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.

Mullen et al. BMC Genomics 2012 13:16   doi:10.1186/1471-2164-13-16

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