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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

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...

Pre-mRNA Processing: RNA Splicing

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Related Experiment Video

Updated: Nov 4, 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

Improved methods for RNAseq-based alternative splicing analysis.

Rebecca F Halperin¹, Apurva Hegde², Jessica D Lang³

¹Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA. rhalperin@tgen.org.

Scientific Reports

|May 25, 2021

Summary

This summary is machine-generated.

This study introduces Bisbee, a novel software for detecting splicing outliers and differential splicing from RNAseq data. Bisbee predicts protein-level effects, improving accuracy for identifying disease-associated splice variants.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Detecting disease-associated splice events from RNAseq data is challenging due to confounding gene expression and limited patient data.
Existing splicing analysis tools often lack the ability to predict the protein-level impact of splice alterations.

Purpose of the Study:

To present a novel statistical approach and software (Bisbee) for robust splicing outlier detection and differential splicing analysis.
To enable prediction of protein-level effects of splice alterations, enhancing the interpretation of RNAseq data.

Main Methods:

Developed a statistical approach testing differences in percentages of sequence reads representing local splice events.
Created the Bisbee software package for splicing analysis and protein-level effect prediction.
Validated Bisbee using matched RNAseq and mass spectrometry data from normal tissues.

Main Results:

Bisbee demonstrated improved sensitivity and specificity compared to existing methods.
Identified tissue-specific splice variants with confirmed protein-level expression via mass spectrometry.
Successfully applied Bisbee to identify pathogenic splicing variants in rare diseases and tumor-specific splice isoforms in melanoma.

Conclusions:

Bisbee offers a powerful new tool for analyzing splicing events and predicting their functional consequences.
The software aids in discovering disease-associated splice variants and validating their protein-level effects.
Bisbee's capabilities were confirmed through validation in rare disease and cancer datasets, including melanoma.