Exploring the relationship between intron retention and chromatin accessibility in plants

BMC Genomics

Table 3 Common enriched footprint-hexamers between arabidopsis and rice

Event type	Region	hexamers	p-value	Motif consensus
IR	5’ Exon	13	1.70×10⁻⁰⁷	CGCCG,(G/C)(G/C)GCGG,(A/G)T(C/T)(G/T)(C/G)A
	Intron	2	0.27	AAGGAG,CGGCGG
	3’ Exon	246	2.25×10⁻¹⁶⁵	AAAA,AAATT,CCGAC,CGCxCG,(C/A)TTT, GCGGC,GxTTT,(T/G)AAA,TTT(C/T) (G/T)T(C/T)(C/G)(G/A)
IE	5’ Exon	0	N/A	-
	Intron	19	2.10×10⁻³²	TTAA(T/A)(T/A),T(T/A)TTT(A/T)
	3’ Exon	0	N/A	-

The number of hexamers in common between the arabidiopsis and rice leaf samples, and the corresponding significance levels of the overlap are shown for all three regions of IR and IE events. The hexamers in each region were clustered, and motif consensus sequences are shown. When there is no clear consensus in a given position, that is denoted by an x. Leading or trailing positions without a clear consensus were omitted, so some consensus sequences are less than 6 nucleotides long. In the intronic region of IR events only 2 hexamers were detected so no clustering was performed. Here, an HMM score cutoff of S=0.20 was used with manual verification of the footprints of the overlapping hexamers

ISSN: 1471-2164