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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...

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 DNA...

RNA Splicing

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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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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 3, 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

Identify alternative splicing events based on position-specific evolutionary conservation.

Liang Chen¹, Sika Zheng

¹Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America. liang.chen@usc.edu

|July 31, 2008

Summary

This summary is machine-generated.

We developed a comparative genomics method to identify conditional exons, which are alternatively spliced. This approach significantly enhances human transcriptome annotation and reveals novel splicing events.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Published on: June 24, 2021

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing significantly expands the human transcriptome.
Identifying all alternative splicing events remains a challenge in the post-genome era.

Purpose of the Study:

To develop a comparative genomics approach to systematically identify alternative splicing events, specifically conditional exons.
To characterize the distinguishing features of conditional exons compared to constitutive exons and introns.

Main Methods:

Utilized differential evolutionary conservation between exons and introns.
Applied the Random Forests algorithm for classification.
Leveraged high-quality ENCODE region annotations.

Main Results:

Identified position-specific conservation score differences between conditional and constitutive exons and their flanking introns.
Achieved high specificities (97% and 95%) and fair sensitivities (64% and 32%) in classifying conditional exons.
Discovered numerous novel conditional exons and introns not present in current annotations, with some experimentally verified.

Conclusions:

Conditional exons exhibit unique, position-specific evolutionary conservation patterns.
The developed method effectively identifies and classifies conditional exons, improving transcriptome annotation.
This work provides a valuable resource for understanding alternative splicing and human genome complexity.