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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 Splicing

RNA Splicing

What is Gene Expression?

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...

What is Gene Expression?

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...

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Updated: Mar 27, 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

A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational

Hong-Dong Li, Gilbert S Omenn, Yuanfang Guan

Briefings in Bioinformatics

|January 8, 2016

Summary

Computational methods can predict protein isoform functions using various data types, including RNA-sequencing. This review highlights current approaches, their limitations, and future directions for improved accuracy in isoform function annotation.

Keywords:

alternatively spliced isoform function prediction functional networks isoform expression selection pressure

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Using the E1A Minigene Tool to Study mRNA Splicing Changes

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Published on: April 22, 2021

Area of Science:

Genomics
Proteomics
Bioinformatics

Background:

Multi-exon genes produce alternatively spliced isoforms with diverse protein functions.
Differentiating and annotating individual isoform functions is crucial but challenging.
Experimental methods are often costly and time-consuming.

Purpose of the Study:

To review computational methods for predicting protein isoform functions.
To discuss the advantages and limitations of various input data sources.
To identify strategies for enhancing prediction accuracy.

Main Methods:

Review of state-of-the-art computational approaches for isoform function prediction.
Analysis of diverse input data, including DNA sequence, RNA expression (RNA-seq), and proteomic data.
Discussion of integrative proteogenomic strategies.

Main Results:

RNA-sequencing provides extensive genome-scale expression data for developing prediction models.
Integrative analysis across molecular levels enhances systematic interrogation of isoform functions.
Current methods vary in input data requirements, advantages, and limitations.

Conclusions:

Computational tools are essential for efficient isoform function annotation.
RNA-seq and proteogenomic approaches offer powerful means for function prediction.
Further improvements in prediction accuracy are achievable through refined methods and data integration.