In Silico Analysis of Noncoding Snps of Human Socs3 Gene and Their Effects on Protein Functions

Background and aim: socs3 is a tumor suppressor that has been identified as upstream of jak/stat3 signaling by specific kinase inhibition. in this study, we describe the role of non-coding mutations in modulating the outcome of cancer mechanisms. we analyzed snps in non-coding regions of socs3 to see the effects of these snps on the function of gene-based on a new 'in silico' approach for identifying regulatory variants. methods: using mirna snp to explore the impact of the 3' and 5' utr snps on mrna:mirna interaction, 25 snps were found to target gain/loss by snps in mirna. snp2tfbs used to identify variations that affect transcription factor binding. among 22 common snps obtained from the ucsc genome browser, snp2tfbs outputs were a table that listed 5 snps and their related factors whose binding sites are significantly affected by these variants. furthermore, the analyses of utrdb showed 3 important untranslated regions (5'-utr and 3'-utr) of socs3 mrna and related snps, which changed functional patterns contained in mrna untranslated regions. results: this study revealed deleterious snps located in the human socs3 gene non-coding region that may alter the protein functions. conclusion: snps are considered the most useful biomarkers for disease diagnosis or prognosis due to their common frequency, ease of analysis, low genotyping costs, and the possibility to carry out association studies based on statistical and bioinformatics tools.