Motif IL_04038.1 Version IL_04038.1 of this group appears in releases 3.15 to 3.45

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3	break		4		5	1-5	2-4	3-4
1	IL_4IOA_102	4IOA	0.7491	2	Decoding loop related (H)	X	LSU rRNA	G	2818	G	2819	C	2820	*	G	2846	C	2849	cWW		cWW
2	IL_2ET8_002	2ET8	0.7154	2	Decoding loop related	A+B	RNA (22-mer)	C	6	A	7	C	8	*	G	38	G	41	cWW		cWW
3	IL_2O3X_002	2O3X	0.7253	2	Decoding loop related	A+B	RNA (23-mer)	C	7	A	8	C	9	*	G	39	G	42	cWW		cWW
4	IL_3C3Z_003	3C3Z	0.7337	2	Decoding loop related	A+B	HIV-1 subtype F genomic RNA	C	15	A	16	C	17	*	G	7	G	10	cWW		cWW
5	IL_3C3Z_002	3C3Z	0.7570	2	Decoding loop related	B+A	HIV-1 subtype F genomic RNA	C	15	A	16	C	17	*	G	7	G	10	cWW		cWW
6	IL_1ZZ5_001	1ZZ5	0.7648	2	Decoding loop related	B+A	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
7	IL_1ZZ5_003	1ZZ5	0.7895	2	Decoding loop related	D+C	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
8	IL_4ZC7_003	4ZC7	0.7474	2	Decoding loop related	B+A	RNA duplex	C	30	G	31	U	32	*	A	16	G	19	cWW		ncWW
9	IL_1T0E_001	1T0E	0.6309	2	Decoding loop related	C+A	RNA (17-mer)	C	16	A	17	C	18	*	G	7	G	10\|\|A	cWW		cWW
10	IL_1ZX7_003	1ZX7	0.5867	2	Decoding loop related	D+C	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
11	IL_1ZX7_005	1ZX7	0.5047	2	Decoding loop related	F+E	RNA (14-mer)	C	26	A	27	C	28	*	G	7	G	10	cWW		cWW
12	IL_2O3X_003	2O3X	0.5754	2	Decoding loop related	B+A	RNA (23-mer)	C	30	A	31	C	32	*	G	16	G	19	cWW		cWW
13	IL_4IOA_046	4IOA	0.4993	1	Intercalated cWW (H)	X	LSU rRNA	G	1241	A	1242	G	1243	*	U	1232	C	1234	cWW		cWW
14	IL_2ET8_001	2ET8	0.3770	1	Stack and bulge	B+A	RNA (22-mer)	G	41	U	42	C	43	*	G	4	C	6	cWW		cWW
15	IL_2O3X_001	2O3X	0.3613	1	Stack and bulge	B+A	RNA (23-mer)	G	42	U	43	C	44	*	G	5	C	7	cWW		cWW
16	IL_5VCI_005	5VCI	0.4731	0	Not an internal loop	A+B	RNA (22-mer) + RNA (12-mer)	G	13	C	14	C	15	*	G	22	C	1	cWW		cWW
17	IL_4WF9_047	4WF9	0.3221	1	Intercalated cWW	X	LSU rRNA	G	1266	A	1267	C	1268	*	G	1257	U	1259	cWW		cWW
18	IL_4LFB_041	4LFB	0.4135	0	Single stack bend	A	SSU rRNA	G	1002	G	1003	G	1003\|\|\|A	*	C	1038	C	1039	cWW		cWW
19	IL_4V83_236	4V83	0.3965	0	Single stack bend	CV	domain 3 of PSIC IGR IRES RNA	C	6155	A	6156	A	6157	*	U	6172	G	6173	cWW		cWW
20	IL_5TBW_375	5TBW	0.3042	0	Single stack bend	AS	5S rRNA	C	47	U	48	G	49	*	C	29	G	30	cWW		cWW
21	IL_5TBW_009	5TBW	0.2752	0	Single stack bend	1	LSU rRNA	C	163	A	164	A	165	*	U	257	G	258	cWW		cWW
22	IL_4IOA_021	4IOA	0.1947	0	Single stack bend (H)	X	LSU rRNA	G	951	A	952	G	953	*	C	850	C	851	cWW		cWW
23	IL_4WF9_028	4WF9	0.2323	0	Single stack bend	X	LSU rRNA	G	984	A	985	G	986	*	C	882	C	883	cWW		cWW
24	IL_4Y4O_201	4Y4O	0.1810	0	Single stack bend (H)	2A	LSU rRNA	G	940	A	941	G	942	*	C	837	C	838	cWW		cWW
25	IL_5J7L_266	5J7L	0.1750	0	Single stack bend	DA	LSU rRNA	G	940	A	941	G	942	*	C	837	C	838	cWW		ncWW
26	IL_5TBW_004	5TBW	0.1920	0	Single stack bend	1	LSU rRNA	G	56	A	57	G	58	*	C	27	C	28	cWW		cWW
27	IL_4V9F_005	4V9F	0.2110	0	Single stack bend	0	LSU rRNA	G	182	A	183	G	184	*	C	153	C	154	cWW		cWW
28	IL_4WF9_007	4WF9	0.1289	0	Single stack bend	X	LSU rRNA	G	215	A	216	G	217	*	C	186	C	187	cWW		cWW
29	IL_4Y4O_183	4Y4O	0.1205	0	Single stack bend (H)	2A	LSU rRNA	G	212	A	213	G	214	*	C	183	C	184	cWW		cWW
30	IL_4IOA_005	4IOA	0.0000	0	Single stack bend (H)	X	LSU rRNA	A	189	A	190	G	191	*	C	160	U	161	cWW		cWW
31	IL_5J7L_249	5J7L	0.1978	0	Single stack bend	DA	LSU rRNA	G	212	A	213	G	214	*	C	183	C	184	cWW		cWW
32	IL_4V9F_081	4V9F	0.2417	0	Single stack bend	0	LSU rRNA	U	2436	A	2437	G	2438	*	C	2454	A	2455	cWW		cWW
33	IL_4IOA_056	4IOA	0.2810	0	Single stack bend (H)	X	LSU rRNA	A	1463	A	1464	G	1465	*	C	1477	U	1478	cWW	ncWW	cWW
34	IL_5J7L_032	5J7L	0.2973	0	Single stack bend	AA	SSU rRNA	A	746	A	747	G	748	*	C	658	U	659	cWW		cWW
35	IL_5J7L_044	5J7L	0.3734	0	Single stack bend	AA	SSU rRNA	G	1041	A	1042	G	1043	*	C	998	C	999	cWW		cWW
36	IL_5J7L_269	5J7L	0.3791	0	Single stack bend	DA	LSU rRNA	G	926	A	927	A	928	*	U	850	C	851	cWW		cWW
37	IL_5TBW_035	5TBW	0.4072	0	Single stack bend	1	LSU rRNA	U	1111	A	1112	G	1113	*	C	969	A	970	cWW		cWW
38	IL_4WF9_089	4WF9	0.3645	0	Single stack bend	X	LSU rRNA	C	2525	C	2526	U	2527	*	A	2480	G	2481	cWW		cWW
39	IL_4IOA_085	4IOA	0.4161	0		X	LSU rRNA	C	2477	C	2478	U	2479	*	A	2432	G	2433	cWW		cWW
40	IL_4Y4O_266	4Y4O	0.4562	0		2A	LSU rRNA	C	2498	C	2499	U	2500	*	A	2453	G	2454	cWW		cWW
41	IL_5TBW_081	5TBW	0.5282	0	Single stack bend	1	LSU rRNA	C	1951	G	1952	G	1953	*	C	2094	G	2095	cWW		cWW
42	IL_3MOJ_004	3MOJ	0.5173	0	Single stack bend	A	LSU rRNA	C	2540	A	2541	A	2542	*	U	2522	G	2523	cWW		cWW
43	IL_6FZ0_001	6FZ0	0.6112	0	Single stack bend	A	SAM-V riboswitch	C	46	U	47	A	48	*	U	20	G	21	cWW		cWW
44	IL_2QWY_008	2QWY	0.5987	0	Single stack bend	C	SAM-II riboswitch	C	43	U	44	A	45	*	U	21	G	22	cWW		cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GAG*CC	10
CAC*GAAG	9
CAA*UG	3
AAG*CU	3
CCU*AG	3
GUC*GUC	2
UAG*CA	2
CUA*UG	2
GGC*GGAC	1
CGU*AAAG	1
GAAG*CAC	1
GAG*UAC	1
GCC*GC	1
GAC*GAU	1
GGG*CC	1
CUG*CG	1
GAA*UC	1
CGG*CG	1

Non-Watson-Crick part of the motif

Sequence	Counts
A*	19
A*AA	9
C*	4
U*	3
A*A	2
U*U	2
G*	2
G*GA	1
G*AA	1
AA*A	1

Release history

Release	3.15	3.16	3.17	3.18	3.19	3.20	3.21	3.22	3.23	3.24	3.25	3.26	3.27	3.28	3.29	3.30	3.31	3.32	3.33	3.34	3.35	3.36	3.37	3.38	3.39	3.40	3.41	3.42	3.43	3.44	3.45
Date	2019-02-08	2019-03-08	2019-04-05	2019-05-03	2019-05-31	2019-06-28	2019-07-26	2019-08-23	2019-09-19	2019-10-16	2019-11-13	2019-12-11	2020-01-08	2020-02-05	2020-03-04	2020-04-01	2020-04-29	2020-05-27	2020-06-24	2020-07-22	2020-08-19	2020-09-16	2020-10-14	2020-11-11	2020-12-09	2021-01-06	2021-02-03	2021-03-03	2021-03-31	2021-04-28	2021-05-26
Status	New id, > 2 parents	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match	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: Single stack bend (20)
Decoding loop related (11)
Single stack bend (H) (5)
Stack and bulge (2)
(2)
Intercalated cWW (H) (1)
Decoding loop related (H) (1)
Intercalated cWW (1)
Not an internal loop (1)
Basepair signature: cWW-L-cWW
Heat map statistics: Min 0.06 | Avg 0.53 | Max 0.98

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Coloring options: Nucleotide numbers

Motif IL_04038.1 Version IL_04038.1 of this group appears in releases 3.15 to 3.45 Download Csv Json

3D structures

Complete motif including flanking bases

Non-Watson-Crick part of the motif

Release history

Parent motifs

Children motifs

Motif IL_04038.1 Version IL_04038.1 of this group appears in releases 3.15 to 3.45

Download

Csv

Json