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Exploring a SNP in mouse

In the paper “Altered metabolic signature in pre-diabetic NOD mice” (PloS One. 2012; 7(4): e35445), Madsen et al. have described several regulatory and coding SNPs, some of them in genes involved in ATP and adenosine metabolism, leading to potentially faulty metabolism of ATP and adenosine. The authors describe that one of the identified SNPs in the murine Entpd2 gene (rs28232063) would lead to increased amounts of available ATP, an immune activator, causing increased cell activation and possibly autoreactive T-cell activation. Use Ensembl to answer the following questions:

  1. Where is the SNP located (chromosome and coordinates)?

  2. What is the HGVS recommendation nomenclature for this SNP?

  3. Why does Ensembl put the G allele first (G/A)?

  4. Are there differences between the genotypes reported in C57BL/6NJ and NOD/ShiLtJ, according to the Mouse Genomes Project?

  1. From the Ensembl homepage, select Mouse from the Species search drop-down and enter rs28232063 in the search box.

    SNP rs28232063 is located on 2:25288362. In Ensembl, its alleles are provided relative to the forward strand.

  2. Click on Show under HGVS names to reveal information about HGVS nomenclature.

    This SNP has got four HGVS names, one at the genomic DNA level (NC_000068.8:g.25288362G>A), two at the transcript level (ENSMUST00000148859.2:n.444-182G>A and ENSMUST00000028328.3:c.446G>A) and one at the protein level (ENSMUSP00000028328.3:p.Arg149Gln).

  3. In Ensembl, the allele that is present in the reference genome assembly is always put first.

    G is the allele for the reference mouse genome strain C57BL/6J

  4. Click on Sample genotypes is the left-hand panel. The table shows genotypes reported for different mouse strains from the Mouse Genomes Project.

    There are indeed differences between the genotypes reported in those two different strains. The genotype reported in C57BL/6NJ is G/G whereas in NOD/ShiLtJ the genotype is A/A.