Motif HL_01609.3 Version HL_01609.3 of this group appears in releases 3.95 to 3.99

Download

Csv

Json

Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name for chain		1		2		3		4		5		6		7	1-7	2-6
1	HL_8CRE_224	8CRE	0.5676	2	T-loop with 1 bulged base	CM	SSU rRNA	G	1581	U	1582	C	1583	U	1585	C	1586	A	1587	C	1589	cWW	tWH
2	HL_2A64_002	2A64	0.2734	1	T-loop with 2 stacked bulged bases	A	RNase P class B	C	69	U	70	G	71	A	72	G	73	A	74	G	76	cWW	tWH
3	HL_4WF9_010	4WF9	0.1579	1	T-loop with 2 stacked bulged bases	X	LSU rRNA	C	348	U	349	G	350	G	351	A	352	A	353	G	355	cWW	tWH
4	HL_9DFE_009	9DFE	0.1436	1	T-loop with 1 bulged base	1A	LSU rRNA	U	305	U	306	G	307	G	308	G	309	A	310	G	312	cWW	tWH
5	HL_5DH6_002	5DH6	0.0976	1	T-loop with 2 stacked bulged bases	A	Hammerhead ribozyme (type III)	C	27	U	28	G	29	G	30	G	31	A	32	G	34	cWW	tWH
6	HL_5J7L_142	5J7L	0.0000	1	T-loop with 2 stacked bulged bases	DA	LSU rRNA	C	305	U	306	G	307	G	308	A	309	A	310	G	312	cWW	tWH
7	HL_7A0S_010	7A0S	0.0975	1	T-loop with 1 bulged base	X	LSU rRNA	C	316	U	317	G	318	G	319	A	320	A	321	G	323	cWW	tWH
8	HL_4FRN_005	4FRN	0.1557	2	T-loop with 2 bulged bases not stacked	B	Cobalamin riboswitch	G	28	U	29	G	30	U	31	A	32	A	33	C	36	cWW	tWH
9	HL_4FRG_001	4FRG	0.1730	2	T-loop with 2 bulged bases not stacked	B	Cobalamin riboswitch	G	28	U	29	G	30	A	31	A	32	A	33	C	36	cWW	tWH
10	HL_6DN2_003	6DN2	0.1571	2	T-loop with 2 bulged bases not stacked	Y	RNA (56-MER)	G	68	U	69	G	70	A	71	A	72	A	73	C	76	cWW	tWH
11	HL_3F2X_004	3F2X	0.1694	2	T-loop with 2 bulged bases not stacked	X	FMN riboswitch (RFN element)	G	68	U	69	G	70	A	71	A	72	A	73	C	76	cWW	tWH
12	HL_3F2X_001	3F2X	0.1271	2	T-loop with 2 bulged bases not stacked	X	FMN riboswitch (RFN element)	G	17	U	18	G	19	A	20	A	21	A	22	C	25	cWW	tWH
13	HL_6DN2_001	6DN2	0.1329	2	T-loop with 2 bulged bases not stacked	X	RNA RIBOSWITCH	G	17	U	18	G	19	A	20	A	21	A	22	C	25	cWW	tWH
14	HL_4V9F_010	4V9F	0.1427	1	T-loop with 2 stacked bulged bases	0	LSU rRNA	U	312	U	313	G	314	G	315	A	316	A	317	A	319	cWW	tWH
15	HL_8P9A_117	8P9A	0.1788	1	T-loop with 1 bulged base	AR	LSU rRNA	U	194	U	195	G	196	G	197	A	198	A	199	A	201	cWW	tWH
16	HL_8CRE_005	8CRE	0.1817	1	T-loop with 1 bulged base	1	LSU rRNA	U	193	U	194	G	195	G	196	A	197	A	198	A	200	cWW	tWH
17	HL_3VJR_001	3VJR	0.3471	2	T-loop with 2 bulged bases not stacked	B	tRNA CCA-acceptor	G	13	U	14	U	15	C	16	G	17	A	18	C	21	cWW	tWH
18	HL_5X2G_003	5X2G	0.6947	2	T-loop related	B	sgRNA	G	73	U	74	U	75	C	77	A	78	A	79	C	81	cWW	tWH

3D structures

Complete motif including flanking bases

Sequence	Counts
GUGAAAUUC	5
CUGGAAAG	3
UUGGAACA	2
GUCAUCAGC	1
CUGAGAUG	1
UUGGGAAG	1
CUGGGAUG	1
GUGUAAUUC	1
UUGGAAUA	1
GUUCGAUCC	1
GUUACAAUC	1

Non-Watson-Crick part of the motif

Sequence	Counts
UGAAAUU	5
UGGAAA	3
UGGAAC	2
UCAUCAG	1
UGAGAU	1
UGGGAA	1
UGGGAU	1
UGUAAUU	1
UGGAAU	1
UUCGAUC	1
UUACAAU	1

Release history

Release	3.95	3.96	3.97	3.98	3.99
Date	2025-03-26	2025-04-23	2025-05-21	2025-06-18	2025-07-16
Status	Updated, 1 parent	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: T-loop with 2 bulged bases not stacked (7)
T-loop with 2 stacked bulged bases (5)
T-loop with 1 bulged base (5)
T-loop related (1)
Basepair signature: cWW-tWH-F-F-F
Heat map statistics: Min 0.07 | Avg 0.30 | Max 0.88

Help

Coloring options: Nucleotide numbers

Copyright 2026 BGSU RNA group. Page generated in 0.4873 s