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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...

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...

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...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: 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 17, 2026

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

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

Published on: December 9, 2016

A statistical method for the detection of alternative splicing using RNA-seq.

Liguo Wang¹, Yuanxin Xi, Jun Yu

¹Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA.

|January 15, 2010

Summary

This study introduces a new metric, Minimal Match on Either Side of exon junction (MMES), to improve the accuracy of detecting mRNA splicing patterns from RNA-sequencing data, especially for low-abundance transcripts.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

RNA sequencing (RNA-seq) enables transcriptome analysis, including mRNA splicing patterns.
Existing methods for detecting exon junctions using junction reads have high false positive/negative rates due to transcriptome complexity.

Purpose of the Study:

To develop a more accurate method for detecting exon junctions from RNA-seq data.
To introduce a novel metric for assessing the quality of junction reads.

Main Methods:

Introduced the Minimal Match on Either Side of exon junction (MMES) metric to measure junction read quality.
Implemented an empirical statistical model for exon junction detection using the MMES metric.
Applied the method to a large dataset (>200M reads) of mouse mRNA sequences.

Main Results:

The MMES-based method demonstrated significantly higher accuracy compared to previous approaches.
The method excels at detecting exon junctions from low-abundance transcripts.
Results were validated using independent transcript databases and real-time RT-PCR assays.

Conclusions:

The MMES metric offers a substantial improvement in exon junction detection accuracy.
This metric can be integrated into various statistical models for enhanced RNA-seq analysis.
The developed method provides a more reliable way to study mRNA splicing patterns.