Motif HL_98984.4 Version HL_98984.4 of this group appears in releases 3.86 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	1-3
1	HL_3WQY_001	3WQY	0.4417	6		C	tRNA	C	1613	A	1614	G	1622	cWW
2	HL_4V9K_033	4V9K	0.3866	8	tRNA D-loop	AW	tRNA	C	13	A	14	G	22	cWW
3	HL_6F4G_001	6F4G	0.2572	10		C	U2-SL4	U	8	A	9	G	20	cWW
4	HL_8G9Z_001	8G9Z	0.0959	3		E	Selenocysteine transfer RNA	G	15\|\|A	U	16\|\|A	C	20\|\|A\|A	cWW
5	HL_8GXB_002	8GXB	0.0834	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	NAD+ II riboswitch	C	23	A	24	G	34	cWW
6	HL_7QR3_002	7QR3	0.1003	9	U1 small nuclear ribonucleoprotein A binding hairpin	C	Mammalian CPEB3 ribozyme	C	43	A	44	G	54	cWW
7	HL_7DLZ_001	7DLZ	0.1183	9	U1 small nuclear ribonucleoprotein A binding hairpin	X	RNA (45-MER)	C	18	A	19	G	29	cWW
8	HL_6F4H_002	6F4H	0.1481	9	U1 small nuclear ribonucleoprotein A binding hairpin	D	U1-SL2	C	6	A	7	G	17	cWW
9	HL_6F4H_001	6F4H	0.1231	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	U1-SL2	C	6	A	7	G	17	cWW
10	HL_8C3A_006	8C3A	0.0000	2		1	LSU rRNA	C	207	A	208	G	211	cWW
11	HL_5TBW_006	5TBW	0.0636	2		1	LSU rRNA	C	208	A	209	G	212	cWW
12	HL_7QR4_002	7QR4	0.1277	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	Mammalian CPEB3 ribozyme	C	43	A	44	G	54	cWW
13	HL_1U6B_003	1U6B	0.2709	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	197-MER	C	1002	A	1003	G	1013	cWW
14	HL_3HHN_008	3HHN	0.1764	9	U1 small nuclear ribonucleoprotein A binding hairpin	E	Class I ligase ribozyme, self-ligation product	C	1004	A	1005	G	1015	cWW
15	HL_3CUL_002	3CUL	0.1236	9	U1 small nuclear ribonucleoprotein A binding hairpin	C	RNA (92-MER)	C	29	A	30	G	40	cWW
16	HL_5DDO_004	5DDO	0.1635	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	L-glutamine riboswitch (58-MER)	C	34	A	35	G	45	cWW
17	HL_5DDO_002	5DDO	0.1451	9	U1 small nuclear ribonucleoprotein A binding hairpin	A	L-glutamine riboswitch (58-MER)	C	34	A	35	G	45	cWW
18	HL_7VTI_001	7VTI	0.0734	4		B	crRNA	C	15	G	16	G	21	cWW
19	HL_3G9C_005	3G9C	0.1318	9	U1 small nuclear ribonucleoprotein A binding hairpin	Q	glmS ribozyme	C	17\|\|\|A	A	17\|\|\|B	G	17\|\|\|L	cWW
20	HL_5FJ4_002	5FJ4	0.1097	9	U1 small nuclear ribonucleoprotein A binding hairpin	H	HMKT-7	C	11	A	12	G	22	cWW
21	HL_8JY0_001	8JY0	0.0883	9	U1 small nuclear ribonucleoprotein A binding hairpin	B	RhoBAST	C	13	A	14	G	24	cWW
22	HL_4C4W_002	4C4W	0.1197	9	U1 small nuclear ribonucleoprotein A binding hairpin	H	TSKT-23	C	11	A	12	G	22	cWW
23	HL_6LAX_001	6LAX	0.0957	9	U1 small nuclear ribonucleoprotein A binding hairpin	A	SAM-VI (S-adenosyl methionine) riboswitch aptamer	C	15	A	16	G	26	cWW
24	HL_8GXB_001	8GXB	0.1212	9	U1 small nuclear ribonucleoprotein A binding hairpin	A	NAD+ II riboswitch	C	23	A	24	G	34	cWW
25	HL_8V1I_004	8V1I	0.1136	3		B	MALAT1-associated small cytoplasmic RNA/MEN beta RNA	G	10	G	11	C	16	cWW
26	HL_7D7V_001	7D7V	0.1700	9	U1 small nuclear ribonucleoprotein A binding hairpin	A	nadA RNA	C	27	A	28	G	38	cWW
27	HL_5DDP_002	5DDP	0.1425	9	U1 small nuclear ribonucleoprotein A binding hairpin	A	glnA	C	34	A	35	G	45	cWW
28	HL_4PKD_001	4PKD	0.1661	9	U1 small nuclear ribonucleoprotein A binding hairpin	V	U1 snRNA stem-loops 1 and 2 (55-MER)	C	64	A	65	G	75	cWW
29	HL_5AMQ_001	5AMQ	0.2280	4		C	RNA	U	3	A	4	A	9	cWW
30	HL_3IWN_002	3IWN	0.1358	9		A	C-di-GMP riboswitch	C	57	A	58	G	68	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CAUUGCACUCCG	19
CAUUGCACCUCG	2
CAGCGGGAG	1
CAGUUGGUUAG	1
UAUUGCAGUACCG	1
GUGGUC	1
CACAG	1
CAUAG	1
CGAUUUG	1
GGUGGC	1
UAGUGUA	1

Non-Watson-Crick part of the motif

Sequence	Counts
AUUGCACUCC	19
AUUGCACCUC	2
AGCGGGA	1
AGUUGGUUA	1
AUUGCAGUACC	1
UGGU	1
ACA	1
AUA	1
GAUUU	1
GUGG	1
AGUGU	1

Release history

Release	3.86
Date	2024-07-17
Status	Updated, 1 parent

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: U1 small nuclear ribonucleoprotein A binding hairpin (20)
(9)
tRNA D-loop (1)
Basepair signature: cWW-F
Heat map statistics: Min 0.05 | Avg 0.28 | Max 0.93

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