Author information: (1)Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene’s function.For people interested in more technical data, several databases of known SNPs are available: by developing and applying cost-effective kompetitive allele specific polymerase chain reaction genotyping assays. The nucleotide sequence of ancestral and variant alleles is available in the ‘dbSNP’. This makes them very useful in old samples with low-quantity DNA template, and/or in degraded samples where the available DNA is fragmented.
Thus, SNP selection on the promoter regions was based in the differences on TF binding pattern between the old and the new allele. Clevenger J(1), Chavarro C(2), Pearl SA(2), Ozias-Akins P(3), Jackson SA(4).
Using this approach we were able to identify SNPs responsible for generating important differences in TFs pattern to a TFBS.We thank Professor Fernando Rodrigues from ICVS, UM for insights into genetic transcriptional organization; QIAGEN’s application specialist, Jorge Posadas; and HapMap’s staff.Therefore, the goal of this study was to develop a method to select SNP in the coding and essentially the promoter regions of genes. Nagy, S.J.
A Single Nucleotide Polymorphism is also known as a SNP or snp (pronounced 'snip').
A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual. A SNP in these regions can change the affinity for the usual TFs and in certain situations lead to the introduction of new ones. Transcriptional regulation involves proteins and TFs that bind to short regulatory sequences, or motifs, in the promoter region, also known as transcription factors binding site (TFBS). The majority of SNPs is biallelic, but tri-allelic and tetra-allelic SNPs have also been reported.At the present time, few data on the use of X-chromosome SNP in forensic analysis have been published, although some studies have already shown their applicability in relationship testing and population characterization. SNPs can also be used to track the inheritance of disease genes within families. Among several difficulties, we are faced with the promiscuity of the TFs. The potential clinical relevance of the new TFs was also evaluated before the final selection. Plant …
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