IL_05642.6

#S	Loop id	PDB	Disc	Annotation	Chain(s)	Standardized name for chain		1		2		3	break		4		5	1-5	3-4
1	IL_9E6Q_038	9E6Q	1.4258	Single bulged C	1	LSU rRNA	U	1032	C	1033	C	1034	*	G	981	A	982	cWW	cWW
2	IL_7A0S_025	7A0S	1.3076	Single bulged C	X	LSU rRNA	G	938	C	939	G	940	*	C	863	C	864	cWW	ncWW
3	IL_8GLP_136	8GLP	0.7545	Single bulged C	L5	LSU rRNA	G	4095	C	4096	G	4097	*	C	4112	U	4113	cWW	cWW
4	IL_8GLP_023	8GLP	0.9191	Single bulged C	L5	LSU rRNA	G	448	C	449	G	450	*	U	1297	C	1298	cWW	cWW
5	IL_9H3G_141	9H3G	0.8226	Single bulged C	A	LSU rRNA	A	3305	C	3306	G	3307	*	C	3375	U	3376	cWW	cWW
6	IL_8B0X_130	8B0X	0.5847	Single bulged C	a	LSU rRNA	G	1733	C	1734	G	1735	*	C	1729	C	1730	cWW	cWW
7	IL_7A0S_010	7A0S	0.7730	Single bulged C	X	LSU rRNA	G	558	C	559	G	560	*	C	552	C	553	cWW	cWW
8	IL_8GLP_269	8GLP	0.6176	Single bulged C	S2	SSU rRNA	G	1422	C	1423	G	1424	*	C	1416	C	1417	cWW	cWW
9	IL_8GLP_055	8GLP	0.6842	Single bulged C	L5	LSU rRNA	G	1484	C	1485	C	1486	*	G	1479	C	1480	cWW	cWW
10	IL_9H3G_080	9H3G	0.4165	Single bulged C	A	LSU rRNA	G	1742	C	1743	G	1744	*	C	1702	U	1703	cWW	cWW
11	IL_5F5H_002	5F5H	0.4918	Single bulged C	D	RNA (21-mer)	G	18	C	19	U	20	*	A	4	C	5	cWW	cWW
12	IL_5F5H_001	5F5H	0.4756	Single bulged C	C	RNA (21-mer)	G	18	C	19	U	20	*	A	4	C	5	cWW	cWW
13	IL_1S03_002	1S03	0.4458	Single bulged C	A	47-MER	G	9	C	10	G	11	*	C	39	C	40	cWW	cWW
14	IL_7KGA_001	7KGA	0.5234	Single bulged C	A	Flavivirus DB element	A	44	C	45	U	46	*	A	10	U	11	cWW	cWW
15	IL_9M86_004	9M86	0.3481	Single bulged C	D	RNA (31-MER)	A	72	C	73	U	74	*	A	50	U	51	cWW	cWW
16	IL_6ZDP_001	6ZDP	0.4953	Single bulged C	B	Chains: B	A	1346	C	1347	U	1348	*	A	1290	U	1291	cWW	cWW
17	IL_8GLP_178	8GLP	0.4354	Single bulged C	L5	LSU rRNA	G	5012	C	5013	A	5014	*	U	5035	C	5036	cWW	cWW
18	IL_6XKO_001	6XKO	0.3790	Single bulged C	A	PreQ1-III riboswitch	G	78	C	79	G	80	*	C	56	C	57	cWW	cWW
19	IL_8GLP_001	8GLP	0.3119	Single bulged C	L8+L5	5.8S rRNA	G	149	C	150	G	151	*	C	6	C	7	cWW	cWW
20	IL_7A0S_032	7A0S	0.1265	Single bulged C	X	LSU rRNA	U	1005	C	1006	A	1007	*	U	1170	A	1171	cWW	cWW
21	IL_8B0X_096	8B0X	0.1191	Single bulged C	a	LSU rRNA	C	996	C	997	A	998	*	U	1161	G	1162	cWW	cWW
22	IL_9DFE_034	9DFE	0.0000	Single bulged C	1A	LSU rRNA	C	994	C	995	A	996	*	U	1159	G	1160	cWW	cWW
23	IL_4WF9_035	4WF9	0.1704	Single bulged C	X	LSU rRNA	C	1038	C	1039	A	1040	*	U	1203	G	1204	cWW	cWW
24	IL_7KGA_004	7KGA	0.2057	Single bulged C	B	Flavivirus DB element	A	44	C	45	U	46	*	A	10	U	11	cWW	cWW
25	IL_7PMM_001	7PMM	0.4022	Single bulged C	D	RNA (45mer) containing HP92 of the 23S rRNA	U	33	C	34	G	35	*	C	13	A	14	cWW	cWW
26	IL_8GLP_009	8GLP	0.3427	Single bulged C	L5	LSU rRNA	G	142	C	143	G	144	*	C	125	C	126	cWW	cWW
27	IL_8GLP_015	8GLP	0.4560	Single bulged C	L5	LSU rRNA	G	244	C	245	G	246	*	C	195	C	196	cWW	cWW
28	IL_8GLP_172	8GLP	0.4273	Single bulged C	L5	LSU rRNA	G	4899	C	4900	G	4901	*	C	4920	C	4921	cWW	cWW
29	IL_1S03_006	1S03	0.2971	Single bulged C	B	47-MER	G	9	C	10	G	11	*	C	39	C	40	cWW	cWW
30	IL_9SUM_176	9SUM	0.3885		CA	SSU rRNA	G	789	C	790	A	791	*	U	821	C	822	cWW	cWW
31	IL_9H3G_169	9H3G	0.4310	Single bulged C	h1	SSU rRNA	U	260	C	261	G	262	*	C	202	A	203	cWW	cWW
32	IL_8GLP_024	8GLP	0.6258	Single bulged C	L5	LSU rRNA	G	695	C	696	G	697	*	C	459	C	460	cWW	cWW
33	IL_3W3S_001	3W3S	0.5901	Single bulged C	B	Selenocysteine transfer RNA	G	11	C	11\|\|\|A	C	12	*	G	23	C	24	cWW	cWW
34	IL_8QYX_165	8QYX	0.7042	Single bulged C	B2	5S rRNA	U	62	C	63	G	64	*	C	15	A	16	cWW	cWW
35	IL_8GLP_044	8GLP	0.5611	Single bulged C	L5	LSU rRNA	U	1209	C	1210	G	1211	*	C	1086	A	1087	cWW	cWW
36	IL_9E6Q_083	9E6Q	0.6511	Single bulged C	1	LSU rRNA	G	2516	C	2517	C	2518	*	G	2532	C	2533	cWW	cWW
37	IL_3SN2_001	3SN2	0.6479	Single bulged C	B	IRE II	U	7	C	8	G	9	*	C	24	A	25	cWW	cWW
38	IL_3SNP_003	3SNP	0.6255	Single bulged C	D	IRE	G	7	C	8	U	9	*	A	24	C	25	cWW	cWW
39	IL_7A0S_055	7A0S	0.5129	Single bulged C	X	LSU rRNA	G	1488	C	1489	U	1490	*	A	1534	C	1535	cWW	cWW
40	IL_8OI5_071	8OI5	0.4731	Single bulged C	1	LSU rRNA	G	1774	C	1775	G	1776	*	C	1665	C	1666	cWW	cWW
41	IL_9SUM_064	9SUM	0.4716	Single bulged C (H)	A	LSU rRNA	G	1721	C	1722	G	1723	*	C	1609	C	1610	cWW	cWW
42	IL_9PN5_068	9PN5	0.4973	Single bulged C	A1	LSU rRNA	G	1778	C	1779	G	1780	*	C	1669	C	1670	cWW	cWW
43	IL_9H3G_076	9H3G	0.4781	Single bulged C	A	LSU rRNA	G	1780	C	1781	G	1782	*	C	1669	C	1670	cWW	cWW
44	IL_9AXU_065	9AXU	0.4753	Single bulged C	2	LSU rRNA	G	1819	C	1820	G	1821	*	C	1704	C	1705	cWW	cWW
45	IL_9H3G_145	9H3G	0.3667	Single bulged C	A	LSU rRNA	G	3327	C	3328	A	3329	*	U	3350	C	3351	cWW	cWW
46	IL_9DE7_001	9DE7	0.4087	Single bulged C	A	RNA (58-MER)	U	4	C	5	U	6	*	A	55	A	56	cWW	cWW
47	IL_5KPY_001	5KPY	0.5215	Single bulged C	A	5-hydroxytryptophan RNA aptamer	U	25	C	26	G	27	*	C	43	A	44	cWW	cWW
48	IL_6CK5_003	6CK5	0.5289	Single bulged C	A	Guanidine-I riboswitch	U	39	C	40	G	41	*	C	21	A	22	cWW	cWW
49	IL_3HHN_003	3HHN	0.3784	Single bulged C	E	Class I ligase ribozyme, self-ligation product	G	46	C	47	U	48	*	A	112	C	113	cWW	cWW
50	IL_8F5G_002	8F5G	0.4334	Single bulged C	D	RNA	G	8	C	9	U	10	*	A	19	C	20	cWW	cWW
51	IL_3IVK_001	3IVK	0.4647	Single bulged C	M	class I ligase product	G	46	C	47	U	48	*	A	112	C	113	ncWW	cWW
52	IL_9PN5_142	9PN5	0.4082	Single bulged C	B5	SSU rRNA	U	24	C	25	A	26	*	U	600	A	601	cWW	cWW
53	IL_9H3G_155	9H3G	0.4996	Single bulged C	h1	SSU rRNA	U	24	C	25	A	26	*	UY1	602	A	603	cWW	cWW
54	IL_9SUM_137	9SUM	0.4112	Single bulged C (H)	CA	SSU rRNA	U	24	C	25	A	26	*	U	589	A	590	cWW	cWW
55	IL_8CRE_390	8CRE	0.6567	Single bulged C	CM	SSU rRNA	U	24	C	25	A	26	*	U	598	A	599	cWW	cWW
56	IL_8GLP_078	8GLP	0.7776	Single bulged C	L5	LSU rRNA	C	1920	C	1921	G	1922	*	C	2062	G	2063	cWW	cWW
57	IL_3DIL_001	3DIL	0.6151	Single bulged C	A	Lysine riboswitch	G	12	C	13	G	14	*	C	78	C	79	cWW	cWW
58	IL_3D0U_001	3D0U	0.7333	Single bulged C	A	Lysine riboswitch	G	9	C	10	G	11	*	C	75	C	76	cWW	cWW
59	IL_8GLP_165	8GLP	0.6804	Single bulged C	L5	LSU rRNA	G	4740	C	4741	G	4742	*	C	4958	U	4959	cWW	cWW
60	IL_4C7O_003	4C7O	0.8098	Single bulged C	E	SRP RNA	C	31	C	32	G	33	*	C	12	G	13	cWW	cWW
61	IL_8GLP_083	8GLP	0.9576	Single bulged C	L5	LSU rRNA	C	2083	C	2084	G	2085	*	C	2272	G	2273	cWW	cWW
62	IL_3SN2_002	3SN2	1.1555	Single bulged C	B	IRE II	G	18	C	19	C	20	*	G	13	C	14	cWW	cWW
63	IL_9SUM_136	9SUM	0.7361	Single bulged U (H)	C	5.8S rRNA	U	86	C	87	A	88	*	U	67	A	68	cWW	cWW
64	IL_8OI5_142	8OI5	0.8071	Single bulged C	4	5.8S rRNA	U	90	C	91	A	92	*	U	67	A	68	cWW	cWW
65	IL_8OI5_002	8OI5	0.7521	Single bulged C	4+1	5.8S rRNA	G	150	C	151	G	152	*	C	6	C	7	cWW	cWW
66	IL_9PN5_001	9PN5	0.7424	Single bulged C	A4+A1	5.8S rRNA	G	150	C	151	G	152	*	C	7	C	8	cWW	cWW
67	IL_9SUM_001	9SUM	0.7542	Single bulged C (H)	C+A	5.8S rRNA	G	146	C	147	G	148	*	C	5	C	6	cWW	cWW
68	IL_9E6Q_047	9E6Q	0.9295	Single bulged C	1	LSU rRNA	G	1158	C	1159	G	1160	*	C	1247	C	1248	cWW	cWW
69	IL_9TKV_001	9TKV	0.6361	Single bulged C	R	31-mer RNA hairpin with 5'pppG-C blunt end mimicking the influenza B virus vRNA promoter (panhandle)	G	23	C	24	U	25	*	A	8	C	9	cWW	cWW
70	IL_1KUQ_002	1KUQ	1.0063	Single bulged C	B	16S RIBOSOMAL RNA FRAGMENT	C	46	C	47	C	48	*	G	21	G	22	cWW	cWW
71	IL_9DFE_107	9DFE	1.4563	Major groove intercalation	1A	LSU rRNA	U	2878	C	2879	C	2880	*	G	2838	G	2839	cWW	cWW
72	IL_8GLP_174	8GLP	1.5924	Single bulged C	L5	LSU rRNA	U	5053	C	5054	G	5055	*	C	4996	G	4997	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GCG*CC	23
GCU*AC	8
UCG*CA	7
UCA*UA	6
GCC*GC	4
ACU*AU	4
GCG*CU	3
GCA*UC	3
CCA*UG	3
CCG*CG	3
UCC*GA	1
GCG*UC	1
ACG*CU	1
UCU*AA	1
UCA*(UY1)A	1
CCC*GG	1
UCC*GG	1
UCG*CG	1

Non-Watson-Crick part of the motif

Sequence	Counts
C*	72

Release history

Release	4.14
Date	2026-09-09
Status	Updated, 1 parent

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Motif IL_05642.6 Version IL_05642.6 of this group appears in releases 4.14 to 4.14 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_05642.6 Version IL_05642.6 of this group appears in releases 4.14 to 4.14

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