Motif HL_97270.1 Version HL_97270.1 of this group appears in releases 0.3 to 1.0

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3		4		5		6		7	1-7	2-6
1	HL_2A64_002	2A64	0.3202	1	T-loop with 2 stacked bulged bases	A	ribonuclease P RNA	C	69	U	70	G	71	A	72	G	73	A	74	G	76	cWW	tWH
2	HL_3DHS_002	3DHS	0.2163	1		A	RNase P RNA	C	69	U	70	G	71	A	72	G	73	A	74	G	76	cWW	tWH
3	HL_2ZJR_009	2ZJR	0.1556	1	T-loop with 2 stacked bulged bases (H)	X	LSU rRNA	C	316	U	317	G	318	G	319	A	320	A	321	G	323	cWW	tWH
4	HL_3V2F_010	3V2F	0.2384	1		A	23S Ribosomal RNA	U	305	U	306	G	307	G	308	G	309	A	310	G	312	cWW	tWH
5	HL_2QBG_011	2QBG	0.1230	1		B	23S rRNA	C	305	U	306	G	307	G	308	A	309	A	310	G	312	cWW	tWH
6	HL_1S72_010	1S72	0.0000	1	T-loop with 2 stacked bulged bases (H)	0	LSU rRNA	U	312	U	313	G	314	G	315	A	316	A	317	A	319	cWW	tWH
7	HL_3U5H_005	3U5H	0.0700	1		5	25S rRNA	U	194	U	195	G	196	G	197	A	198	A	199	A	201	cWW	tWH
8	HL_4A1B_005	4A1B	0.1516	1		1	26S RRNA	U	194	U	195	G	196	G	197	A	198	A	199	A	201	cWW	tWH
9	HL_2HOJ_002	2HOJ	0.5252	1		A	thi-box riboswitch	G	66	A	67	U	68	A	69	A	70	U	71	C	73	cWW
10	HL_2GDI_002	2GDI	0.5276	1	Other HL	X	TPP riboswitch	G	66	A	67	U	68	A	69	A	70	U	71	C	73	cWW
11	HL_2GDI_004	2GDI	0.4963	1		Y	TPP riboswitch	G	66	A	67	U	68	A	69	A	70	U	71	C	73	cWW
12	HL_3U5F_006	3U5F	0.3608	1		6	18S rRNA	G	243	A	244	U	245	G	246	A	247	U	248	C	250	cWW
13	HL_2XZM_006	2XZM	0.4349	1		A	18S RRNA	G	240	A	241	U	242	G	243	A	244	A	245	C	247	cWW
14	HL_1S72_039	1S72	0.5628	0	Other HL (H)	0	LSU rRNA	C	1594	G	1595	U	1596	A	1597	A	1598	U	1599	G	1600	cWW
15	HL_4A1B_037	4A1B	0.5904	0		1	26S RRNA	G	1743	A	1744	U	1745	U	1746	A	1747	U	1748	C	1749	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
UUGGAACA	3
GAUAAUGC	3
CUGAGAUG	2
CUGGAAAG	2
UUGGGAAG	1
GAUGAUUC	1
GAUGAAUC	1
CGUAAUG	1
GAUUAUC	1

Non-Watson-Crick part of the motif

Sequence	Counts
UGGAAC	3
AUAAUG	3
UGAGAU	2
UGGAAA	2
UGGGAA	1
AUGAUU	1
AUGAAU	1
GUAAU	1
AUUAU	1

Release history

Release	0.3	0.4	0.5	0.6	0.7	0.8	1.0
Date	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-02-17	2013-03-04
Status	> 2 parents	Exact match	Exact match	Exact match	Exact match	Exact match	Exact match

Parent motifs

Parent motif	Common motif instances	Only in HL_97270.1	Only in the parent motif
HL_05993.1 Compare	HL_2ZJR_009, HL_1S72_010, HL_2QBG_011, HL_2A64_002, HL_3DHS_002	HL_3V2F_010, HL_2GDI_002, HL_4A1B_005, HL_3U5F_006, HL_2HOJ_002, HL_2XZM_006, HL_4A1B_037, HL_1S72_039, HL_3U5H_005, HL_2GDI_004	HL_2D6F_003, HL_2AZX_006, HL_2ZUE_003, HL_3A3A_004, HL_1U0B_003, HL_2AZX_003, HL_3F4G_001, HL_2QBG_019, HL_2DU3_003, HL_2DER_003, HL_3ADC_004, HL_2DER_006, HL_3O58_014, HL_3AL0_003, HL_3ICQ_002, HL_2ZM5_003, HL_3ADC_008, HL_1QU2_003, HL_2D6F_006, HL_2QBG_034, HL_1S72_034, HL_2NR0_007, HL_2CSX_003, HL_2ZJR_032, HL_2NR0_004, HL_2AKE_003, HL_2ZZN_006, HL_3ICQ_005, HL_2ZZN_003, HL_2FK6_002, HL_1WZ2_004, HL_3A2K_006, HL_3A2K_003, HL_3Q1Q_011, HL_3AM1_004, HL_2CV1_003, HL_1WZ2_008, HL_3OUY_001, HL_1O0C_003, HL_2NRE_003, HL_3EPH_006, HL_1J1U_003, HL_3F4G_004, HL_3G78_001, HL_3O58_005, HL_2ZZM_004, HL_2CV1_006, HL_1J2B_004, HL_3PYO_032, HL_1J2B_002, HL_3ADD_008, HL_2NR0_010, HL_3L0U_003, HL_2NR0_013, HL_2DU6_003, HL_2ZNI_003, HL_3PYO_010, HL_2ZNI_006, HL_2DR8_001, HL_2NQP_004, HL_2BTE_008, HL_1GAX_003, HL_1GAX_006, HL_3ADD_004, HL_3O58_031, HL_2BTE_004, HL_3OVA_001
HL_78735.2 Compare	HL_2GDI_002, HL_2GDI_004, HL_2HOJ_002	HL_3V2F_010, HL_4A1B_005, HL_3U5F_006, HL_2A64_002, HL_2XZM_006, HL_4A1B_037, HL_2QBG_011, HL_1S72_039, HL_2ZJR_009, HL_1S72_010, HL_3DHS_002, HL_3U5H_005	HL_1U9S_003, HL_3D2V_002, HL_3NPB_003, HL_3D2V_004, HL_2XZM_008, HL_1FJG_006, HL_2AW7_006, HL_3O30_007, HL_3Q1Q_005
HL_68221.1 Compare	HL_2XZM_006, HL_1S72_039	HL_3V2F_010, HL_2GDI_002, HL_4A1B_005, HL_3U5F_006, HL_2A64_002, HL_2HOJ_002, HL_4A1B_037, HL_2QBG_011, HL_2ZJR_009, HL_1S72_010, HL_3U5H_005, HL_3DHS_002, HL_2GDI_004	HL_3DIR_004, HL_3OUY_002, HL_2ZJR_017, HL_3PYO_018

Children motifs

Child motif	Common motif instances	Only in HL_97270.1	Only in the child motif
HL_97270.2 Compare	HL_3V2F_010, HL_2GDI_002, HL_4A1B_005, HL_2GDI_004, HL_2HOJ_002, HL_2XZM_006, HL_4A1B_037, HL_2A64_002, HL_2QBG_011, HL_1S72_039, HL_3U5F_006, HL_1S72_010, HL_3DHS_002, HL_3U5H_005	HL_2ZJR_009	HL_4IOA_009

Annotations: (10)
T-loop with 2 stacked bulged bases (H) (2)
Other HL (H) (1)
T-loop with 2 stacked bulged bases (1)
Other HL (1)
Basepair signature: cWW-tWH-R-R-R
Heat map statistics: Min 0.07 | Avg 0.41 | Max 0.75

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Coloring options: Nucleotide numbers

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