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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...

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...

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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.
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Related Experiment Video

Updated: Sep 6, 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

Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder.

Philipp Markolin^1,2,3, Gunnar Rätsch^1,2,3, André Kahles^4,5,6

¹Biomedical Informatics Group, Department of Computer Science, ETH Zurich, Zurich, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)

|June 25, 2022

Summary

This summary is machine-generated.

Alternative splicing (AS) is a key RNA maturation process. SplAdder tool enhances AS event identification and quantification using RNA-sequencing data for deeper biological insights.

Keywords:

Alternative splicing Bioinformatics Data analysis RNA-sequencing Sequence analysis Transcriptomics

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Last Updated: Sep 6, 2025

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing (AS) is a crucial post-transcriptional regulation mechanism in eukaryotes.
RNA sequencing (RNA-Seq) offers high-resolution data for studying transcriptomes and AS.
Understanding AS is vital for gene regulation, population genetics, and disease research.

Purpose of the Study:

To introduce SplAdder, a graph-based bioinformatics toolbox for analyzing alternative splicing.
To demonstrate how SplAdder integrates RNA-Seq data with existing annotations to discover novel AS events.
To showcase SplAdder's capability in quantifying and confirming AS events and detecting differential splicing.

Main Methods:

Utilizing a graph-based approach to represent and analyze splicing patterns.
Integrating multiple RNA-Seq alignment files with annotation data.
Augmenting existing gene annotations with RNA-Seq evidence.
Developing methods for identifying, quantifying, and statistically testing AS events.

Main Results:

SplAdder successfully augments gene annotations using RNA-Seq data.
The toolbox enables comprehensive identification and quantification of AS events.
SplAdder facilitates the detection of significant quantitative differences in splicing between sample groups.

Conclusions:

SplAdder is an effective tool for in-depth analysis of alternative splicing from RNA-Seq data.
The toolbox enhances the discovery and characterization of AS events.
SplAdder aids in understanding the biological and clinical implications of alternative splicing.