Motif IL_65553.5 Version IL_65553.5 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		5		6		7	break		8		9		10		11		12	1-5	1-12	2-3	2-11	4-11	5-9	5-10	5-12	6-9	6-10	7-8	10-11
1	IL_3RW6_002	3RW6	0.6179	4	Kink-turn with non-sequential stacking	H	constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA	C	43	A	44	A	45	G	47	A	48	C	49	G	50	*	U	11	A	12	C	16	A	17	G	18	ncsS	cWW		tsS	tSH	tHW				cwW	cWW
2	IL_3U5F_019	3U5F	0.7169	2		6	18S rRNA	U	348	U	349	U	350	A	352	A	353	C	354	G	355	*	U	311	A	312	C	314	A	315	A	316	ncsS	cWW		tsS	ntSH	tHW				cwW	cWW
3	IL_2XZM_017	2XZM	0.7245	2		A	18S RRNA	C	339	A	340	G	341	C	343	A	344	C	345	G	346	*	U	302	A	303	C	305	A	306	G	307		cWW		ntsS		ncBW				cwW	ncWW
4	IL_2AW7_014	2AW7	0.6943	2		A	16S ribosomal RNA	C	277	G	278	A	279	G	281	A	282	U	283	C	284	*	G	242	A	243	U	245	A	246	G	247	ncsS	cWW	ncSH		tSH	tHW				cWw	cWW
5	IL_1S72_032	1S72	0.5483	2	Kink-turn (H)	0	LSU rRNA	C	1026	G	1027	U	1028	G	1031	A	1032	C	1033	G	1034	*	C	936	C	937	G	938	A	939	G	940		ncWW		ntsS	tSH				cBW		cWW
6	IL_3U5F_051	3U5F	0.4959	1		6	18S rRNA	C	910	U	911	U	912	G	914	A	915	U	916	U	917	*	G	895	U	896	C	897	A	898	G	899	ncsS	cWW		ntsS	tSH			tSs			ncWW
7	IL_4IOA_004	4IOA	0.4668	1	Kink-turn	X	LSU rRNA	C	96	U	97	U	98	G	100	A	101	C	102	U	103	*	A	80	C	81	G	82	A	83	G	84		cWW		tsS	tSH				cBW		cWW
8	IL_4GMA_003	4GMA	0.4696	1	Kink-turn	Z	Adenosylcobalamin riboswitch	G	143	G	144	A	145	G	147	A	148	G	149	U	150	*	A	93	G	94	G	95	A	96	C	97	ncsS	cWW		ntsS	tSH			ntSs	tHS		ncWW
9	IL_1T0K_001	1T0K	0.3471	1	Kink-turn	D+C	RNA (16-mer)	C	54	A	55	G	56	G	58	A	59	U	60	G	61	*	C	9	G	10	G	11	A	12	G	13		cWW		tsS	ntSH				ntHS		cWW
10	IL_4GXY_005	4GXY	0.3524	1	Kink-turn	A	Adenosylcobalamin riboswitch	C	139	G	140	A	141	G	143	A	144	U	145	C	146	*	G	82	G	83	G	84	A	85	G	86	ncsS	cWW		ntsS	tSH				tHS		cWW
11	IL_3V2F_004	3V2F	0.3883	1		A	23S Ribosomal RNA	C	97	G	98	U	99	G	102	A	103	U	104	C	105	*	G	81	G	82	G	83	A	84	G	85		cWW		ntsS	tSH			ntSs	tHS		cWW
12	IL_1S72_004	1S72	0.3515	1	Kink-turn (H)	0	LSU rRNA	C	93	G	94	A	95	G	97	A	98	A	99	C	100	*	G	77	G	78	G	79	A	80	G	81		cWW		ntsS	tSH		ntHS	ntSs	tHS		cWW
13	IL_4AOB_002	4AOB	0.3364	1	Kink-turn	A	SAM-I riboswitch	U	31	G	32	A	33	G	35	A	36	C	37	C	38	*	G	17	C	18	A	19	A	20	G	21		cWW		tsS	tSH				cBW		cWW
14	IL_3NPB_003	3NPB	0.4019	1		A	TL5 RNA	C	31	G	32	A	33	G	35	A	36	A	37	G	38	*	C	17	A	18	G	19	A	20	G	21		cWW		tsS							cWW	ncSH
15	IL_3V7E_006	3V7E	0.1496	1	Kink-turn (H)	D	SAM-I riboswitch	C	231	G	232	A	233	G	235	A	236	A	237	A	238	*	U	217	G	218	G	219	A	220	G	221		cWW		ntsS	tSH				tHS		cWW
16	IL_3GX5_002	3GX5	0.0000	1		A	RNA (94-MER)	C	31	G	32	A	33	G	35	A	36	A	37	A	38	*	U	17	G	18	G	19	A	20	G	21		cWW		tsS	tSH		tHS		tHS		cWW
17	IL_3V2F_044	3V2F	0.1550	1		A	23S Ribosomal RNA	C	1208	G	1209	A	1210	G	1212	A	1213	A	1214	G	1215	*	U	1234	G	1235	G	1236	A	1237	G	1238		cWW			tSH		tHS		tHS		cWW
18	IL_3U5H_064	3U5H	0.2195	1		5	25S rRNA	U	1388	G	1389	A	1390	G	1392	A	1393	A	1394	G	1395	*	U	1415	C	1416	G	1417	A	1418	A	1419		cWW		tsS	tSH		tHS		tHS		cWW
19	IL_2QBG_047	2QBG	0.3196	1		B	23S rRNA	C	1208	U	1209	G	1210	G	1212	A	1213	A	1214	G	1215	*	U	1234	G	1235	G	1236	A	1237	G	1238		cWW			ntSH		ntHS		tHS		cWW
20	IL_4IOA_045	4IOA	0.3175	1	Kink-turn	X	LSU rRNA	C	1221	G	1222	G	1223	G	1225	A	1226	A	1227	G	1228	*	U	1247	G	1248	G	1249	A	1250	G	1251		cWW			tSH		tHS		tHS		cWW
21	IL_1S72_048	1S72	0.3039	1	Kink-turn (H)	0	LSU rRNA	G	1312	A	1313	U	1314	G	1316	A	1317	A	1318	G	1319	*	U	1338	G	1339	G	1340	A	1341	C	1342		cWW		ntsS	tSH		tHS		tHS		cWW
22	IL_4A1B_062	4A1B	0.3345	1		1	26S RRNA	C	1414	C	1415	U	1416	G	1418	A	1419	A	1420	G	1421	*	U	1441	G	1442	G	1443	A	1444	G	1445		cWW		ntsS	tSH		ntHS		tHS		cWW

3D structures

Complete motif including flanking bases

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

Non-Watson-Crick part of the motif

Sequence	Counts
GAUGAA*GGA	2
AAUGAC*AAGACA	1
UUCAAC*AUCA	1
AGUCAC*AUCA	1
GACGAU*AUUA	1
GUUUGAC*CGA	1
UUGGAU*UCA	1
UUUGAC*CGA	1
GAUGAG*GGA	1
AGAGAU*GGA	1
GAGGAU*GGA	1
GUGGAU*GGA	1
GAAGAA*GGA	1
GAUGAC*CAA	1
GACGAA*AGA	1
GACGAA*GGA	1
GACGAA*CGA	1
UGCGAA*GGA	1
GGAGAA*GGA	1
AUGGAA*GGA	1
CUAGAA*GGA	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_65553.5	Only in the parent motif
IL_65553.4 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_4IOA_004, IL_4IOA_045	IL_2ZJR_004, IL_2ZJR_043

Children motifs

Child motif	Common motif instances	Only in IL_65553.5	Only in the child motif
IL_65553.6 Compare	IL_1S72_032, IL_3U5H_064, IL_3U5F_019, IL_2QBG_047, IL_3V7E_006, IL_3U5F_051, IL_4GXY_005, IL_4IOA_045, IL_1S72_004, IL_4A1B_062, IL_3GX5_002, IL_3V2F_044, IL_2AW7_014, IL_1T0K_001, IL_4AOB_002, IL_4IOA_004, IL_3NPB_003, IL_1S72_048, IL_4GMA_003, IL_3RW6_002, IL_3V2F_004	IL_2XZM_017	IL_4BPP_017

Annotations: (11)
Kink-turn (6)
Kink-turn (H) (4)
Kink-turn with non-sequential stacking (1)
Basepair signature: cWW-cSS-tSS-L-tSH-tSS-tHS-tHW-cWW-tHS-cWW
Heat map statistics: Min 0.15 | Avg 0.46 | Max 0.87

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Coloring options: Nucleotide numbers

Motif IL_65553.5 Version IL_65553.5 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_65553.5 Version IL_65553.5 of this group appears in releases 1.1 to 1.4

Download

Csv

Json