Table 5

Non-synonymous SNPs between C57BL6/J and FVB/NJ in Ath11

Chromosome 10 position

Ref/FVB

dbSNP ID

MGP

Gene name, Ensembl gene ID and description

Trans.

Protein domain


5016217

G/C

None

8

Syne1

ENSMUSG00000019769

Synaptic nuclear envelope 1

1/4

Spectrin repeat

5380387

C/A

rs29315913

13

Esr1

ENSMUSG0000001976

Estrogen receptor 1

1/5

Nuclear hormone receptor, ligand-binding, core

5977100

A/C

None

16

Zbtb2

ENSMUSG00000075327

Zinc finger and BTB domain containing 2

2/2

None

6338741

A/G

rs29378605

15

Mthfd1l

ENSMUSG00000040675

Methylenetetrahydrofolate dehydrogenase (NAD P+ dependent) 1-like

3/3

Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain

6367833

A/G

rs29320259

14

Mthfd1l

ENSMUSG00000040675

Methylenetetrahydrofolate dehydrogenase (NAD P+ dependent) 1-like

3/3

Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain

7309964

T/C

rs29376214

6

Lrp11

ENSMUSG00000019796

Low density lipoprotein receptor-related protein 11

4/6

    Polycystic Kidney Disease
(PKD) domain

21108744

A/G

rs49757404

12

Aldh8a1

ENSMUSG00000037542

Aldehyde dehydrogenase 8 family

1/2

Aldehyde dehydrogenase domain

21787374

C/T

rs47037014

8

4930444G20Rik

ENSMUSG00000069712

RIKEN cDNA 4930444G20 gene

1/1

None

21787451

A/C

rs50088182

9

4930444G20Rik

ENSMUSG00000069712

RIKEN cDNA 4930444G20 gene

1/1

None

21864292

C/T

rs49453000

8

E030030I06Rik

ENSMUSG00000055657

RIKEN cDNA E030030I06 gene

1/1

None

21868313

T/C

None

9

E030030I06Rik

ENSMUSG00000055657

RIKEN cDNA E030030I06 gene

1/1

None

21868315

T/A

None

9

E030030I06Rik

ENSMUSG00000055657

RIKEN cDNA E030030I06 gene

1/1

None


Wolfrum et al. [34] characterized two narrowed regions, 10a and 10b, within Ath11 containing 28 genes. This table describes additional non-synonymous SNPs discovered by sequencing of the FVB/NJ genome. Listed are the reference allele and FVB/NJ allele (Ref/FVB), the dbSNP ID (build 128) for sites previously identified as polymorphic in other mouse strains, and the number of strains in the Mouse Genomes Project (MGP) with the same allele as FVB/NJ. Also listed is the number of protein-coding transcripts (Trans.) affected and the protein domain involved. Gene and protein domain models were obtained from Ensembl version 64.

Wong et al. Genome Biology 2012 13:R72   doi:10.1186/gb-2012-13-8-r72

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