TAILIEUCHUNG - Identification and prediction of the consequences of nonsynonymous SNPs in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish Danio rerio
The recent progress in DNA sequencing and computational algorithms dramatically heightened the value of single nucleotide polymorphism (SNP) databases. The experimental studies of mutation for the particular gene of interest are laborious and timeconsuming. | Turkish Journal of Biology Research Article Turk J Biol (2016) 40: 43-54 © TÜBİTAK doi: Identification and prediction of the consequences of nonsynonymous SNPs in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish Danio rerio Kiran Dashrath RASAL*, Vemulawada CHAKRAPANI, Swagat Kumar PATRA, Sasmita JENA, Shibani Dutta MOHAPATRA, Swapnarani NAYAK, Jitendra Kumar SUNDARAY, Pallipuram JAYASANKAR, Hirak Kumar BARMAN Fish Genetics and Biotechnology Division, Central Institute of Freshwater Aquaculture, Indian Council of Agricultural Research, Bhubaneswar, Odisha, India Received: Accepted/Published Online: Final Version: Abstract: The recent progress in DNA sequencing and computational algorithms dramatically heightened the value of single nucleotide polymorphism (SNP) databases. The experimental studies of mutation for the particular gene of interest are laborious and timeconsuming. In this study, we used several computational algorithms to investigate the structural and functional consequences of SNPs on the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish (Danio rerio). The GAPDH gene is involved in multiple cellular activities, in addition to its association with classical glycolytic pathway. It has most commonly been used as the housekeeping gene for differential gene expression profiling, including western blots. The computational analysis, which used sequence-based tools such as SIFT, PANTHER, PROVEAN, and , predicted deleterious nonsynonymous SNPs (nsSNPs) at in the GAPDH gene. The SWISS Model tool generated a homology-modeled 3D structure of GAPDH by applying homologous protein structures retrieved from the RCSB PDB databank (PDB ID: 1U8F_O, 1ZNQ_O, 1J0X_O, 3GPD_R, and 1SZJ_G). The sequence identities of the above selected models were 86%, 86%, 86%, 83%, and 75%, respectively. The Procheck quality assessment in .
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