Deleterious single nucleotide polymorphisms of protein kinase R identified by the computational approach

Melzer, Anna Maria; Palanisamy, Navaneethan

doi:10.1016/j.molimm.2018.05.026

Cited by 2 publications

(1 citation statement)

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“…Although there is no previous antecedents in fish, the SNP effect on the protein structure has been evaluated on genes of immunologic interest (Jang et al, 2017;Majumdar et al, 2017;Melzer and Palanisamy, 2018), including human glutathione-Stransferase superfamily (Kitteringham et al, 2007). The structure of GSTO-1 is composed mainly of an N-terminal domain of the thioredoxin type which consists of four central b-sheets surrounded at each end by a-helices, and a C-terminal end which is mainly made of a-helices (Board et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar)

Vallejos‐Vidal¹,

Reyes-Cerpa²,

Rivas‐Pardo³

et al. 2020

Front. Genet.

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Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ccl19], integrin b2 (itb2, also named cd18), glutathione transferase omega-1 [gsto-1], heat shock 70 KDa protein [hsp70], major histocompatibility complex class I [mhc-I]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5'-untranslated region (UTR) or 3'-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itb2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (DRSCU) showed one negative (hsp70 c.1950C > T) and two positive DRSCU values (itb2 c.2275G > A; gsto-1 c.558G > A), suggesting that these

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