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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

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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: Mar 25, 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

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.

André Kahles¹, Cheng Soon Ong², Yi Zhong¹

¹Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA and.

Bioinformatics (Oxford, England)

|February 14, 2016

Summary

SplAdder enhances transcriptome analysis by identifying and quantifying alternative splicing events from RNA-Seq data. This toolbox improves annotation accuracy and aids in understanding complex gene expression regulation.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing (AS) is crucial for transcriptome complexity in higher eukaryotes.
RNA sequencing (RNA-Seq) enables deep measurement of AS transcript diversity.
Novel transcripts are frequently discovered in under-annotated organisms, disease contexts, or large populations.

Purpose of the Study:

To present SplAdder, a novel toolbox for alternative splicing analysis.
To augment existing gene annotations using RNA-Seq evidence.
To identify, quantify, and statistically compare alternative splicing events.

Main Methods:

Input: RNA-Seq alignments and gene annotation files.
Annotation augmentation based on RNA-Seq data.
Identification and quantification of AS events within an augmented annotation graph.
Statistical testing for differential AS event usage between samples.

Main Results:

SplAdder augments gene annotations with RNA-Seq evidence.
The toolbox identifies, quantifies, and confirms AS events.
SplAdder enables testing for significant quantitative differences in AS events between samples.
Focus on performance, accuracy, and usability in AS analysis.

Conclusions:

SplAdder provides a robust framework for analyzing alternative splicing.
The tool facilitates deeper understanding of transcriptome regulation.
SplAdder is valuable for studies involving novel transcripts or complex populations.