Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

Table 5 Effects of SNPs located in the 5' UTR of IGFBP5, MAPK9 and GCK on predicted transcription factor binding sites.

Entrez Gene ID	Chr.	Position	Allele	Strand	Matrix Family	Core similarity	Matrix similarity	Site sequence	Detailed Family Information
IGFBP5	2	108855684	T	(-)	V$ZF07	1.00	0.94	ggtccCTCCtctcag	C2H2 zinc finger transcription factors 7
				(+)	V$PLAG	1.00	0.89	gaGAGGagggacccaggggaggg	Pleomorphic adenoma gene
MAPK9	7	871347	C	(+)	V$NFKB	1.00	0.93	aacgggtgTTCCttc	Nuclear factor kappa B/c-rel
				(+)	V$EREF	1.00	0.81	cagggaggactgtgtGACCtggt	Estrogen response elements
				(-)	V$PPAR	0.76	0.71	aacCAGGtcacacagtcctccct	Peroxisome proliferator activated receptor homodimers
			G	(-)	V$PAX3	1.00	0.87	caggTCACacagtcctccc	PAX-3 binding sites
GCK	11	74275999		(-)	V$EREF	1.00	0.93	aaaccagGTCAcacagtcctccc	Estrogen response elements
				(-)	V$RORA	1.00	0.96	agaaaaccaGGTCacacagtcct	v-ERB and RAR-related orphan receptor alpha
				(+)	V$GREF	0.75	0.86	ggaggactgtgTGATctgg	Glucocorticoid responsive and related elements
			A	(-)	V$GATA	0.85	0.90	accaGATCacaca	GATA binding factors
				(-)	V$RXRF	1.00	0.79	agcaaaGGTCagaaaaccagatcac	RXR heterodimer binding sites

The "core sequence" of a matrix is defined as the (usually 4) consecutive highest conserved positions of the matrix (marked in uppercase letters). A perfect match between the consensus bovine sequence and the matrix gets a score of 1.00 (each sequence position corresponds to the highest conserved nucleotide at that position in the matrix); a "good" match to the matrix usually has a similarity of >0.80.

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