IL_65553.11

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3		4		5		6		7	break		8		9		10		11		12	1-5	1-12	2-3	2-11	4-5	4-9	4-11	5-9	5-10	5-12	6-8	6-9	6-10	7-8	10-11	11-12
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		cWW		tSS			tSH	tHW		ntSS			cWW	cWW		ncSS
2	IL_4BPP_017➜	4BPP	0.7226	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	cSS	cWW		tSS		ntSH	ncSW	tHW		tSS			cWW	cWW		ncSS
3	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		cWW		tSS			ntSH	tHW					cWW	cWW
4	IL_3J7A_016➜	3J7A	0.6832	2		A	SSU rRNA	C	354	U	355	A	356	G	358	A	359	C	360	G	361	*	U	317	A	318	C	320	A	321	G	322	cSS	cWW		tSS			tSH	tHW		tSS			cWW	cWW
5	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	cSS	cWW	ncSH				tSH	tHW		tSS			cWW	cWW
6	IL_1S72_032➜	1S72	0.5483	2		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		cWW		ntSS			tSH		ntHS	tSS				cWW
7	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	cSS	cWW		ntSS			tSH		ntHS	tSS	ntHW	ntHW		cWW
8	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		ntHS	ntSS				cWW
9	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	cSS	cWW	ncSH				tSH		tHS	tSS		tHS		cWW
10	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			tSH		ntHS			ntHS		cWW
11	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		cWW	ncSS				tSH		ntHS	ntSS		ntHS		cWW		ncSS
12	IL_4QCN_004➜	4QCN	0.3957	1		A	23S Ribosomal RNA	C	96	G	97	U	98	G	100	A	101	U	102	C	103	*	G	80	G	81	G	82	A	83	G	84		cWW		tSS			tSH		ntHS	tSS		tHS		cWW	ncSH
13	IL_1S72_004➜	1S72	0.3515	1		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					tSH		tHS	tSS		tHS		cWW
14	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		ntHS	tSS				cWW		ncSS
15	IL_4C4W_001➜	4C4W	0.2710	1		D	TSKT-23	U	26	G	27	A	28	G	30	A	31	C	32	C	33	*	G	3	C	4	A	5	A	6	G	7		cWW		ntSS			tSH		tHS			ntHS		cWW
16	IL_4KQY_002➜	4KQY	0.2484	1	Kink-turn	A	SAM-I riboswitch	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	ncSS	ntSS	ncSH		tSH		tHS			ntHS		cWW
17	IL_3V7E_006➜	3V7E	0.1496	1		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					tSH					tHS		cWW
18	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
19	IL_4QCN_043➜	4QCN	0.1577	1		A	23S Ribosomal RNA	C	1253	G	1254	A	1255	G	1257	A	1258	A	1259	G	1260	*	U	1280	G	1281	G	1282	A	1283	G	1284		cWW	ncSS				tSH		tHS			tHS		cWW
20	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	ncSS	tSS			tSH		tHS			tHS		cWW
21	IL_4CUV_066➜	4CUV	0.2240	1		1	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	ncSS	ntSS			tSH		tHS			tHS		cWW
22	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		ntSS			tSH		tHS			tHS		cWW
23	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	ncSH				tSH		tHS			tHS		cWW
24	IL_1S72_048➜	1S72	0.3039	1		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		tSS			tSH		tHS			tHS		cWW		ncSS
25	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		tHS			tHS		cWW
26	IL_1VX6_065➜	1VX6	0.3072	1		A	28S ribosomal RNA	U	1536	G	1537	U	1538	G	1540	A	1541	A	1542	G	1543	*	U	1563	G	1564	G	1565	A	1566	A	1567		cWW							tHS			tHS		cWW
27	IL_4QCN_083➜	4QCN	0.3342	1		A	23S Ribosomal RNA	C	2151	U	2152	G	2153	G	2155	A	2156	A	2157	C	2158	*	G	2177	G	2178	G	2179	A	2180	G	2181		cWW	ncSS		cSH		tSH		tHS			cWS		cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
UGACGAAG*UCGAA	2
UGAUGACC*GCAAG	2
CGAUGAAG*UGGAG	1
CGAUGAAA*UGGAG	1
CGACGAAG*CAGAG	1
CGACGAAA*UGGAG	1
CGGAGAAG*UGGAG	1
CUGUGAAC*GGGAG	1
UGUUGAAG*UGGAA	1
CCUAGAAG*UGGAG	1
GAUGGAAG*UGGAC	1
CUGCGAAG*UGGAG	1
CGAAGAAC*GGGAG	1
CGACGAUC*GAUUAG	1
CGUUUGACG*CCGAG	1
CUAUGACG*UAUCAG	1
UAUCAA*UUUCAACG	1
CAGUCACG*UAUCAG	1
GUCAG*CUUGGAUU	1
CUUUGACU*ACGAG	1
CGUGGAUC*GGGAG	1
CGAGGAUC*GGGAG	1
CAGAGAUG*CGGAG	1
GGAUGAGU*AGGAC	1
CAAUGACG*UAAGACAG	1

Non-Watson-Crick part of the motif

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

Release history

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

Parent motifs

Parent motif	Common motif instances	Only in IL_65553.11	Only in the parent motif
IL_65553.10 Compare	IL_4KQY_002, IL_4GXY_005, IL_4CUV_066, IL_2AW7_014, IL_1S72_048, IL_3U5H_064, IL_2QBG_047, IL_1S72_004, IL_3GX5_002, IL_3V7E_006, IL_4BPP_017, IL_4IOA_045, IL_4C4W_001, IL_4A1B_062, IL_4IOA_004, IL_3RW6_002, IL_3U5F_051, IL_1S72_032, IL_1T0K_001, IL_4GMA_003, IL_3U5F_019, IL_4AOB_002	IL_4QCN_083, IL_3J7A_016, IL_1VX6_065, IL_4QCN_043, IL_4QCN_004	IL_4NVV_046, IL_4NVV_004

Children motifs

Child motif	Common motif instances	Only in IL_65553.11	Only in the child motif
IL_65553.12 Compare	IL_3U5F_019, IL_4GXY_005, IL_4CUV_066, IL_2AW7_014, IL_1S72_004, IL_3U5H_064, IL_4QCN_043, IL_4QCN_004, IL_1S72_048, IL_3GX5_002, IL_1VX6_065, IL_4QCN_083, IL_3V7E_006, IL_4BPP_017, IL_4IOA_045, IL_4C4W_001, IL_4A1B_062, IL_4IOA_004, IL_3RW6_002, IL_3U5F_051, IL_1S72_032, IL_1T0K_001, IL_2QBG_047, IL_4GMA_003, IL_4KQY_002, IL_4AOB_002, IL_3J7A_016		IL_4W21_090, IL_4W23_017

Motif IL_65553.11 Version IL_65553.11 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_65553.11 Version IL_65553.11 of this group appears in releases 1.17 to 1.17

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Csv

Json