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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...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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: Jul 4, 2026

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

FIRMA: a method for detection of alternative splicing from exon array data.

E Purdom¹, K M Simpson, M D Robinson

¹Department of Statistics, University of California at Berkeley, 367 Evans Hall #3860, Berkeley, CA 94720-3860, USA. epurdom@stat.berkeley.edu

Bioinformatics (Oxford, England)

|June 25, 2008

Summary

New methods are needed to analyze alternative splicing data from exon arrays. Finding Isoforms Using Robust Multichip Analysis (FIRMA) detects differential alternative splicing and confirms gene exons.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing is a widespread mechanism in gene expression.
Exon and tiling microarrays enable genome-wide measurement of alternative splicing.
Novel analytical methods are required for this high-throughput data.

Purpose of the Study:

To develop and evaluate a novel method for detecting differential alternative splicing from exon array data.
To address the need for robust analysis of genome-wide alternative splicing experiments.

Main Methods:

The study presents Finding Isoforms Using Robust Multichip Analysis (FIRMA).
FIRMA is designed for Affymetrix exon arrays but is extensible to other array types.
The method was validated using simulated data and real biological datasets.

Main Results:

FIRMA effectively detects differential alternative splicing in exon array data.
The method was applied to human tissue and matched normal/tumor colon tissue datasets.
FIRMA identified exons in multiple genes, validated by reverse transcriptase PCR.

Conclusions:

FIRMA provides a robust approach for analyzing alternative splicing from exon array data.
The method has potential applications in various genomic and transcriptomic studies.
R code for FIRMA is available within the aroma.affymetrix package.