scholarly journals dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation

1999 ◽  
Vol 9 (8) ◽  
pp. 677-679 ◽  
Author(s):  
Stephen T. Sherry ◽  
Minghong Ward ◽  
Karl Sirotkin
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dbsnp Database

In Silico Analysis of Non Synonymous Single Nucleotide Polymorphisms (nsSNPs) of SMPX Gene in Hearing Impairment

2018 ◽  
Author(s):  
Md. Arifuzzaman ◽  
Sarmistha Mitra ◽  
Amir Hamza ◽  
Raju Das ◽  
Nurul Absar ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Protein Stability ◽  
In Silico Analysis ◽  
Normal Activity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Stability Change ◽  
And Function ◽  
Dbsnp Database

ABSTRACTBackgroundMutations in SMPX gene can disrupt the normal activity of the SMPX protein which is involved in hearing process.ObjectiveIn this study, deleterious non-synonymous single nucleotide polymorphisms were isolated from the neutral variants by using several bioinformatics tools.MethodFirstly, dbSNP database hosted by NCBI was used to retrieve the SNPs of SMPX gene, secondly, SIFT was used primarily to screen the damaging SNPs. Further, for validation PROVEAN, PredictSNP and PolyPhen 2 were used. I-Mutant 3 was utilized to analyze the protein stability change and MutPred predicted the molecular mechanism of protein stability change. Finally evolutionary conservation was done to study their conservancy by using ConSurf server.ResultsA total of 26 missense (0.6517%) and 3 nonsense variants (0.075%) were retrieved and among them 4 mutations were found deleterious by all the tools of this experiment and are also highly conserved according to ConSurf server. rs772775896, rs759552778, rs200892029 and rs1016314772 are the reference IDs of deleterious mutations where the substitutions are S71L, N19D, A29T and K54N. Loss of Ubiquitination, loss of methylation, loss of glycosylation, and loss of MoRF binding motifs are the root causes of protein stability change.ConclusionThis is the first study regarding nsSNPs of SMPX gene where the most damaging SNPs were screened that are associated with the SMPX gene and can be used for further research to study their effect on protein structure and function, their dynamic behavior and how they actually affect protein’s flexibility.

scholarly journals Identification of 1093-bp intron A, SNPS and indels discovered in the porcine pregnancy-associated glycoprotein 2-like (pPAG2-L) gene subfamily in pigs

Genetika ◽  
2020 ◽  
Vol 52 (3) ◽  
pp. 851-866
Author(s):  
Martyna Bieniek-Kobuszewska ◽  
Grzegorz Panasiewicz ◽  
Bożena Szafranska
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
General Knowledge ◽  
Nucleotide Polymorphisms ◽  
Porcine Genome ◽  
Large White ◽  
Bac Clone ◽  
Single Nucleotide ◽  
Noncoding Regions ◽  
Gene Subfamily

The objective of this study was to identify the intron A sequence (between exons 1 and 2) of pPAG2-L, novel single nucleotide polymorphisms (SNPs) and mutations (InDels) within intron A in the crossbreed (Landrace x Large White), Hirshmann hybrid and Duroc pigs. Genomic templates were isolated from leukocytes, amplified, and the gel-out were purified and then sequenced. Positive amplification control included CH242-60C13 BAC clone (Duroc) containing pPAG1-L and pPAG2-L. This is the first report that describes the 1093-bp intron A sequence from the pPAG2-L (Acc. No. KF471015; GenBank), which increased general knowledge of the porcine genome. Novel SNPs/InDels were identified within the intron A of the pPAG2-L in the crossbreeds (72), Duroc (45) and Hirshmann hybrids (17). This is a pioneer study describing identification of the intron A and SNPs/InDels in crossbreeds that provides a novel major pattern that represents a large portion of the genetic variation within the porcine genome. This information should be valuable when genotyping (coding and noncoding regions) multiparous sows from many breeds, in which reproductive phenotypes are known.

Phylogeny and genetic variation in the genus Eranthis using nrITS and cpIS single nucleotide polymorphisms

2019 ◽  
Vol 60 (2) ◽  
pp. 239-252 ◽  
Author(s):  
Seo Young Park ◽  
Mi Jin Jeon ◽  
Sang Hoon Ma ◽  
Eric Wahlsteen ◽  
Keenan Amundsen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Impact of Genetic Variability on Physiological Responses to Caffeine in Humans: A Systematic Review

Nutrients ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 1373 ◽  
Author(s):  
Jacob Fulton ◽  
Petros Dinas ◽  
Andres Carrillo ◽  
Jason Edsall ◽  
Emily Ryan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Analysis ◽  
Physiological Responses ◽  
Controlled Trials ◽  
Nucleotide Polymorphisms ◽  
Caffeine Consumption ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Aryl Hydrocarbon

Emerging research has demonstrated that genetic variation may impact physiological responses to caffeine consumption. The purpose of the present review was to systematically recognize how select single nucleotide polymorphisms (SNPs) impact habitual use of caffeine as well as the ergogenic and anxiogenic consequences of caffeine. Two databases (PubMed and EBSCO) were independently searched using the same algorithm. Selected studies involved human participants and met at least one of the following inclusion criteria: (a) genetic analysis of individuals who habitually consume caffeine; (b) genetic analysis of individuals who underwent measurements of physical performance with the consumption of caffeine; (c) genetic analysis of individuals who underwent measurements of mood with the consumption of caffeine. We included 26 studies (10 randomized controlled trials, five controlled trials, seven cross-sectional studies, three single-group interventional studies and one case-control study). Single nucleotide polymorphisms in or near the cytochrome P450 (CYP1A2) and aryl hydrocarbon receptor (AHR) genes were consistently associated with caffeine consumption. Several studies demonstrated that the anxiogenic consequences of caffeine differed across adenosine 2a receptor (ADORA2A) genotypes, and the studies that investigated the effects of genetic variation on the ergogenic benefit of caffeine reported equivocal findings (CYP1A2) or warrant replication (ADORA2A).

scholarly journals Cannabis labelling is associated with genetic variation in terpene synthase genes

Nature Plants ◽  
2021 ◽  
Vol 7 (10) ◽  
pp. 1330-1334
Author(s):  
Sophie Watts ◽  
Michel McElroy ◽  
Zoë Migicovsky ◽  
Hugo Maassen ◽  
Robin van Velzen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
Terpene Synthase ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Tandem Arrays

AbstractAnalysis of over 100 Cannabis samples quantified for terpene and cannabinoid content and genotyped for over 100,000 single nucleotide polymorphisms indicated that Sativa- and Indica-labelled samples were genetically indistinct on a genome-wide scale. Instead, we found that Cannabis labelling was associated with variation in a small number of terpenes whose concentrations are controlled by genetic variation at tandem arrays of terpene synthase genes.

scholarly journals Correction to: Phylogeny and genetic variation in the genus Eranthis using nrITS and cpIS single nucleotide polymorphisms

2019 ◽  
Vol 60 (3) ◽  
pp. 453-453
Author(s):  
Seo Young Park ◽  
Mi Jin Jeon ◽  
Sang Hoon Ma ◽  
Eric Wahlsteen ◽  
Keenan Amundsen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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