Motif HL_22280.4 Version HL_22280.4 of this group appears in releases 3.86 to 3.86

Download

Csv

Json

Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	Annotation	Chain(s)	Standardized name		1		2		3		4		5		6		7		8		9	1-9	2-6
1	HL_4V9K_035	4V9K	0.4071	T-loop with 2 stacked bulged bases	AW	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	A	59	U	60	C	61	cWW	ntWH
2	HL_3WFS_003	3WFS	0.1995	T-loop with 2 stacked bulged bases	A	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	U	60	C	61	cWW	tWH
3	HL_7UZ0_003	7UZ0	0.1858	T-loop with 2 stacked bulged bases	A	tRNA	G	68	U	69	U	70	C	71	G	72	A	73	G	74	U	75	C	76	cWW	tWH
4	HL_4TUE_035	4TUE	0.2090	T-loop with 2 stacked bulged bases	QV	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	ncWW	tWH
5	HL_4GCW_002	4GCW	0.1800	T-loop with 2 stacked bulged bases	B	TRNA(THR)	G	53	U	54	U	55	C	56	G	57	A	58	G	59	C	60	C	61	cWW	tWH
6	HL_7EQJ_006	7EQJ	0.1648	T-loop with 2 stacked bulged bases	B	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	C	60	C	61	cWW	tWH
7	HL_6CU1_001	6CU1	0.2242	T-loop with 2 stacked bulged bases	A	Y RNA-like	G	24	U	25	U	26	C	27	G	28	A	29	G	30	A	31	C	32	cWW	tWH
8	HL_7K98_003	7K98	0.1980	T-loop with 2 stacked bulged bases	C	tRNA	G	54	U	55	U	56	C	57	G	58	A	59	U	60	C	61	C	62	cWW	tWH
9	HL_1U0B_003	1U0B	0.2090	T-loop with 2 stacked bulged bases	A	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	C	59	U	60	C	61	cWW	tWH
10	HL_1QU2_003	1QU2	0.1961	T-loop with 2 stacked bulged bases	T	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	G	59	U	60	C	61	cWW	tWH
11	HL_6PMO_005	6PMO	0.1790	T-loop with 2 stacked bulged bases	B	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	A	59	U	60	C	61	cWW	tWH
12	HL_4V90_034	4V90	0.2166	T-loop with 2 stacked bulged bases	AV	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	U	60	C	61	cWW	tWH
13	HL_4V87_109	4V87	0.2639	T-loop with 2 stacked bulged bases	BB	tRNA	G	64	U	65	U	66	C	67	A	68	A	69	G	70	U	71	C	72	cWW	ntWH
14	HL_5B63_004	5B63	0.2111	T-loop with 2 stacked bulged bases	D	tRNA	G	954	U	955	U	956	C	957	G	958	A	959	A	960	U	961	C	962	cWW	tWH
15	HL_2AZX_006	2AZX	0.0000	T-loop with 2 stacked bulged bases	D	72-MER	G	553	U	554	U	555	C	556	G	557	A	558	A	559	U	560	C	561	ncWW	tWH
16	HL_7UQ6_003	7UQ6	0.1528	T-loop with 2 stacked bulged bases	B	tRNA	G	64	U	65	U	66	C	67	G	68	A	69	G	70	U	71	C	72	cWW	tWH
17	HL_7YSE_003	7YSE	0.1746	T-loop with 2 stacked bulged bases	E	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	G	59	U	60	C	61	cWW	tWH
18	HL_1J2B_002	1J2B	0.2778	T-loop with 2 stacked bulged bases	C	tRNA(Val)	G	954	U	955	U	956	C	957	A	958	A	959	G	960	U	961	C	962	cWW	tWH
19	HL_2CSX_003	2CSX	0.2481	T-loop with 2 stacked bulged bases	C	RNA (75-MER)	G	53	U	54	U	55	C	56	G	57	A	58	G	59	U	60	C	61	cWW	tWH
20	HL_1GAX_006	1GAX	0.4827	T-loop with 2 stacked bulged bases	D	TRNA(VAL)	G	952	U	953	U	954	C	955	A	956	A	957	G	958	U	959	C	960	cWW	tWH
21	HL_4V8N_145	4V8N	0.2367	T-loop with 2 stacked bulged bases	CV	tRNA	G	55	U	56	U	57	C	58	G	59	A	60	A	61	U	62	C	63	cWW	tWH
22	HL_4WJ4_003	4WJ4	0.1604	T-loop with 2 stacked bulged bases	B	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	G	59	U	60	C	61	cWW	tWH
23	HL_7LYF_003	7LYF	0.1504	T-loop with 2 stacked bulged bases	A	Dengue virus SLA	G	116	U	117	U	118	C	119	A	120	A	121	G	122	U	123	C	124	cWW	tWH
24	HL_8UO6_008	8UO6	0.1666	T-loop with 2 stacked bulged bases	B	HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold	G	111	U	112	U	113	C	114	A	115	A	116	G	117	U	118	C	119	cWW	tWH
25	HL_8UO6_004	8UO6	0.1444	T-loop with 2 stacked bulged bases	A	HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold	G	111	U	112	U	113	C	114	A	115	A	116	G	117	U	118	C	119	cWW	tWH
26	HL_3AL0_003	3AL0	0.1650	T-loop with 2 stacked bulged bases	E	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	G	59	U	60	C	61	cWW	tWH
27	HL_6UFM_003	6UFM	0.1656	T-loop with 2 stacked bulged bases	A	tRNA	G	54	U	55	U	56	C	57	G	58	A	59	G	60	U	61	C	62	cWW	tWH
28	HL_4RDX_003	4RDX	0.1543	T-loop with 2 stacked bulged bases	C	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	G	59	U	60	C	61	cWW	tWH
29	HL_7KJT_003	7KJT	0.1687	T-loop with 2 stacked bulged bases	A	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	cWW	tWH
30	HL_2ZUE_003	2ZUE	0.1692	T-loop with 2 stacked bulged bases	B	tRNA-Arg	G	953	U	954	U	955	C	956	A	957	A	958	A	959	U	960	C	961	cWW	tWH
31	HL_5AH5_008	5AH5	0.1462	T-loop with 2 stacked bulged bases	D	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	G	59	U	60	C	61	cWW	tWH
32	HL_2BTE_004	2BTE	0.1894	T-loop with 2 stacked bulged bases	B	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	G	59	U	60	C	61	cWW	tWH
33	HL_4JXZ_003	4JXZ	0.1813	T-loop with 2 stacked bulged bases	B	tRNA	G	953	U	954	U	955	C	956	G	957	A	958	A	959	U	960	C	961	cWW	tWH
34	HL_1J1U_003	1J1U	0.1743	T-loop with 2 stacked bulged bases	B	tRNA(Tyr)	G	554	U	555	U	556	C	557	A	558	A	559	A	560	U	561	C	562	cWW	tWH
35	HL_4YCO_003	4YCO	0.1459	T-loop with 2 stacked bulged bases	D	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	U	60	C	61	cWW	tWH
36	HL_5AXM_003	5AXM	0.1599	T-loop with 2 stacked bulged bases	P	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	C	60	C	61	cWW	tWH
37	HL_7MRL_003	7MRL	0.1520	T-loop with 2 stacked bulged bases	A	tRNA	G	56	U	57	U	58	C	59	A	60	A	61	G	62	U	63	C	64	cWW	tWH
38	HL_5X6B_003	5X6B	0.1957	T-loop with 2 stacked bulged bases	P	tRNA	G	52	U	53	U	54	C	55	A	56	A	57	A	58	U	59	C	60	cWW	tWH
39	HL_2ZZM_004	2ZZM	0.2158	T-loop with 2 stacked bulged bases	B	RNA (84-MER)	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	cWW	tWH
40	HL_5HR6_003	5HR6	0.1912	T-loop with 2 stacked bulged bases	C	tRNA	G	52	U	53	U	54	C	55	G	56	A	57	A	58	U	59	C	60	cWW	tWH
41	HL_5HR7_006	5HR7	0.1689	T-loop with 2 stacked bulged bases	D	tRNA	G	52	U	53	U	54	C	55	G	56	A	57	A	58	U	59	C	60	cWW	tWH
42	HL_4YYE_003	4YYE	0.1695	T-loop with 2 stacked bulged bases	C	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	cWW	tWH
43	HL_1QTQ_003	1QTQ	0.1827	T-loop with 2 stacked bulged bases	B	tRNA	G	953	U	954	U	955	C	956	G	957	A	958	A	959	U	960	C	961	cWW	tWH
44	HL_7E8O_003	7E8O	0.1698	T-loop with 2 stacked bulged bases	X	tRNA	G	52	U	53	U	54	C	55	G	56	A	57	A	58	U	59	C	60	cWW	tWH
45	HL_3WQY_003	3WQY	0.1428	T-loop with 2 stacked bulged bases	C	tRNA	G	1653	U	1654	U	1655	C	1656	A	1657	A	1658	A	1659	U	1660	C	1661	cWW	tWH
46	HL_2ZZN_006	2ZZN	0.1568	T-loop with 2 stacked bulged bases	D	RNA (71-MER)	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	cWW	tWH
47	HL_8V1H_002	8V1H	0.3228	T-loop with 2 stacked bulged bases	A	MALAT1-associated small cytoplasmic RNA/MEN beta RNA	G	38	U	39	U	40	C	41	A	42	A	43	A	44	U	45	C	46	cWW	tWH
48	HL_8S95_005	8S95	0.1743	T-loop with 2 stacked bulged bases	C	Enterovirus 5' cloverleaf cis-acting replication element	G	133	U	134	U	135	C	136	A	137	A	138	G	139	U	140	C	141	cWW	tWH
49	HL_4WT8_217	4WT8	0.1780	T-loop with 2 stacked bulged bases	D4	tRNA	G	54	U	55	U	56	C	57	A	58	A	59	A	60	U	61	C	62	cWW	tWH
50	HL_4V9Q_215	4V9Q	0.1772	T-loop with 2 stacked bulged bases	DV	tRNA	G	53	U	54	U	55	C	56	A	57	A	58	A	59	U	60	C	61	cWW	tWH
51	HL_1WZ2_008	1WZ2	0.2060	T-loop with 2 stacked bulged bases	D	tRNA	G	965	U	966	U	967	C	968	G	969	A	970	A	971	U	972	C	973	cWW	tWH
52	HL_3AMU_003	3AMU	0.2225	T-loop with 2 stacked bulged bases	B	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	A	59	U	60	C	61	cWW	tWH
53	HL_2D6F_006	2D6F	0.2283	T-loop with 2 stacked bulged bases	F	tRNA	G	953	U	954	U	955	C	956	G	957	A	958	C	959	U	960	C	961	cWW	tWH
54	HL_5UD5_003	5UD5	0.2407	T-loop with 2 stacked bulged bases	C	tRNA	G	53	U	54	U	55	A	56	G	57	A	58	U	59	U	60	C	61	cWW	tWH
55	HL_2DRA_001	2DRA	0.2692	T-loop with 2 stacked bulged bases	B	tRNA (34-MER)	G	12	U	13	U	14	C	15	G	16	A	17	U	18	U	19	C	20	cWW	tWH
56	HL_7MDL_004	7MDL	0.2100	T-loop with 2 stacked bulged bases	E	Selenocysteine transfer RNA	G	53\|\|A	U	54\|\|A	U	55\|\|A	C	56\|\|A	A	57\|\|A	A	58\|\|A	U	59\|\|A	U	60\|\|A	C	61\|\|A	cWW	tWH
57	HL_3OVB_001	3OVB	0.2471	T-loop with 2 stacked bulged bases	C	RNA (35-MER)	G	12	U	13	U	14	C	15	A	16	A	17	G	18	U	19	C	20	cWW	tWH
58	HL_3VJR_001	3VJR	0.3119	T-loop with 2 bulged bases not stacked	B	tRNA CCA-acceptor	G	13	U	14	U	15	C	16	G	17	A	18	U	19	C	20	C	21	cWW	tWH
59	HL_6NWY_035	6NWY	0.3322	T-loop with 2 stacked bulged bases	QV	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	A	59	U	60	C	61	cWW	ntWH
60	HL_2ZNI_003	2ZNI	0.3686	T-loop with 2 stacked bulged bases	C	bacterial tRNA	G	53	U	54	G	55	A	56	A	57	A	58	C	59	U	60	C	61	cWW	tWH
61	HL_6ORD_037	6ORD	0.4743	T-loop with 2 stacked bulged bases	QY	tRNA	G	53	U	54	U	55	C	56	G	57	A	58	U	59	C	60	C	61	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GUUCGAAUC	13
GUUCAAGUC	13
GUUCAAAUC	12
GUUCGAGUC	7
GUUCGAUCC	5
GUUCGAUUC	4
GUUCGACUC	2
GUUCGAGCC	1
GUUCGAGAC	1
GUUAGAUUC	1
GUUCAAUUC	1
GUGAAACUC	1

Non-Watson-Crick part of the motif

Sequence	Counts
UUCGAAU	13
UUCAAGU	13
UUCAAAU	12
UUCGAGU	7
UUCGAUC	5
UUCGAUU	4
UUCGACU	2
UUCGAGC	1
UUCGAGA	1
UUAGAUU	1
UUCAAUU	1
UGAAACU	1

Release history

Release	3.86
Date	2024-07-17
Status	Updated, 2 parents

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: T-loop with 2 stacked bulged bases (60)
T-loop with 2 bulged bases not stacked (1)
Basepair signature: cWW-tWH-F-F-F-F-F
Heat map statistics: Min 0.06 | Avg 0.21 | Max 0.81

Help

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/package.js

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/corejmol.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__8576354335022445__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8576354335022445__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://rna.bgsu.edu/rna3dhub/motif/view/HL_22280.4","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8576354335022445__","codePath":"https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8576354335022445","bgcolor":"white" }

setting document base to "https://rna.bgsu.edu/rna3dhub/motif/view/HL_22280.4"

Jmol Version: 14.4.4_2016.04.25 2016-04-26 17:41

java.vendor: Java2Script (HTML5)

java.version: 2016-04-21 14:47:41 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/corescript.z.js

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__8576354335022445__ ready

script 1 started

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/coretext.z.js

Script completed

Jmol script terminated

script 2 started

Script completed

Jmol script terminated

script 3 started

Script completed

Jmol script terminated

script 4 started

Script completed

Jmol script terminated

Coloring options: Nucleotide numbers

Motif HL_22280.4 Version HL_22280.4 of this group appears in releases 3.86 to 3.86 Download Csv Json

3D structures

Complete motif including flanking bases

Non-Watson-Crick part of the motif

Release history

Parent motifs

Children motifs

Motif HL_22280.4 Version HL_22280.4 of this group appears in releases 3.86 to 3.86

Download

Csv

Json