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Single Nucleotide Polymorphisms-SNPs

Single 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,...

Comparing Copy Number Variations and SNPs

Comparing 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%...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

Alternative RNA Splicing

Alternative 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...

RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

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Related Experiment Video

Updated: Jun 20, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database.

Jin Ok Yang¹, Woo-Yeon Kim, Jong Bhak

¹Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.

|September 18, 2009

Summary

Single nucleotide polymorphisms (SNPs) at splice sites significantly impact gene function and disease risk. The ssSNPTarget database offers a comprehensive resource for studying these splice site SNPs (ssSNPs) in humans and mice.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing affects over 90% of human genes, influencing protein diversity.
Splice site recognition is crucial for accurate exon-intron boundary processing.
Single nucleotide polymorphisms (SNPs) in splice sites can alter mRNA translation and disease susceptibility.

Purpose of the Study:

To develop and present the ssSNPTarget database, a novel resource for splice site SNPs (ssSNPs).
To provide comprehensive information on ssSNPs in human and mouse genes, including their distribution and functional impact.

Main Methods:

Curated and integrated data on ssSNPs from various sources.
Analyzed SNP effects on junction strength, protein domains, and alternative splicing events.
Incorporated splice site conservation data and disease associations from OMIM, GAD, and HGMD.

Main Results:

The ssSNPTarget database contains 1,576 human ssSNPs across 1,193 genes and 538 mouse ssSNPs across 281 genes.
Detailed information on ssSNP distribution, functional consequences, conservation, and disease links is provided.
User-friendly query options via gene symbol, SNP rs number, transcript ID, or genomic position.

Conclusions:

ssSNPTarget serves as a valuable resource for researchers investigating the role of ssSNPs in gene regulation and disease.
Facilitates the study of alternative splicing variations and their implications for human and mouse genetics.