Motif IL_29549.9 Version IL_29549.9 of this group appears in releases 3.62 to 3.76

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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	3-10	3-11	4-7	4-9	5-6	5-10	6-10	7-8
1	IL_3RW6_002	3RW6	0.5971	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
2	IL_4LFB_011	4LFB	0.5620	2	Kink-turn with non-sequential stacking	A	SSU rRNA	C	242	A	243	C	245	A	246	G	247	*	C	277	G	278	A	279	G	281	A	282	C	283	G	284	cWW	tWH			cWw	ntSs	tHS	cWW		ncsS
3	IL_6CZR_123	6CZR	0.5762	2	Kink-turn with non-sequential stacking	1a	SSU rRNA	C	238	A	239	C	241	A	242	G	243	*	C	273	G	274	A	275	G	277	A	278	C	279	G	280	cWW	tWH			cWw	ntSs	tHS	cWW
4	IL_4V88_402	4V88	0.6490	2	Kink-turn with non-sequential stacking	A6	SSU 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
5	IL_5J7L_014	5J7L	0.6047	2	Kink-turn with non-sequential stacking	AA	SSU rRNA	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
6	IL_4V9F_031	4V9F	0.5000	2	Kink-turn	0	LSU rRNA	C	936	C	937	G	938	A	939	G	940	*	U	1026	G	1027	U	1028	G	1031	A	1032	C	1033	G	1034	cWW		cWB			ntSs	tHS	cWW
7	IL_4WF9_004	4WF9	0.3922	1	Kink-turn	X	LSU rRNA	G	81	G	82	G	83	A	84	G	85	*	C	97	U	98	U	99	G	101	A	102	U	103	C	104	cWW		tSH	ntsS		ntSs	ntHS	cWW
8	IL_6UFG_001	6UFG	0.2722	1	Kink-turn	A	RNA (166-MER)	G	23	G	24	G	25	A	26	G	27	*	C	3	A	4	U	5	G	7	A	8	U	9	C	10	cWW		tSH			ntSs	tHS	cWW
9	IL_7A0S_004	7A0S	0.3240	1	Kink-turn	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		cWB				ntHS	cWW
10	IL_4V88_434	4V88	0.3402	1	Kink-turn	A6	SSU 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
11	IL_6UFH_001	6UFH	0.2593	1	Kink-turn	A	RNA (167-MER)	G	23	G	24	G	25	A	26	G	27	*	C	3	A	4	U	5	G	7	A	8	U	9	C	10	cWW		tSH			ntSs	tHS	cWW		ncsS
12	IL_7RQB_004	7RQB	0.1649	1	Kink-turn	1A	LSU rRNA	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			tSs	tHS	cWW	ntsS
13	IL_4GXY_005	4GXY	0.1363	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_6UFM_001	6UFM	0.0000	1	Kink-turn	B	RNA (98-MER)	G	23	G	24	G	25	A	26	G	27	*	C	3	G	4	A	5	G	7	A	8	U	9	C	10	cWW		tSH			tSs	tHS	cWW
15	IL_1T0K_001	1T0K	0.1887	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
16	IL_4V9F_004	4V9F	0.2158	1	Kink-turn	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
17	IL_4AOB_002	4AOB	0.2218	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
18	IL_4C4W_002	4C4W	0.3611	1	Kink-turn	H	TSKT-23	G	3	C	4	A	5	A	6	G	7	*	U	26	G	27	A	28	G	30	A	31	C	32	C	33	cWW		ncWB	tSH		ntSs	tHS	cWW
19	IL_5G4U_006	5G4U	0.3267	1	Kink-turn	I+J	HMKT-7	G	13	U	14	G	15	A	16	G	17	*	C	3	G	4	A	5	G	7	A	8	U	9	C	10	cWW		ncwW	tSH		ntSs	tHS	cWW
20	IL_5G4U_005	5G4U	0.3427	1	Kink-turn	J+I	HMKT-7	G	13	U	14	G	15	A	16	G	17	*	C	3	G	4	A	5	G	7	A	8	U	9	C	10	cWW		ncwW	tSH		tSs	tHS	cWW
21	IL_4KQY_002	4KQY	0.3335	1	Kink-turn	A	SAM-I riboswitch	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			ntSH		tSs	ntHS	cWW
22	IL_5Y7M_008	5Y7M	0.3013	1	Kink-turn	D	RNA (52-MER)	G	29	G	30	G	31	A	32	U	33	*	A	17	G	18	A	19	G	21	A	22	U	23	C	24	cWW		ntSH	ntSH		tSs	tHS	cWW
23	IL_5G4T_002	5G4T	0.3427	1	Kink-turn	B+A	HMKT-7	G	13	G	14	G	15	A	16	G	17	*	C	3	G	4	A	5	G	7	A	8	A	9	C	10	cWW		tSH	tSH		ntSs	tHS	cWW
24	IL_5FJC_002	5FJC	0.3458	1	Kink-turn	A	SAM-I riboswitch	G	17	G	18	G	19	A	20	G	21	*	C	31	G	32	A	33\|\|A	G	35	A	36	A	37	C	38	cWW		tSH	tSH		tSs	tHS	cWW
25	IL_3U4M_004	3U4M	0.3998	1	Kink-turn	B	LSU rRNA	G	2155	G	2156	G	2157	A	2158	G	2159	*	C	2129	U	2130	G	2131	G	2133	A	2134	A	2135	C	2136	cWW		tSH	tSH		tSs	tHS	cWW
26	IL_3V7E_002	3V7E	0.4032	1	Kink-turn	C	SAM-I riboswitch	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			tSs	tHS	cWW
27	IL_7RQB_047	7RQB	0.4236	1	Kink-turn	1A	LSU rRNA	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		ntSs	tHS	cWW
28	IL_5J7L_288	5J7L	0.4474	1	Kink-turn	DA	LSU 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	tSH		tSs	tHS	cWW
29	IL_5TBW_059	5TBW	0.4209	1	Kink-turn	1	LSU 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
30	IL_7A0S_043	7A0S	0.4894	1	Kink-turn	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	ntSH		ntSs	tHS	cWW
31	IL_4V9F_048	4V9F	0.4491	1	Kink-turn	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
32	IL_4WF9_046	4WF9	0.5570	1	Kink-turn	X	LSU rRNA	U	1272	G	1273	G	1274	A	1275	G	1276	*	C	1246	G	1247	U	1248	G	1250	A	1251	A	1252	G	1253	cWW		tSH	ntSH				cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GGGAG*CGAAGAAC	3
CAUCAG*CGACGACG	2
GGGAG*CAUCGAUC	2
GCAAG*UGAUGACC	2
GUGAG*CGAAGAUC	2
UAAGACAG*CAAUGACG	1
UAUCAA*UUUCAACG	1
GAUUAG*CGACGAUC	1
CCGAG*UGUUUGACG	1
GGGAG*CUUUGAUC	1
ACGAG*CUUUGACU	1
GUCAG*CUUGGAUU	1
GGGAG*CGUGGAUC	1
GGGAG*CGAGGAUC	1
GGGAG*CGACGAUC	1
CGGAG*CAGAGAUG	1
CAGAG*CGACGAAG	1
GGGAU*AGACGAUC	1
GGGAG*CUGUGAAC	1
UGGAG*CGAUGAAA	1
UGGAG*CGAUGAAG	1
UGGAG*CUGCGAAG	1
UCGAA*UGACGAAG	1
UGGAG*CGGAGAAG	1
UGGAC*GAUGGAAG	1
UGGAG*CGUUGAAG	1

Non-Watson-Crick part of the motif

Sequence	Counts
GGA*GAAGAA	3
AUCA*GACGAC	2
GGA*AUCGAU	2
GGA*GACGAU	2
CAA*GAUGAC	2
UGA*GAAGAU	2
GGA*GAUGAA	2
AAGACA*AAUGAC	1
AUCA*UUCAAC	1
AUUA*GACGAU	1
CGA*GUUUGAC	1
GGA*UUUGAU	1
CGA*UUUGAC	1
UCA*UUGGAU	1
GGA*GUGGAU	1
GGA*GAGGAU	1
GGA*AGAGAU	1
AGA*GACGAA	1
GGA*UGUGAA	1
GGA*UGCGAA	1
CGA*GACGAA	1
GGA*GGAGAA	1
GGA*AUGGAA	1
GGA*GUUGAA	1

Release history

Release	3.62	3.63	3.64	3.65	3.66	3.67	3.68	3.69	3.70	3.71	3.72	3.73	3.74	3.75	3.76
Date	2022-10-12	2022-11-09	2022-12-07	2023-01-04	2023-02-01	2023-03-01	2023-03-29	2023-04-26	2023-05-24	2023-06-21	2023-07-19	2023-08-16	2023-09-13	2023-10-11	2023-11-08
Status	Updated, 1 parent	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: Kink-turn (27)
Kink-turn with non-sequential stacking (5)
Basepair signature: cWW-tSH-tSH-tHS-tSS-R-cWW
Heat map statistics: Min 0.07 | Avg 0.44 | Max 0.79

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