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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.