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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...

RNA Splicing

RNA Splicing

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

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

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

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Related Experiment Video

Updated: Mar 14, 2026

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

Does conservation account for splicing patterns?

Michael Wainberg¹, Babak Alipanahi¹, Brendan Frey^2,3,4

¹Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, Canada.

|October 9, 2016

Summary

This summary is machine-generated.

Alternative mRNA splicing generates protein diversity. A new computational model reveals splice site conservation predicts splicing patterns, suggesting novel regulatory elements and proteins drive evolutionary changes in gene expression.

Keywords:

Alternative splicing Conservation Splicing regulation

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Published on: June 30, 2022

Area of Science:

Genetics and Genomics
Molecular Biology
Bioinformatics

Background:

Alternative mRNA splicing, particularly exon skipping, is crucial for proteomic diversity and organismal differentiation.
Understanding the regulatory mechanisms of alternative splicing is key to deciphering gene expression complexity.

Purpose of the Study:

To develop a computational model for predicting alternative splicing with high accuracy.
To identify key sequence features that govern alternative splicing patterns.
To investigate the evolutionary role of splicing regulation.

Main Methods:

Development of a novel computational model for predicting percent-spliced-in values of cassette exons.
Utilized splice junction conservation scores (e.g., phastCons) as primary predictive features.
Defined and analyzed intronic splicing regulatory elements (ISREs) independent of known motifs.

Main Results:

The model accurately predicts alternative splicing without relying on handcrafted biological features.
Conservation of splice junctions and flanking introns is a powerful predictor of splicing outcomes.
Intronic splicing regulation is localized near splice sites, and conserved intronic elements act as regulators.
Increased flanking intron conservation correlates with decreased exon inclusion.
Identified novel intronic splicing regulatory elements (ISREs) not matching known binding sites.

Conclusions:

The emergence of cis-acting splicing inhibitors may explain the evolutionary shift from constitutive to alternative splicing.
The identified ISREs suggest the existence of novel RNA-binding proteins or uncharacterized roles for known proteins in splicing regulation.