, IL_4GMA_003, IL_3NPB_003, IL_1S72_004, IL_2XZM_017, IL_3RW6_002, IL_3V2F_004	IL_2ZJR_004, IL_2ZJR_043	IL_4IOA_004, IL_4IOA_045

Annotations: (11)
Kink-turn (H) (6)
Kink-turn (4)
Kink-turn with non-sequential stacking (1)
Basepair signature: cWW-tSH-tWH-cWW-tSH-tHS-tSS-tSS-R-cWW
Heat map statistics: Min 0.15 | Avg 0.47 | Max 0.87

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