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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
RNA Splicing01:32

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...
RNA Splicing01:32

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...
Alternative RNA Splicing02:18

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...
Alternative RNA Splicing02:18

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...
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).

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Related Experiment Video

Updated: Jun 5, 2026

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
08:53

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

Context-dependent robustness to 5' splice site polymorphisms in human populations.

Zhi-xiang Lu1, Peng Jiang, James J Cai

  • 1Department of Internal Medicine, University of Iowa, 3294 CBRB, 285 Newton Rd, Iowa City, IA 52242, USA.

Human Molecular Genetics
|January 13, 2011
PubMed
Summary

Genetic variations in 5' splice sites show surprising robustness in human cells. Specific intronic elements, like poly-G runs, protect exons from mutations, revealing insights into the splicing code.

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Last Updated: Jun 5, 2026

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
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ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Alternative splicing exhibits significant diversity across human populations.
  • Genetic variants at the 5' splice site are linked to splicing variations and human diseases.
  • Understanding 5' splice site recognition is crucial for deciphering gene regulation.

Purpose of the Study:

  • To investigate natural variations in splicing and their impact on 5' splice site recognition.
  • To identify genetic signals that modify the effects of 5' splice site polymorphisms.
  • To explore the robustness of the human transcriptome to 5' splice site variations.

Main Methods:

  • Analysis of single nucleotide polymorphisms (SNPs) in 5' splice sites across diverse human cell lines.
  • Quantitative examination of splicing impact for selected SNPs using minigene assays.
  • Bioinformatic analysis to identify modifying sequence motifs and regulatory elements.

Main Results:

  • Identified 1174 SNPs within consensus 5' splice sites; 129 were tested for splicing impact.
  • Surprisingly, only ~14% of tested SNPs altered splicing outside the essential GT dinucleotide.
  • Discovered that strong 3' splice sites and downstream intronic motifs, particularly poly-G runs, confer robustness to 5' splice site polymorphisms.
  • The poly-G run was significantly enriched downstream of exons unaffected by 5' splice site SNPs.

Conclusions:

  • Human transcriptomes exhibit widespread context-dependent robustness to 5' splice site polymorphisms.
  • Certain exons are more vulnerable to 5' splice site mutations due to a lack of protective elements.
  • Genetic diversity in alternative splicing provides valuable insights into the mammalian splicing code.