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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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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...
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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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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Single Nucleotide Polymorphisms-SNPs01:05

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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,...
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Updated: Jun 14, 2025

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SpliceVarDB: A comprehensive database of experimentally validated human splicing variants.

Patricia J Sullivan1, Julian M W Quinn2, Weilin Wu2

  • 1Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.

American Journal of Human Genetics
|September 3, 2024
PubMed
Summary
This summary is machine-generated.

SpliceVarDB is a new database that consolidates over 50,000 splicing variants from thousands of genes. This resource aids in interpreting genetic variants that affect gene splicing, improving diagnostic accuracy.

Keywords:
canonical splice sitegenomicspathogenicsplice regionsplice sitesplicingsplicing regulatory elementtranscriptomicsvariant interpretationwhole-genome sequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Splicing variants contribute significantly to genetic diseases but are challenging to predict using DNA data alone.
  • Current RNA-based analyses are resource-intensive, and validated splicing variant data is fragmented and underrepresented in public databases like ClinVar.
  • This fragmentation hinders variant interpretation and leads to redundant validation efforts.

Purpose of the Study:

  • To develop SpliceVarDB, a centralized online database for variants affecting gene splicing.
  • To standardize and harmonize splicing variant validation data from diverse experimental sources.
  • To facilitate the interpretation of splicing variants and support the development of improved in silico prediction tools.

Main Methods:

  • Compiled over 50,000 variants impacting splicing across more than 8,000 human genes.
  • Systematically evaluated over 500 published data sources for variant spliceogenicity.
  • Established a spliceogenicity scale to classify variants based on evidence strength.

Main Results:

  • Classified variants into "splice-altering" (~25%), "not splice-altering" (~25%), and "low-frequency splice-altering" (~50%) categories.
  • Identified that 55% of splice-altering variants in SpliceVarDB are located outside canonical splice sites, including deep intronic regions.
  • Demonstrated the utility of SpliceVarDB for variant curation and the development of predictive models.

Conclusions:

  • SpliceVarDB provides a comprehensive, harmonized resource for splicing variant data, addressing a critical gap in genetic variant interpretation.
  • The database supports diagnostic workflows and the advancement of in silico splicing prediction tools.
  • SpliceVarDB is publicly accessible at https://splicevardb.org, promoting collaborative research and improving genetic disease diagnostics.