Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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

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...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: 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...

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...

Long-patch Base Excision Repair

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Host-endophyte (Epichloë occultans) interaction impacts on annual ryegrasses (Lolium persicum and Lolium rigidum): ecological and breeding implications.

Planta·2025

Same author

An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes.

Molecular biology and evolution·2025

Same author

Chemotypic diversity of bioprotective grass endophytes based on genome analyses, with new insights from a Mediterranean-climate region in Isfahan Province, Iran.

Mycologia·2024

Same author

RNA-clique: a method for computing genetic distances from RNA-seq data.

BMC bioinformatics·2024

Same author

Temporal gene expression during asexual development of the apicomplexan <i>Sarcocystis neurona</i>.

mSphere·2024

Same author

Anti-herbivory defences delivered by Epichloë fungal endophytes: a quantitative review of alkaloid concentration variation among hosts and plant parts.

Annals of botany·2024

Same journal

Rapid Evolution of Expression Levels in Hepatocellular Carcinoma.

International journal of computational biology and drug design·2021

Same journal

Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations.

International journal of computational biology and drug design·2021

Same journal

PATH: An interactive web platform for analysis of time-course high-dimensional genomic data.

International journal of computational biology and drug design·2021

Same journal

Modelling of hypoxia gene expression for three different cancer cell lines.

International journal of computational biology and drug design·2020

Same journal

Brain-wide structural connectivity alterations under the control of Alzheimer risk genes.

International journal of computational biology and drug design·2020

Same journal

Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.

International journal of computational biology and drug design·2019

See all related articles

Search research articles

Related Experiment Video

Updated: May 18, 2026

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Published on: November 9, 2020

A linear-time algorithm for finding a maximum-length ORF in a splice graph.

Jerzy W Jaromczyk¹, Neil Moore, Christopher L Schardl

¹Department of Computer Science, University of Kentucky, Lexington, KY, USA. jurek@cs.uky.edu

International Journal of Computational Biology and Drug Design

|September 28, 2012

Summary

This summary is machine-generated.

We developed a fast algorithm to find the longest protein-encoding region (Open Reading Frame or ORF) in complex gene structures called splice graphs. This method efficiently identifies the longest ORF across all possible gene variants.

More Related Videos

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Related Experiment Videos

Last Updated: May 18, 2026

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Published on: November 9, 2020

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Area of Science:

Genomics
Transcriptomics
Bioinformatics

Background:

Identifying protein-encoding regions is crucial for genomic and transcriptomic analysis.
Long Open Reading Frames (ORFs) can serve as reliable predictors of these regions.
Splice graphs offer a compact representation for complex gene structures with numerous alternative splicing events.

Purpose of the Study:

To present a linear-time, deterministic algorithm for locating the longest ORF within a splice graph.
To improve the efficiency of finding potential protein-encoding regions in alternatively spliced genes.

Main Methods:

Developed a deterministic algorithm with linear time complexity.
Implemented a search space pruning strategy to limit the number of reading frames evaluated at each vertex.
Ensured the pruned search space retains at least one longest ORF.

Main Results:

The algorithm successfully finds a longest ORF in a splice graph.
Achieved linear time complexity relative to the size of the splice graph.
Efficiently handles genes with a potentially exponential number of splice variants.

Conclusions:

The presented algorithm provides an efficient and accurate method for identifying longest ORFs in alternatively spliced genes.
This approach enhances the analysis of genomic and transcriptomic data by optimizing the detection of protein-coding sequences.