Skip to main content

Table 2 Genomic features of polymorphic positions at the CAR locus.

From: Functional constraints on the constitutive androstane receptor inferred from human sequence variation and cross-species comparisons

Positiona

Location

Nucleotide presentb

    

Derived allele frequency

Possible consequencesc

  

Human

Chimp

Cow

Dog

Rat

Mouse

AA

Han

EU

 

28187

5' sequence

G/A

G

n/a

n/a

n/a

n/a

0.02

0

0

Disrupts NF-1 site

41893

Intron 2

A/G

A

A

G

A

A

0

0

0.02

 

42202

Intron 2

G/C

G

G

G

-

-

0.04

0

0

Disrupts HNF-1 site

42218

Intron 2

T/C

T

T

T

C

C

0.07

0

0

Disrupts NF-1 site

42221

Intron 2

C/T

C

C

C

C

C

0

0

0.02

Disrupts NF-1 site

42225

Intron 2

C/A

C

C

C

C

C

0.07

0.18

0.21

Disrupts NF-1 site

42267

Intron 2

C/T

C

C

C

A

A

0.04

0

0

Disrupts C/EBP, USF sites

44896

Intron 3

C/T

C

C

C

C

C

0.29

0.47

0.31

 

45014

Exon 4

C/G

C

C

C

C

C

0.02

0

0

 

45045

Exon 4

C/T

C

C

C

C

C

0.02

0

0

Radical NS change; Disrupts predicted ESE

45518

Exon 5

C/T

C

C

C

C

G

0.16

0.45

0.42

 

45567

Intron 5

A/G

A

A

G

C

G

0.05

0

0.02

Disrupts HNF-1 site

47331

Intron 7

G/-

G

G

-

-

-

0.02

0

0

 

47537

Intron 8

A/C

A

G

G

C

C

0.05

0.15

0.21

Disrupts NF-1 site

47636

Intron 8

T/G

T

T

T

T

T

0.26

0.09

0.23

 

48318

Intron 8

T/C

T

n/a

-

C

T

0.02

0

0.02

 

48342

Intron 8

G/A

G

n/a

C

G

G

0.04

0

0

 

48419

Exon 9

G/A

G

n/a

G

A

A

0

0

0.02

 

48621

3' sequence

G/A

G

C

T

C

C

0

0

0.02

 

48692

3' sequence

A/T

A

A

T

G

G

0.02

0

0.02

 

48734

3' sequence

A/T

A

A

A

A

A

0

0.02

0

 
  1. a Positions are based on the reverse complement of AL50974.
  2. b Nucleotides in bold are identical to that observed in chimpanzee. 'n/a' denotes missing data, while '-' indicates that the position is absent relative to human.
  3. c Transcription factor binding site predictions are based on output from Match; exon splice enhancer (ESE) predictions are based on predictions from ESEfinder (see Methods).
  4. Abbreviations: C/EBP, CCAAT enhancer binding protein; HNF, hepatocyte nuclear factor; NF, nuclear factor; USF, upsteam stumulatory factor.