Motif HL_01057.2 Version HL_01057.2 of this group appears in releases 3.85 to 3.86

Download

Csv

Json

Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2	1-2
1	HL_5NDH_001	5NDH	0.1148	4	Pseudoknot geometry with 3' bulge	A	RNA (16-mer)	G	6	C	11	cWW
2	HL_5VJ9_003	5VJ9	0.0000	4	Pseudoknot geometry with 3' bulge	C	RNA (16-mer)	G	6	C	11	cWW
3	HL_5NDI_002	5NDI	0.1262	4	Pseudoknot geometry with 3' bulge	B	RNA (20-mer)	G	8	C	13	cWW
4	HL_7RQB_041	7RQB	0.3439	4	Pseudoknot geometry with 3' bulge (H)	1A	LSU rRNA	C	1631	G	1635	cWW
5	HL_5TBW_022	5TBW	0.5421	4	Externally structured	1	LSU rRNA	C	958	G	963	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GACGAC	3
CAAGAG	1
CCUCAG	1

Non-Watson-Crick part of the motif

Sequence	Counts
ACGA	3
AAGA	1
CUCA	1

Release history

Release	3.85	3.86
Date	2024-06-19	2024-07-17
Status	Updated, 2 parents	Exact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: Pseudoknot geometry with 3' bulge (3)
Externally structured (1)
Pseudoknot geometry with 3' bulge (H) (1)
Basepair signature: cWW
Heat map statistics: Min 0.11 | Avg 0.27 | Max 0.58

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__8776898424440507__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8776898424440507__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://rna.bgsu.edu/rna3dhub/motif/view/HL_01057.2","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8776898424440507__","codePath":"https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8776898424440507","bgcolor":"white" }

setting document base to "https://rna.bgsu.edu/rna3dhub/motif/view/HL_01057.2"

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__8776898424440507__ 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