Table 3

Selected transcription factor binding motifs in the ANK1 promoter predicted by TESS, TRANSFAC and MatInspector prediction tools

*SNPs

Putative

Transcription Factors

Prediction

tool

Created

with

Recognition

Sequence

Start

End


rSNP1 (-24), C/T

GAL4

TESS

C

CCC

    C

-27

-24


E-box binding factors

MatInspector

C

AGACCCCGTGTC

    C

-36

-27


USF

TRANSFAC MatInspector

C

CCC

    C
GTGTCC

-27

-18


GR

MatInspector

TRANSFAC

TESS

T

CAGGGACAC

    A
GGGTCTAGG*

ACCC

    T
GTGTCC

    T
GTGTC

-15

-28

-24

-33

-18

-19


pSNP2 (-307), C/T

T-Ag

TESS

C

GC

    C
GC

-309

-305


Sp1

TRANSFAC

T

AAGC

    T
GCTCC

-311

-302


rSNP3 (-672), A/G

Sp1

TRANSFAC

TESS

A

GCC

    A
GGCCCCTCAGC

    A
GGCCCC

-675

-672

-661

-666


NF-1

TESS

A

TGG

    A

-675

-672


NF-Kappa-B

TRANSFAC

G

GG

    G
GGTTTCC

-674

-665


GAL4

TESS

G

GG

    G
G

-674

-671


MIG1

TESS

G

CTGG

    G
G

-676

-671


rSNP4 (-687), C/G

Sp1

TRANSFAC

TESS

C

ATGGCC

    C
GGCCCCT

GCC

    C
GGCCCC

-666

-669


-690

-681


Oct-01

TRANSFAC

C

GCC

    C
GGCCCC

-690

-681


NF-1

TRANSFAC

C

TGGC

    C
GGGCC

-691

-682


Sp1

TRANSFAC

G

GGCC

    G
GGCCCCTCA

-691

-678


YY1

TRANSFAC TESS

G

GATGGCC

    G
G

-694

-686


GCF

TESS

G

SC

    G
SSSC

-689

-683


Krueppel like

MatInspector

G

CTGAGGGGCC

    G
GGCCAT*

-677

-693


Nuclear factor Kappa B/C-Rel

MatInspector

G

TGGG

    G
ATGGCCCG

-698

-686


GC-box factors SP1/GC

MatInspector

G

GAGGGG

    C
CGGGCCAT*

-679

-693


pSNP5 (-733), C/T

Oct-01

TRANSFAC

C

TG

    C
TTTGCCC

-737

-728


Lvc

TESS

C

CCTG

    C

-737

-733


GCF

TESS

C

GSSS

    C
GS

-737

-731


Sn

TESS

T

ACCTG

    T
T

-738

-732


Grainyhead-like factors

MatInspector

T

GGAACCTG

    T
TTTG

-741

-729


pSNP6 (944), C/T

Oct-01

TRANSFAC

C

CTG

    C
TTTGCC

-947

-938


Glucocorticoid receptor

TESS

T

TGT

    T
GT

    T
GTCCC

-947

-944

-942

-939


Krueppel like factors

MatInspector

T

C

    A
ACAAAGGATGAGATG*

-943

-959


rSNP7 (961), A/C

CAC-binding

TESS

MatInspector

C

CCA

    C
C

TCCA

    C
CCATCTCATC

-964

-965

-960

-651


*Only the SNPs that create putative transcription factor binding sites were listed. *Minus strand. SNP positions in the recognition sequence are underlined.

Aslan et al. BMC Genetics 2010 11:111   doi:10.1186/1471-2156-11-111

Open Data