Table 1

Identified SNPs within the ACSL1 locus and positions on the bovine genome assemblies

SNP ID

relative to coding sequence*

Gene region

Variation relative to reference sequence

Position on NW_001494406.2 (Btau4.2)

Position on NW_003104605.1 (UMD_3.1)

Allele

frequency

SNP accession number (dbSNP, NCBI ss#)


c.-569_570del AC

Promoter

Indel TG

1918795

389858

Not analyzed

ss469271165

c.-224_225del GG

Promoter

Indel (C)5-7

1918451

389615

Not analyzed

ss469271166

c.-196G>A

Promoter

C>T

1918422

3894586

Not analyzed

ss469271167

c.-167G>C

Promoter

C>G

1918393

3894557

Not analyzed

ss469271168

c.-151G>C

Promoter

C>G

1918377

3894541

Not analyzed

ss469271169

c.-122G>A

Promoter

C>T

1918348

3894512

0.67 (G)/0.33 (A)

ss469271170

c.481-233A>G

Intron 5

T>C

1876389

3852106

0.73 (A)/0.27 (G)

ss469271171

c.516C>G

Exon 6

G>C

1876121

3852284

0.57 (C)/0.43 (G)

ss469271172

c.580+114C>G

Intron 6

G>C

1875943

3852552

0.33 (C)/0.67 (G)

ss469271173

c.584A>G

Exon 7

T>C

1875838

3852001

0.07 (G)/0.94 (A)

ss469271174

c.845-58T>G

Intron 9

A>C

1871919

3848082

0.75 (T)/0.21 (G)5

ss469271175

c.1267-100C>T

Intron 13

G>A

1864210

3840373

0.24 (T)/0.76 (C)

ss469271176

c.1525-131C>T

Intron 16

G>A

1859370

3835533

Not analyzed

ss469271177

c.1938T>G

Exon 20

A>C

Not annotated

3831586

0.75 (T)/0.25 (G)

ss469271178

c.1959+56G>A

Intron 20

C>T

Not annotated

3831509

0.24 (A)/0.76 (G)

ss469271179

c.2099+1023del A

3'UTR

Indel A

1853870

3829944

Not analyzed

ss469271180

c.2099+1030 C>A

3'UTR

C>A

1853863

3829937

Not analyzed

ss469271181

c.2099+1032 A>C

3'UTR

A>C

1853861

3829935

Not analyzed

ss469271182

c.2099+1034 C>A

3'UTR

C>A

1853859

3829933

Not analyzed

ss469271183


*SNP nomenclature according to the translation start codon ATG, reference sequence NM_001076085.1. SNPs marked in bold were included in the association analysis. Genomic positions of the SNPs were inferred from the current versions of the refererence and alternative bovine genome assemblies Btau4.2 and UMD_3.1 available at NCBI (http://www.ncbi.nlm.nih.gov/genome/guide/cow/index.html webcite).

Widmann et al. BMC Genetics 2011 12:96   doi:10.1186/1471-2156-12-96

Open Data