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

68.6K
Overview
68.6K
RNA Splicing01:32

RNA Splicing

56.3K
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...
56.3K
Exon Recombination02:32

Exon Recombination

3.6K
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...
3.6K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
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...
9.9K
From DNA to Protein03:06

From DNA to Protein

18.3K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
18.3K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.6K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.6K

You might also read

Related Articles

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

Sort by
Same author

Construction of Dinucleotide Circular Codes Based on Nucleotide Probabilities.

Acta biotheoretica·2025
Same author

Genome Galaxy Identified by the Circular Code Theory.

Bulletin of mathematical biology·2024
Same author

Circular code identified by the codon usage.

Bio Systems·2024
Same author

Circular cut codes in genetic information.

Bio Systems·2024
Same author

Circular mixed sets.

Bio Systems·2023
Same author

Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory.

Bulletin of mathematical biology·2023
Same journal

Ruliological Resilience: Pattern Restoration and Robustness in Wolfram Patterns. A Basis for Regeneration, Not Just in Cone Shells?

Bio Systems·2026
Same journal

The Quantum-to-Classical Transducer: A Thermodynamic and Quantum Mechanical Framework for the Emergence of Bioenergetics.

Bio Systems·2026
Same journal

Forward-backward gene expression binarization for boolean state inference over a known regulatory network.

Bio Systems·2026
Same journal

Partial-label metric ceilings for evaluating gene regulatory networks inferred from single-cell foundation models.

Bio Systems·2026
Same journal

The impedance mismatch theory: A non-equilibrium thermodynamic framework for a shared energetic stress pathway in neurodegeneration.

Bio Systems·2026
Same journal

Immune signal-status misclassification: A theoretical framework for biological status assignment and failed status resolution.

Bio Systems·2026
See all related articles

Related Experiment Video

Updated: Jun 28, 2025

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

7.3K

Circular code in introns.

Christian J Michel1

  • 1Theoretical Bioinformatics, ICube, C.N.R.S., University of Strasbourg, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.

Bio Systems
|April 19, 2024
PubMed
Summary
This summary is machine-generated.

Statistical analysis reveals introns in 10 out of 12 groups possess coding properties. This suggests introns may play a role in reading frame retrieval, challenging previous assumptions about their function.

Keywords:
Circular code periodicityIntronsPeriodicities modulo 2, 3, 6Trinucleotides N(1)N(2)N(1)

More Related Videos

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.2K
In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
10:27

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

1.5K

Related Experiment Videos

Last Updated: Jun 28, 2025

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

7.3K
Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.2K
In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
10:27

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

1.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Eukaryotic introns were traditionally considered non-coding sequences.
  • The circular code X, a pattern in gene sequences, has known properties related to reading frame retrieval.
  • Previous studies have not extensively explored intron periodicity in relation to coding potential.

Purpose of the Study:

  • To investigate the statistical properties of the circular code X within eukaryotic introns.
  • To determine if introns exhibit periodicities indicative of a coding function.
  • To explore the taxonomic distribution of these periodicities.

Main Methods:

  • Massive statistical analysis using the autocorrelation function of the circular code X.
  • Analysis of periodicity modulo 3, modulo 2, and modulo 6 in various intron groups.
  • Examination of specific trinucleotides (N1N2N1) and their impact on observed periodicities.

Main Results:

  • A circular code periodicity of 0 modulo 3 was found in 5 intron groups (birds, ascomycetes, basidiomycetes, green algae, land plants), suggesting a coding property.
  • Periodicity of 1 modulo 2 was observed in 6 intron groups (amphibians, fishes, mammals, other animals, reptiles, apicomplexans).
  • Insects showed mixed periodicity (modulo 2 and 3), with a common subperiodicity of 3 modulo 6 across analyzed groups.
  • Removing N1N2N1 trinucleotides revealed the hidden 0 modulo 3 periodicity in 5 additional intron groups, indicating 10 out of 12 groups have coding properties.
  • A hexanucleotide code is proposed to explain the 3 modulo 6 subperiodicity.

Conclusions:

  • A significant number of introns across diverse taxa (10/12) exhibit statistical properties related to reading frame retrieval.
  • These findings challenge the view of introns as solely non-coding and suggest a potential role in gene expression regulation.
  • The observed periodicities may hint at more complex, ancient circular codes influencing gene structure and function.