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Updated: Jul 18, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay
Areum Han1, Woo-Yeon Kim, Seong-Min Park
1Korean Bioinformation Center, KRIBB, Daejeon 305-806, Korea.
Bioinformatics (Oxford, England)
|November 24, 2006
Summary
SNP2NMD is a new database for human single nucleotide polymorphisms (SNPs) that cause premature termination codons (PTCs) and trigger nonsense-mediated mRNA decay (NMD). This resource aids disease association studies by providing genetic information on SNPs, genes, and diseases.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Genetic polymorphisms play a crucial role in disease association studies.
- Single nucleotide polymorphisms (SNPs) can lead to premature termination codons (PTCs).
- Nonsense-mediated mRNA decay (NMD) is a key cellular surveillance pathway affected by PTCs.
Purpose of the Study:
- To develop a comprehensive database, SNP2NMD, for human SNPs that trigger NMD.
- To facilitate research in disease association by providing detailed genetic information.
Main Methods:
- Database development focused on cataloging human SNPs.
- Integration of information on SNPs, associated genes, and relevant diseases.
- Implementation of web interfaces for data retrieval and visualization.
Main Results:
- The SNP2NMD database provides extensive genetic information on SNPs.
- Graphical views of queried SNPs, genes, and disease terms are available.
- The database serves as a valuable resource for researchers in genetics and disease studies.
Conclusions:
- SNP2NMD enhances the study of genetic polymorphisms and their impact on gene networks.
- The database supports disease association studies by linking SNPs, PTCs, and NMD.
- Accessible web interfaces improve the usability of genetic and disease information.
Related Concept Videos
02:27Nonsense-mediated mRNA Decay
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
02:27Nonsense-mediated mRNA Decay
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
02:31Nuclear Export of mRNA
Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
02:18Alternative RNA Splicing
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...