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

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

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
  1. 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.