Skip to main content

Table 3 Selected transcription factor binding motifs in the ANK1 promoter predicted by TESS, TRANSFAC and MatInspector prediction tools

From: Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

*SNPs

Putative

Transcription Factors

Prediction

tool

Created

with

Recognition

Sequence

Start

End

rSNP1 (-24), C/T

GAL4

TESS

C

CCCC

-27

-24

 

E-box binding factors

MatInspector

C

AGACCCCGTGTCC

-36

-27

 

USF

TRANSFAC MatInspector

C

CCCC GTGTCC

-27

-18

 

GR

MatInspector

TRANSFAC

TESS

T

CAGGGACACA GGGTCTAGG*

ACCCT GTGTCC

T GTGTC

-15

-28

-24

-33

-18

-19

pSNP2 (-307), C/T

T-Ag

TESS

C

GCC GC

-309

-305

 

Sp1

TRANSFAC

T

AAGCT GCTCC

-311

-302

rSNP3 (-672), A/G

Sp1

TRANSFAC

TESS

A

GCCA GGCCCCTCAGC

A GGCCCC

-675

-672

-661

-666

 

NF-1

TESS

A

TGGA

-675

-672

 

NF-Kappa-B

TRANSFAC

G

GGG GGTTTCC

-674

-665

 

GAL4

TESS

G

GGG G

-674

-671

 

MIG1

TESS

G

CTGGG G

-676

-671

rSNP4 (-687), C/G

Sp1

TRANSFAC

TESS

C

ATGGCCC GGCCCCT

GCCC GGCCCC

-666

-669

     

-690

-681

 

Oct-01

TRANSFAC

C

GCCC GGCCCC

-690

-681

 

NF-1

TRANSFAC

C

TGGCC GGGCC

-691

-682

 

Sp1

TRANSFAC

G

GGCCG GGCCCCTCA

-691

-678

 

YY1

TRANSFAC TESS

G

GATGGCCG G

-694

-686

 

GCF

TESS

G

SCG SSSC

-689

-683

 

Krueppel like

MatInspector

G

CTGAGGGGCCG GGCCAT*

-677

-693

 

Nuclear factor Kappa B/C-Rel

MatInspector

G

TGGGG ATGGCCCG

-698

-686

 

GC-box factors SP1/GC

MatInspector

G

GAGGGGC CGGGCCAT*

-679

-693

pSNP5 (-733), C/T

Oct-01

TRANSFAC

C

TGC TTTGCCC

-737

-728

 

Lvc

TESS

C

CCTGC

-737

-733

 

GCF

TESS

C

GSSSC GS

-737

-731

 

Sn

TESS

T

ACCTGT T

-738

-732

 

Grainyhead-like factors

MatInspector

T

GGAACCTGT TTTG

-741

-729

pSNP6 (944), C/T

Oct-01

TRANSFAC

C

CTGC TTTGCC

-947

-938

 

Glucocorticoid receptor

TESS

T

TGTT GT

T GTCCC

-947

-944

-942

-939

 

Krueppel like factors

MatInspector

T

CA ACAAAGGATGAGATG*

-943

-959

rSNP7 (961), A/C

CAC-binding

TESS

MatInspector

C

CCAC C

TCCAC CCATCTCATC

-964

-965

-960

-651

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