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Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

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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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%...

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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
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Related Experiment Video

Updated: Aug 28, 2025

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

Comprehensive and scalable quantification of splicing differences with MntJULiP.

Guangyu Yang¹, Sarven Sabunciyan², Liliana Florea^3,4

¹Department of Computer Science, Johns Hopkins University, 733 N Broadway, MRB 462, Baltimore, MD, 21205, USA.

|September 14, 2022

Summary

MntJULiP offers a novel, accurate method for quantifying splicing differences across multiple conditions. This tool identifies thousands of differentially spliced introns, including novel ones, enhancing our understanding of phenotypic variation.

Keywords:

Alternative splicing Differential splicing RNA-seq Transcriptomics

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Last Updated: Aug 28, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts

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Published on: October 9, 2016

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Existing tools for differential splicing detection lack comprehensiveness and consistency.
Accurate quantification of splicing variation is crucial for understanding biological processes.

Purpose of the Study:

To introduce MntJULiP, a novel computational method for comprehensive and accurate quantification of splicing differences.
To address limitations of current tools in detecting splicing variations.

Main Methods:

Development of MntJULiP, a novel algorithm for differential splicing analysis.
Application of MntJULiP to analyze 1398 GTEx brain samples.

Main Results:

MntJULiP accurately quantifies changes in intron splicing ratios and absolute splicing levels.
Identified over 29,000 differentially spliced introns, including 11,242 novel introns.
Demonstrated high scalability, processing thousands of samples efficiently.

Conclusions:

MntJULiP provides a comprehensive and accurate approach to differential splicing analysis.
The method reveals splicing variations previously overlooked by other tools.
MntJULiP facilitates the study of splicing's role in phenotypic differentiation.