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Table 8 In-silico analysis of transcription factor binding site motifs at SNP sites in the PRKAG3 promoter region

From: SNP variation in the promoter of the PRKAG3gene and association with meat quality traits in pig

SNPs

Putative transcription factors

Predictor

Recognition sequence

Created with

Start

End

g.-995A>G

CCAAT/enhancer-binding protein (α and ß)

TFSEARCH

CCCTTAGGCAATAT a

A

−1004

−991

  

TESS

CTTAGGCAATAT

   
  

MatInspector

CCCCTTAGGCAATAT

  

−991

  

Matchâ„¢ ALIBABA2

CCCCTTAGGCAATATAGG

  

−991

     

−1002

−989

     

−1005

 
 

HNF-4

Matchâ„¢

CCTTAGGCAATA AA c

  

−992

      

−992

   

CCTGCCCCTTAGGCAAT

 

−1005

 
     

−100

−1010

g.-480C>T

Pax-4

Matchâ„¢

CCGGGACCACCCACGAACTCC b, c

C

−481

−460

g.-461C>T

SP1

TFSEARCH

GCTGGGGAGGCGGAG a b

C

−472

−458

  

TESS

CGGAGT

GGGGAGGCGGA

 

−462

−457

  

ALIBABA2

  

−469

−459

g.-311A>G

IK-1

Matchâ„¢

TFSEARCH

CGGTGGGAACACA a, c

G

−315

−303

g.-221G>A

Myoblast Determining Factors

MatInspector

CGAGGACAGGTGAGAAG b, c

G

−221

−205

g.-30C>T

RFX1

Matchâ„¢

CTGTATCTGGGCAACAC b, c

T

−33

−17

  1. 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.
  2. a Transcription factor binding site prediction changes on substitution to alternate allele.
  3. b Minus strand.
  4. c Muscle specific.