Table 8

In-silico analysis of transcription factor binding site motifs at SNP sites in the PRKAG3 promoter region
SNPs Putative transcription factors Predictor Recognition sequence Created with Start End
g.-995A>G CCAAT/enhancer-binding protein (α and ß) TFSEARCH CCCTTAGGC
    A
ATAT a
A −1004 −991
TESS CTTAGGC
    A
ATAT
MatInspector CCCCTTAGGC
    A
ATAT
−991
Match™ ALIBABA2 CCCCTTAGGC
    A
ATATAGG
−991
−1002 −989
−1005
HNF-4 Match™ CCTTAGGC
    A
ATA AA c
−992
−992
CCTGCCCCTTAGGC
    A
AT
−1005
−100 −1010
g.-480C>T Pax-4 Match™ C
    C
GGGACCACCCACGAACTCC b, c
C −481 −460
g.-461C>T SP1 TFSEARCH GCTGGGGAGGC
    G
GAG a b
C −472 −458
TESS

C

    G
GAGT

GGGGAGGC

    G
GA

−462 −457
ALIBABA2 −469 −459
g.-311A>G IK-1

Match™

TFSEARCH

CGGT
    G
GGAACACA a, c
G −315 −303
g.-221G>A Myoblast Determining Factors MatInspector
    C
GAGGACAGGTGAGAAG b, c
G −221 −205
g.-30C>T RFX1 Match™ CTGTATCTGGGCA
    A
CAC b, c
T −33 −17

SNP positions in recognition sequence are underlined. No transcription factor motifs were found in positions g.-968G>A, g.-671A>G, g.-583C>T, g.-158C>G.

a Transcription factor binding site prediction changes on substitution to alternate allele.

b Minus strand.

c Muscle specific.

Ryan et al.

Ryan et al. BMC Genetics 2012 13:66   doi:10.1186/1471-2156-13-66

Open Data