Motif HL_46680.1 Version HL_46680.1 of this group appears in releases 3.80 to 3.86

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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	1-5
1	HL_3V7E_001	3V7E	0.5169	2	Pseudoknot geometry	C	SAM-I riboswitch	G	23	U	26	G	27	G	28	C	29	cWW
2	HL_5FJC_001	5FJC	0.4547	2	Pseudoknot geometry	A	SAM-I riboswitch	G	23	U	26	G	27	G	28	C	29	cWW
3	HL_4AOB_001	4AOB	0.4374	2	Pseudoknot geometry	A	SAM-I riboswitch	G	23	U	26	G	27	G	28	C	29	cWW
4	HL_6MWN_004	6MWN	0.4358	2	Pseudoknot geometry	B	IRES	G	650	G	653	G	654	A	655	C	656	cWW
5	HL_4KQY_001	4KQY	0.3823	2	Pseudoknot geometry	A	SAM-I riboswitch	G	23	U	26	G	27	G	28	C	29	cWW
6	HL_6VMY_003	6VMY	0.4494	2	Pseudoknot geometry	A	Cobalamin riboswitch	G	268	C	271	C	272	G	273	C	274	cWW
7	HL_5U30_002	5U30	0.4146	2	Pseudoknot geometry	B	sgRNA	U	43	C	46	C	47	A	48	G	49	cWW
8	HL_1U6B_002	1U6B	0.3415	1	Pseudoknot geometry	B	197-MER	C	70	C	72	C	73	C	74	G	75	cWW
9	HL_5TBW_066	5TBW	0.0000	1	Ribsomal LSU H95	1	LSU rRNA	U	3068	A	3070	U	3071	C	3072	A	3073	cWW
10	HL_8C3A_067	8C3A	0.0844	1	Ribsomal LSU H95	1	LSU rRNA	U	3040	A	3042	U	3043	C	3044	A	3045	cWW
11	HL_4V9F_067	4V9F	0.1787	1	Ribsomal LSU H95	0	LSU rRNA	C	2737	A	2739	G	2740	A	2741	G	2742	cWW
12	HL_6UFM_005	6UFM	0.2338	1	Pseudoknot geometry	B	RNA (98-MER)	G	50	A	52	A	53	A	54	C	55	cWW
13	HL_5J7L_198	5J7L	0.2291	1	Ribsomal LSU H95	DA	LSU rRNA	U	2701	C	2703	C	2704	A	2705	A	2706	cWW
14	HL_7A0S_064	7A0S	0.2096	1	Ribsomal LSU H95	X	LSU rRNA	U	2680	C	2682	C	2683	A	2684	A	2685	cWW
15	HL_4WF9_061	4WF9	0.2513	1	Ribsomal LSU H95	X	LSU rRNA	U	2728	C	2730	C	2731	A	2732	A	2733	cWW
16	HL_4PQV_002	4PQV	0.4069	2	Pseudoknot geometry	A	Flavivirus 3' UTR stem loop IV	C	28	C	30	C	31	G	32	G	34	cWW
17	HL_7A0S_037	7A0S	0.6545	2		X	LSU rRNA	G	1508	A	1510	A	1511	A	1512	C	1514	ncWW
18	HL_5J7L_166	5J7L	0.7189	2	Pseudoknot geometry with 3' bulge	DA	LSU rRNA	G	1324	U	1326	A	1327	A	1328	C	1330	cWW
19	HL_4V9F_035	4V9F	0.6774	2	Pseudoknot geometry with 3' bulge	0	LSU rRNA	G	1430	U	1432	G	1433	A	1434	C	1436	cWW
20	HL_4WF9_033	4WF9	0.6768	2	Pseudoknot geometry with 3' bulge	X	LSU rRNA	G	1361	U	1363	C	1364	G	1365	C	1367	cWW
21	HL_7RQB_034	7RQB	0.7410	2	Pseudoknot geometry with 3' bulge (H)	1A	LSU rRNA	G	1324	U	1326	C	1327	G	1328	C	1330	cWW
22	HL_7A0S_033	7A0S	0.7562	2	Pseudoknot geometry with 3' bulge	X	LSU rRNA	G	1337	U	1339	C	1340	G	1341	C	1343	cWW
23	HL_8C3A_032	8C3A	0.8449	2	Pseudoknot geometry with 3' bulge	1	LSU rRNA	A	1502	C	1504	A	1505	G	1506	U	1508	cWW
24	HL_5TBW_032	5TBW	0.8300	2	Pseudoknot geometry with 3' bulge	1	LSU rRNA	A	1506	C	1508	A	1509	G	1510	U	1512	cWW
25	HL_5J7L_170	5J7L	0.7045	2	Pseudoknot geometry with 3' bulge	DA	LSU rRNA	G	1492	A	1494	A	1495	A	1496	C	1498	cWW
26	HL_7RQB_038	7RQB	0.6969	2	Pseudoknot geometry with 3' bulge (H)	1A	LSU rRNA	G	1492	A	1494	A	1495	A	1496	C	1498	cWW
27	HL_4OQU_002	4OQU	0.7559	4	Pseudoknot geometry	A	SAM-I/IV riboswitch	G	32	G	36	A	37	C	38	C	40	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GACUGGC	4
UGAUCA	2
UGCCAA	2
GGUCGUC	2
AGCAGUU	2
GCAAAUC	2
GCUGGAC	1
GUCCCGC	1
UUUCCAG	1
CGCCCG	1
CGAGAG	1
GGAAAC	1
UACCAA	1
CGCCGAG	1
GAAAAUC	1
GUUAAUC	1
GCUGAUC	1
GCUCGUC	1
GACGGACAC	1

Non-Watson-Crick part of the motif

Sequence	Counts
ACUGG	4
GAUC	2
GCCA	2
GUCGU	2
GCAGU	2
CAAAU	2
CUGGA	1
UCCCG	1
UUCCA	1
GCCC	1
GAGA	1
GAAA	1
ACCA	1
GCCGA	1
AAAAU	1
UUAAU	1
CUGAU	1
CUCGU	1
ACGGACA	1

Release history

Release	3.80	3.81	3.82	3.83	3.84	3.85	3.86
Date	2024-01-31	2024-02-28	2024-03-27	2024-04-24	2024-05-22	2024-06-19	2024-07-17
Status	New id, 2 parents	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: Pseudoknot geometry (11)
Pseudoknot geometry with 3' bulge (7)
Ribsomal LSU H95 (6)
Pseudoknot geometry with 3' bulge (H) (2)
(1)
Basepair signature: cWW-F-F-F
Heat map statistics: Min 0.06 | Avg 0.54 | Max 0.94

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