PMC:1482699 / 20862-22778 JSONTXT

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The coding region of each gene was sequenced from the CAST strain and compared to the publicly available B6 sequence to identify polymorphisms (Additional File 4). A total of 94.492 kbp was sequenced (75.378 kbp CDS and 19.114 Kbp 5' and 3' untranslated region (UTR)), representing 25,083 amino acids. Comparison with the public B6 assembly (May 2004 University of California, Santa Cruz (UCSC [28]) mm5 genome assembly, National Center for Biotechnology Information (NCBI) Build 33) identified 307 polymorphisms between CAST and B6. Of these, 295 were single nucleotide polymorphisms (SNP) and 12 were insertions or deletions in CAST (Additional File 4). All 12 insertions or deletions were located within 5' and 3' UTRs. Fifty-six nonsynonomous SNP (nsSNP) were identified in 14 different genes (Additional File 4). PolyPhen [29] and SIFT [30] are software programs designed to identify nsSNP which potentially alter protein function by evaluating evolutionary conservation at specific amino acid residues using a multiple sequence alignment of protein sequences homologous to the query. When applied to our data set PolyPhen, SIFT or both programs predicted that 15 of the 56 nsSNP in 9 different genes would possibly alter protein function (Table 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