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Related Concept Videos

RNA Splicing01:32

RNA Splicing

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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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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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Alternative RNA Splicing02:18

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Chromatin Structure and RNA Splicing02:41

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Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
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Related Experiment Video

Updated: Nov 4, 2025

Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts
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Quantifying splice-site usage: a simple yet powerful approach to analyze splicing.

Craig I Dent1, Shilpi Singh1, Sourav Mukherjee2

  • 1School of Biological Sciences, Monash University, VIC 3800, Australia.

NAR Genomics and Bioinformatics
|May 21, 2021
PubMed
Summary

This study introduces a novel method to measure individual splice site usage, revealing genetic factors influencing gene splicing. This approach links genetic variations to splice site strength, impacting phenotypes across organisms.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • RNA splicing and alternative splicing are crucial for eukaryotic gene regulation and phenotypic diversity.
  • Splicing variations link genetic differences to diseases in humans and environmental responses in plants.
  • Current methods quantify isoforms or splicing events but not individual splice site usage.

Purpose of the Study:

  • To develop a simple approach for quantifying individual splice site usage and strength.
  • To link genetic variation to splice site selection using quantitative phenotypes.
  • To identify genomic determinants of splice site choice via Genome-Wide Association Studies (GWAS).

Main Methods:

  • Quantification of empirical usage of individual splice sites.
  • Analysis of splice site strength as a quantitative phenotype.
  • Genome-Wide Association Studies (GWAS) to identify genetic determinants.

Main Results:

  • A new method to measure individual splice site usage was developed.
  • Splice site usage was directly linked to genetic variation.
  • Pilot GWAS in *Arabidopsis thaliana* suggests *cis*-acting sequence divergence influences splicing variations.

Conclusions:

  • The developed approach enables direct measurement of splice site strength and usage.
  • This method facilitates the study of genomic determinants of splice site choice.
  • Findings have broad implications for understanding gene regulation in agriculture and medicine.