Motif IL_13730.8 Version IL_13730.8 of this group appears in releases 3.45 to 3.47

Download

Csv

Json

Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2	break		3		4	1-4	2-3
1	IL_4Y4O_273	4Y4O	0.7278	2	Multiple bulged bases	2A	LSU rRNA	C	2512	G	2513	*	C	2571	G	2574	cWW	cWW
2	IL_4IOA_092	4IOA	0.7110	2	Multiple bulged bases	X	LSU rRNA	C	2491	G	2492	*	C	2550	G	2553	cWW	cWW
3	IL_3IGI_013	3IGI	0.5631	2	Multiple bulged bases	A	Group IIC intron	U	365	A	366	*	U	375	G	378	cWW	cWW
4	IL_1KXK_003	1KXK	0.4647	2	Multiple bulged bases	A	ai5g group II Self-splicing intron	U	28	G	29	*	C	42	G	45	cWW	cWW
5	IL_4WF9_103	4WF9	0.3920	2	Multiple bulged bases	X	LSU rRNA	U	2722	U	2723	*	A	2738	G	2741	cWW	cWW
6	IL_5J7L_349	5J7L	0.3920	2	Multiple bulged bases	DA	LSU rRNA	U	2695	U	2696	*	A	2711	G	2714	cWW	cWW
7	IL_5TBW_119	5TBW	0.5455	2	Multiple bulged bases	1	LSU rRNA	C	3063	U	3064	*	A	3077	G	3080	cWW	cWW
8	IL_5TBW_109	5TBW	0.6785	2	Multiple bulged bases	1	LSU rRNA	C	2881	U	2882	*	A	2940	G	2943	cWW	cWW
9	IL_4V9F_088	4V9F	0.6914	2	Multiple bulged bases	0	LSU rRNA	C	2547	C	2548	*	G	2606	G	2609	cWW	cWW
10	IL_5TBW_136	5TBW	0.7747	2	Multiple bulged bases	1	LSU rRNA	C	3349	C	3350	*	G	3353	G	3356	ncWW	cWW
11	IL_1U9S_008	1U9S	0.6088	1	Stack outside cWW	A	RIBONUCLEASE P	G	217	C	219	*	G	195	C	196	cWW	cWW
12	IL_6JXM_001	6JXM	0.6705	2	Multiple bulged bases	B	tRNA	G	53	U	56	*	A	34	C	35	cWW	cWW
13	IL_5T83_004	5T83	0.5373	2	Multiple bulged bases	A	Guanidine-I riboswitch	G	33	C	36	*	G	22	C	23	cWW	cWW
14	IL_6DLR_004	6DLR	0.5107	2	Multiple bulged bases	A	Guanidine-I riboswitch	G	36	C	39	*	G	22	C	23	cWW	cWW
15	IL_5WTK_001	5WTK	0.4367	2	Multiple bulged bases	B	RNA (58-MER)	G	20	U	23	*	A	3	C	4	cWW	cWW
16	IL_4V88_392	4V88	0.3981	2	Multiple bulged bases	A6	SSU rRNA	U	113	U	116	*	A	300	A	301	cWW	cWW
17	IL_5XWP_001	5XWP	0.5219	2	Multiple bulged bases	C	RNA (59-MER)	G	22	U	25	*	A	5	C	6	cWW	cWW
18	IL_5WLH_001	5WLH	0.3068	2	Multiple bulged bases	B	pre-crRNA	C	-7	U	-4	*	A	-23	G	-22	cWW	cWW
19	IL_5W1H_001	5W1H	0.3041	2	Multiple bulged bases	B	mature crRNA	C	-7	U	-4	*	A	-23	G	-22	cWW	cWW
20	IL_5LYS_007	5LYS	0.3205	2	Major groove intercalation	B	7SK RNA	A	39	G	42	*	C	67	U	68	cWW	cWW
21	IL_1XOK_001	1XOK	0.3041	2	Major groove intercalation	A	alfalfa mosaic virus RNA 3' UTR	A	864	G	867	*	C	846	U	847	cWW	cWW
22	IL_1XOK_002	1XOK	0.3862	2	Major groove intercalation	B+A	alfalfa mosaic virus RNA 3' UTR	G	877	G	880	*	C	868	C	869	cWW	cWW
23	IL_6IV9_001	6IV9	0.3447	2	Multiple bulged bases	B	crRNA (50-MER)	G	-9	U	-6	*	A	-29	C	-28	cWW	cWW
24	IL_5LYS_006	5LYS	0.3376	2	Stack outside cWW	B	7SK RNA	G	70	G	73	*	C	36	C	37	cWW	cWW
25	IL_387D_001	387D	0.4378	2	Multiple bulged bases	A	RNA Pseudoknot	G	15	A	18	*	U	1	C	2	cWW	cWW
26	IL_1R3E_002	1R3E	0.4692	3	Multiple bulged bases	E+D	RNA (17-mer)	G	408	G	412	*	C	415	C	416	cWW	cWW
27	IL_1R3E_001	1R3E	0.4404	3	Multiple bulged bases	E+D	RNA (17-mer)	C	415	C	416	*	G	408	G	412	cWW	cWW
28	IL_4KZD_006	4KZD	0.3300	2	Stack outside cWW	R	RNA (84-MER)	G	49	G	52	*	C	30	C	31	cWW	cWW
29	IL_1NTA_001	1NTA	0.3659	1	Stack outside cWW	A+B	RNA (22-mer) + RNA (18-mer)	C	5	C	7	*	G	114	G	115	cWW	cWW
30	IL_1NBS_009	1NBS	0.2416	2	Major groove intercalation	B	RNase P class B	U	228	A	231	*	U	181	G	182	cWW	cWW
31	IL_1U9S_003	1U9S	0.2303	2	Major groove intercalation	A	RIBONUCLEASE P	C	224	A	227	*	U	116	G	117	cWW	cWW
32	IL_4WF9_071	4WF9	0.2981	2	Major groove intercalation	X	LSU rRNA	U	1925	A	1928	*	U	1868	G	1869	cWW	cWW
33	IL_4IOA_067	4IOA	0.2442	2	Multiple bulged bases	X	LSU rRNA	U	1881	A	1884	*	U	1833	G	1834	cWW	cWW
34	IL_6CZR_119	6CZR	0.2639	2	Multiple bulged bases	1a	SSU rRNA	U	123	C	126	*	G	227	G	228	cWW	cWW
35	IL_4LFB_007	4LFB	0.1761	2	Multiple bulged bases	A	SSU rRNA	U	129	C	131	*	G	231	G	232	cWW	cWW
36	IL_6JQ6_001	6JQ6	0.1516	1	Stack outside cWW	U	Hatchet ribozyme	U	62\|\|\|\|11_555	C	64\|\|\|\|11_555	*	G	31\|\|\|\|11_555	G	32\|\|\|\|11_555	cWW	cWW
37	IL_6JQ6_004	6JQ6	0.1516	1	Stack outside cWW	U	Hatchet ribozyme	U	62	C	64	*	G	31	G	32	cWW	cWW
38	IL_3IWN_004	3IWN	0.1229	2	Multiple bulged bases	A	C-di-GMP riboswitch	U	76	C	79	*	G	46	G	47	cWW	cWW
39	IL_3MXH_004	3MXH	0.0000	2	Multiple bulged bases	R	c-di-GMP riboswitch	U	81	C	84	*	G	56	G	57	cWW	cWW
40	IL_1FUF_002	1FUF	0.0846	2	Multiple bulged bases	A+B	RNA (14-mer)	U	5	C	8	*	G	23	G	24	cWW	cWW
41	IL_1FUF_003	1FUF	0.0811	2	Multiple bulged bases	B+A	RNA (14-mer)	U	19	C	22	*	G	9	G	10	cWW	cWW
42	IL_6JQ5_001	6JQ5	0.1666	1	Stack outside cWW	A	Hatchet ribozyme	U	62	C	64	*	G	31	G	32	cWW	cWW
43	IL_4IOA_084	4IOA	0.1616	1	Major groove platform	X	LSU rRNA	U	2380	C	2382	*	G	2393	G	2394	cWW	cWW
44	IL_5TBW_085	5TBW	0.1274	2	Major groove intercalation	1	LSU rRNA	U	2241	A	2244	*	U	2200	G	2201	cWW	cWW
45	IL_4V9F_067	4V9F	0.1717	2	Major groove intercalation	0	LSU rRNA	U	1939	A	1942	*	U	1897	G	1898	cWW	cWW
46	IL_5J7L_315	5J7L	0.1620	2	Major groove intercalation	DA	LSU rRNA	U	1898	A	1901	*	U	1841	G	1842	cWW	cWW
47	IL_6CF2_002	6CF2	0.1857	2	Major groove intercalation	G	RNA (35-MER)	C	22	G	25	*	C	10	G	11	cWW	cWW
48	IL_6CZR_117	6CZR	0.3281	2	Multiple bulged bases	1a	SSU rRNA	C	64	G	67	*	C	97	G	98	cWW	cWW
49	IL_5J7L_005	5J7L	0.3151	2	Multiple bulged bases	AA	SSU rRNA	C	63	A	66	*	U	103	G	104	cWW	cWW
50	IL_4LFB_005	4LFB	0.3614	2	Multiple bulged bases	A	SSU rRNA	C	63	G	66	*	C	103	G	104	cWW	cWW
51	IL_4V9F_021	4V9F	0.3247	2	Multiple bulged bases	0	LSU rRNA	C	699	G	702	*	C	726	G	727	cWW	cWW
52	IL_1NTA_002	1NTA	0.3447	5	Major groove intercalation	A+B	RNA (22-mer) + RNA (18-mer)	C	7	G	13	*	C	113	G	114	cWW	cWW
53	IL_4YAZ_008	4YAZ	0.4195	2	Multiple bulged bases	R	Cyclic di-GMP-I riboswitch	C	64	C	67	*	G	51	G	52	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
UAAA*UG	4
UGC*GG	3
CG*CACG	2
GACU*AC	2
CAAU*AG	2
UGAC*GG	2
UAGC*GG	2
UUUC*GG	2
CGUG*CG	2
UA*UACG	1
UG*CACG	1
UU*AUAG	1
UU*ACUG	1
CU*AUUG	1
CU*AACG	1
CC*GUCG	1
CC*GUUG	1
GGC*GC	1
GAUU*AC	1
GGUC*GC	1
GGAC*GC	1
UCGU*AA	1
AUUG*CU	1
AAUG*CU	1
GAUG*CC	1
GUCU*AC	1
GCUG*CC	1
GGAA*UC	1
GUUCG*CC	1
CC*GUUCG	1
GUUG*CC	1
CGC*GG	1
CAAA*UG	1
UGAA*UG	1
UAC*GG	1
UCAA*UG	1
CUGG*CG	1
CGAA*UG	1
CAUG*CG	1
CAUUUGG*CG	1
CAGC*GG	1

Non-Watson-Crick part of the motif

Sequence	Counts
AA*	7
GA*	6
*AC	5
G*	5
AU*	4
UU*	4
GU*	3
AG*	3
*UU	2
AC*	2
*UA	1
*CU	1
*UC	1
CG*	1
UC*	1
CU*	1
UUC*	1
*UUC	1
A*	1
CA*	1
UG*	1
AUUUG*	1

Release history

Release	3.45	3.46	3.47
Date	2021-05-26	2021-06-23	2021-07-21
Status	Updated, 1 parent	Exact match	Exact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: Multiple bulged bases (34)
Major groove intercalation (11)
Stack outside cWW (7)
Major groove platform (1)
Basepair signature: cWW-cWW
Heat map statistics: Min 0.02 | Avg 0.45 | Max 0.99

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__758825706312584__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__758825706312584__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://rna.bgsu.edu/rna3dhub/motif/view/IL_13730.8","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__758825706312584__","codePath":"https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"758825706312584","bgcolor":"white" }

setting document base to "https://rna.bgsu.edu/rna3dhub/motif/view/IL_13730.8"

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__758825706312584__ 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