Motif IL_28947.3 Version IL_28947.3 of this group appears in releases 1.14 to 1.14

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name for chain		1		2	break		3		4	1-4	2-3
1	IL_4NVV_107	4NVV	0.1986	1		B	5S Ribosomal RNA	C	17	G	18	*	C	65	G	67	cWW	cWW
2	IL_1S72_099	1S72	0.1734	1	Major groove intercalation (H)	9	5S rRNA	C	15	G	16	*	C	64	G	66	cWW	cWW
3	IL_1S72_022	1S72	0.0982	2	Multiple bulged bases (H)	0	LSU rRNA	C	726	G	727	*	C	699	G	702	cWW	cWW
4	IL_2QBG_060	2QBG	0.0000	1		B	23S rRNA	C	1499	G	1500	*	C	1489	G	1491	cWW	cWW
5	IL_2AW7_005	2AW7	0.0913	2		A	16S ribosomal RNA	U	103	G	104	*	C	63	A	66	cWW	cWW
6	IL_1FJG_005	1FJG	0.1120	2	Multiple bulged bases (H)	A	SSU rRNA	C	103	G	104	*	C	63	G	66	cWW	cWW
7	IL_2NZ4_007	2NZ4	0.1531	1		R+G	GlmS ribozyme	C	52	G	53	*	C	5	G	7	cWW	cWW
8	IL_3U5H_137	3U5H	0.2393	1		5	25S rRNA	C	3324	G	3325	*	U	3381	G	3383	cWW	cWW
9	IL_4NVV_061	4NVV	0.2324	1		A	23S Ribosomal RNA	C	1545	G	1546	*	U	1535	G	1537	cWW	cWW
10	IL_2QBG_086	2QBG	0.3005	1		B	23S rRNA	U	2220	G	2221	*	U	2202	G	2204	cWW	cWW
11	IL_4A1B_063	4A1B	0.2761	1		1	26S RRNA	U	1437	A	1438	*	U	1424	G	1426	cWW	cWW
12	IL_1S72_042	1S72	0.2313	1	Single bulged G (H)	0	LSU rRNA	C	1225	G	1226	*	U	1136	G	1138	cWW	cWW
13	IL_4NVV_072	4NVV	0.3324	2		A	23S Ribosomal RNA	U	1872	G	1873	*	U	1920	A	1923	cWW	cWW
14	IL_4IOA_067	4IOA	0.3955	2	Multiple bulged bases	X	LSU rRNA	U	1833	G	1834	*	U	1881	A	1884	cWW	cWW
15	IL_4NVV_034	4NVV	0.4685	1		A	23S Ribosomal RNA	G	927	G	928	*	U	941	C	943		cWW
16	IL_1XOK_001	1XOK	0.4239	2	Major groove intercalation	A	alfalfa mosaic virus RNA 3' UTR	C	846	U	847	*	A	864	G	867	cWW	cWW
17	IL_1XOK_002	1XOK	0.5122	2	Major groove intercalation	A+B	alfalfa mosaic virus RNA 3' UTR	C	868	C	869	*	G	877	G	880	cWW	cWW
18	IL_387D_001	387D	0.5905	2	Multiple bulged bases	A	RNA Pseudoknot	U	1	C	2	*	G	15	A	18	cWW	cWW
19	IL_1U9S_008	1U9S	0.7593	1	Stack outside cWW	A	RIBONUCLEASE P	G	195	C	196	*	G	217	C	219	cWW	cWW
20	IL_4FAW_014	4FAW	0.7955	2		A	Group II catalytic intron D1-D4-3	U	365	A	366	*	U	375	G	378	cWW	cWW
21	IL_4C7O_003	4C7O	0.8595	1	Single bulged C	E	SRP RNA	C	12	G	13	*	C	31	G	33	cWW	cWW
22	IL_3U5H_063	3U5H	0.8187	1		5	25S rRNA	C	1420	G	1421	*	C	1385	G	1387	cWW	cWW
23	IL_1KXK_003	1KXK	0.8472	2	Multiple bulged bases	A	ai5g group II Self-splicing intron	U	28	G	29	*	C	42	G	45	cWW	cWW
24	IL_3U5H_019	3U5H	0.5476	1		5	25S rRNA	U	512	G	513	*	C	577	G	579	cWW	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CG*CAG	5
UG*UGAA	2
CG*CAUG	1
UG*CGAA	1
CG*CGUG	1
CG*UUG	1
CG*UAG	1
UG*UUG	1
UA*UUG	1
CG*UGG	1
GG*UAC	1
CU*AAUG	1
CC*GAUG	1
UC*GGAA	1
GC*GGC	1
UA*UACG	1
CG*CCG	1
UG*CACG	1
UG*CAG	1

Non-Watson-Crick part of the motif

Sequence	Counts
*A	8
*GA	4
*AU	3
*U	3
*G	2
*AC	2
*GU	1
*C	1

Release history

Release	1.14
Date	2014-04-27
Status	Updated, 1 parent

Parent motifs

Parent motif	Common motif instances	Only in IL_28947.3	Only in the parent motif
IL_28947.2 Compare	IL_2QBG_086, IL_387D_001, IL_4IOA_067, IL_1S72_042, IL_3U5H_063, IL_2NZ4_007, IL_2QBG_060, IL_4A1B_063, IL_1KXK_003, IL_3U5H_137, IL_4C7O_003, IL_1S72_022, IL_1XOK_001, IL_1FJG_005, IL_1XOK_002, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014, IL_1U9S_008	IL_4NVV_034, IL_4NVV_107, IL_4NVV_061, IL_4NVV_072	IL_3V2F_069, IL_3V2F_059

Children motifs

Child motif	Common motif instances	Only in IL_28947.3	Only in the child motif
IL_04465.1 Compare	IL_2QBG_086, IL_2NZ4_007, IL_1S72_042, IL_3U5H_063, IL_4A1B_063, IL_2QBG_060, IL_4NVV_034, IL_3U5H_137, IL_4NVV_061, IL_4C7O_003, IL_1S72_022, IL_1FJG_005, IL_4NVV_107, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014	IL_387D_001, IL_4IOA_067, IL_1U9S_008, IL_1KXK_003, IL_4NVV_072, IL_1XOK_001, IL_1XOK_002	IL_2QBG_107, IL_1U9S_006, IL_1S72_045, IL_4CUV_143, IL_3D0U_005, IL_3U5F_033, IL_1FJG_022, IL_4CUX_033, IL_4CUV_067, IL_4BPP_033, IL_2AW7_029, IL_4IOA_101, IL_4CUV_108, IL_4IOA_024
IL_84950.1 Compare	IL_387D_001, IL_1U9S_008, IL_1XOK_001, IL_1KXK_003, IL_4NVV_072, IL_4IOA_067, IL_1XOK_002	IL_2QBG_086, IL_2NZ4_007, IL_1S72_042, IL_3U5H_063, IL_4A1B_063, IL_2QBG_060, IL_4NVV_034, IL_3U5H_137, IL_4NVV_061, IL_4C7O_003, IL_1S72_022, IL_1FJG_005, IL_4NVV_107, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014	IL_3U5F_086, IL_4CUX_087

Annotations: (13)
Multiple bulged bases (3)
Multiple bulged bases (H) (2)
Major groove intercalation (2)
Single bulged G (H) (1)
Major groove intercalation (H) (1)
Stack outside cWW (1)
Single bulged C (1)
Basepair signature: cWW-cWW
Heat map statistics: Min 0.09 | Avg 0.51 | Max 0.97

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Coloring options: Nucleotide numbers

Motif IL_28947.3 Version IL_28947.3 of this group appears in releases 1.14 to 1.14 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_28947.3 Version IL_28947.3 of this group appears in releases 1.14 to 1.14

Download

Csv

Json