Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Organization of Genes02:07

Organization of Genes

Overview
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Multi-species Conserved Sequences02:51

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...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

You might also read

Related Articles

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

Sort by
Same author

Host transcriptional responses identify putative diagnostic biomarkers for bovine tuberculosis in cattle and buffalo.

Tuberculosis (Edinburgh, Scotland)·2026
Same author

Integrated Canine-Assisted Services and Art Therapy in Prison: Pilot Study of Animal Well-Being Aspects and Its Impact on Inmate Critical Events.

Animals : an open access journal from MDPI·2026
Same author

Intestinal Dysbiosis Relating to Gut-Brain Axis and Behavior in Dogs: A Systematic Review with Text Mining Approach.

Animals : an open access journal from MDPI·2026
Same author

Behavior in Australian Shepherd Dogs Assessed Using the C-BARQ: A Preliminary Study of Associations with Coat Color, Sex, and Neutering Status.

Veterinary sciences·2026
Same author

Expression of VEGF-A/VEGFR-2 pathway in feline oral squamous cell carcinoma in vitro and anti-tumour effect of Bevacizumab in a xenograft model.

Veterinary journal (London, England : 1997)·2026
Same author

Exploring alternative cytokines as potential biomarkers for <i>Mycobacterium bovis</i> infection in cattle.

Frontiers in immunology·2026

Related Experiment Video

Updated: Jun 6, 2026

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression
08:54

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

Decoding exonic intron retention from sequence: an exploratory study in the human genome.

Luca Faretra1, Francesco Napolitano1, Massimo Pancione1

  • 1Bioinformatics Lab-Department of Science and Technology, University of Sannio, Benevento, Italy.

Frontiers in Bioinformatics
|June 5, 2026
PubMed
Summary
This summary is machine-generated.

Intron retention in humans is driven by a combination of sequence features, not a single factor. Intron length and GC content are key, with splice sites and RNA-binding proteins also playing significant roles.

Keywords:
alternative splicingfeature selectionintron retentionmachine learningrna sequence

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Related Experiment Videos

Last Updated: Jun 6, 2026

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression
08:54

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Alternative splicing allows one gene to produce multiple transcripts.
  • Intron retention, a form of alternative splicing, is common in plants and animals.
  • The sequence features causing selective intron retention are not fully understood.

Purpose of the Study:

  • To explore sequence-level determinants of intron retention in the human genome.
  • To identify individual and combined sequence features that predispose introns to retention.
  • To develop a computational framework for studying post-transcriptional gene regulation.

Main Methods:

  • Systematic extraction of exon-intron-exon units from human transcript annotations.
  • Characterization of events using sequence features: intron/exon architecture, splice site strength, nucleotide composition, transposable elements, and RNA-binding protein (RBP) patterns.
  • Application of Random Forest and LASSO models to assess feature importance.

Main Results:

  • Intron retention predisposition arises from a synergistic interplay of multiple sequence features.
  • Intron length and GC content are dominant predictors.
  • Splice site strength, transposable elements, and RBP binding signatures contribute significantly, with RBP features showing substantial predictive power alone.

Conclusions:

  • No single factor explains intron retention; it's a multifactorial sequence-driven process.
  • RNA-binding proteins play a crucial role in regulating intron retention.
  • The study provides a framework for understanding human intron retention and its potential dysregulation.