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Functional element SNPs database

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FESD
Content
DescriptionFunctional Element SNPs Database in human.
OrganismsHomo sapiens
Contact
AuthorsHyo Jin Kang
Primary citationKang & al. (2005)[1]
Access
Websitehttp://combio.kribb.re.kr/ksnp/resd/

The Functional Element SNPs Database (FESD) is a database of SNPs in the human Molecular biology.[1]

The Functional Element SNPs Database (FESD) tool is designed to organize functional elements into categories in human gene regions and to output their sequences needed for genotyping experiments as well as provide a set of SNPs that lie within each area. The database defines functional elements with ten units: promoter regions, CpG islands,5_-untranslated regions (5_-UTRs), translation start sites, splice sites, coding exons, introns, translation stop sites, polyadenylation signals, and 3_-UTRs.[2]

Functional Elements


Functional Elements A functional element is taken to mean a piece of DNA that acts out a function.

  • The promoter region is located in the 2Kb upstream of the transcription start site.
  • CpG islands are associated with genes and are typically common near transcription start sites in vertebrates.
  • Slice sites are considered the first and the last 2 bp in introns.

[3]

People may reference this database when haplotyping a gene or chromosome, in hopes of discovering mutations that cause disease. By utilizing the database, researchers can manually choose a group of SNPs of special interest for certain functional elements along with their corresponding sequences.[4] Also, FESD can be used to dteremine predisposition to diseases and conditions.[5] Although the database is useful, it relies on chromosome position and cytogenic banding patterns meaning it cannot recognized manually entered SNPs.

Single Nucleotide Polymorphisms

(SNPs) or single nucleotide polymorphisms are useful genetic markers for molecular diagnosis, drug response, and predisposition to diseases.Several methods have been developed to detect single nucleotide polymorphisms. An SNP is a mutation with a single DNA base substitution observed. Studies have shown that SNPs occur about every hundred bases. SNPs can either be intronic or exonic. Intronic SNPs are located in silent regions of the DNA, and are thought not to have any effect on protein produced if translated. Exonic SNPs are expressed and are found in coding regions of DNA.[6] Nonsynonymous SNPs are exonic SNPs which result in amino acid variants in the protein produced or changes in protein length due to their effects and possibility of a premature stop codon. Also, SNPs are responsible for most individual variability of a population. DNA insertions and deletions of both multiple and single bases are found during SNP sequencing, and are also recorded in SNP databases.[7]

References

  1. ^ a b Kang, Hyo Jin (2005). "FESD: a Functional Element SNPs Database in human". Nucleic Acids Res. (in eng). 33 (Database issue). England: D518-22. doi:10.1093/nar/gki082. PMC 540036. PMID 15608252. {{cite journal}}: Cite has empty unknown parameters: |laydate=, |laysource=, and |laysummary= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help); Unknown parameter |quotes= ignored (help)CS1 maint: unrecognized language (link)
  2. ^ MAH, JAMES T. L., and K. S. CHIA. "A Gentle Introduction To Snp Analysis:: Resources And Tools." Journal Of Bioinformatics & Computational Biology 5.5 (2007): 1123-1138. Academic Search Premier. Web. 9 Sept. 2013
  3. ^ GA Coetzee, et al. "Comprehensive Functional Annotation Of Seventy-One Breast Cancer Risk Loci." Plos One 8.5 (n.d.): Science Citation Index. Web. 6 Sept. 2013.
  4. ^ Chang Hsueh-Wei, et al. "Dynamic Programming For Single Nucleotide Polymorphism ID Identification In Systematic Association Studies." Kaohsiung Journal Of Medical Sciences 25.(n.d.): 165-176. ScienceDirect. Web. 9 Sept. 2013.
  5. ^ F. ( 2 ) Takagi, et al. "Novel High-Speed Droplet-Allele Specific-Polymerase Chain Reaction: Application In The Rapid Genotyping Of Single Nucleotide Polymorphisms." Clinica Chimica Acta 424.(2013): 39-46. Scopus®. Web. 18 Sept. 2013.
  6. ^ MAH, JAMES T. L., and K. S. CHIA. "A Gentle Introduction To Snp Analysis:: Resources And Tools." Journal Of Bioinformatics & Computational Biology 5.5 (2007): 1123-1138. Academic Search Premier. Web. 9
  7. ^ Haja N. Kadarmideen, et al. "Functsnp: An R Package To Link Snps To Functionalknowledge And Dbautomaker: A Suite Of Perlscripts To Build SNP Databases." BMC Bioinformatics 11.(2010): 311-319. Academic Search Premier. Web. 18 Sept. 2013.


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