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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.3K
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...
3.3K
Conservation of Protein Domains02:26

Conservation of Protein Domains

2.9K
2.9K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.7K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.1K
Conserved Binding Sites01:49

Conserved Binding Sites

1.1K
1.1K
Complementation Tests00:49

Complementation Tests

4.9K
A complementation test is a simple cross to identify whether the two mutations are located on the same gene or different genes. It was first performed by Edward Lewis in the 1940s while working on fruit flies. He developed the test to identify the location and arrangement of different mutations on chromosomes.
Organisms heterozygous for different mutations are crossed pairwise in all combinations. If present on different genes, the mutations can complement each other by providing the missing...
4.9K

You might also read

Related Articles

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

Sort by
Same author

Novel examples of NMD escape through alternative intronic polyadenylation.

NAR genomics and bioinformatics·2026
Same author

Ancestral intronic splicing regulatory elements in the SCNα gene family.

RNA (New York, N.Y.)·2026
Same author

Ancestral intronic splicing regulatory elements in the SCN<i>α</i> gene family.

bioRxiv : the preprint server for biology·2026
Same author

Unveiling Functional Long-Range RNA Structures via RIC-seq Analysis.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Translon: a single term for translated regions.

Nature methods·2025
Same author

Human introns contain conserved tissue-specific cryptic poison exons.

NAR genomics and bioinformatics·2024
Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026
Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026
Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026
Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026
Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026
Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026
See all related articles

Related Experiment Video

Updated: Apr 25, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

9.6K

IRBIS: a systematic search for conserved complementarity.

Dmitri D Pervouchine1

  • 1Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia dp@crg.eu.

RNA (New York, N.Y.)
|August 22, 2014
PubMed
Summary
This summary is machine-generated.

IRBIS is a new computational pipeline for identifying conserved RNA structures in unaligned sequences. It enables large-scale RNA-RNA interaction analysis and predicts novel RNA structures influencing gene regulation.

Keywords:
Ca-α1DDystoninRNA–RNA interactionalternative splicingevolutionary conservationexon skippinglncRNAlong-range RNA structuresnoRNA

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

16.2K
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.0K

Related Experiment Videos

Last Updated: Apr 25, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

9.6K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

16.2K
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.0K

Area of Science:

  • Computational biology
  • Genomics
  • Bioinformatics

Background:

  • Detecting conserved RNA structures in orthologous sequences is crucial for understanding gene regulation.
  • Existing methods face challenges with scalability and accuracy for large-scale analyses.

Purpose of the Study:

  • To introduce IRBIS, a novel computational pipeline for identifying conserved complementary regions in unaligned orthologous sequences.
  • To enable large-scale analyses of intra- and intermolecular RNA-RNA interactions.

Main Methods:

  • IRBIS employs a "first-fold-then-align" principle, searching all complementary k-mer combinations for simultaneous conservation.
  • A novel trimming procedure is utilized to reduce the search space and enhance performance.
  • The method is benchmarked on simulated and real biological data.

Main Results:

  • Stringent predictions of intramolecular RNA structures in placental mammals, drosophilids, and nematodes.
  • Identification of long-range RNA structures potentially affecting alternative splicing in Dystonin and Ca-α1D genes.
  • Discovery that small nucleolar RNAs (snoRNAs) and long noncoding RNAs (lncRNAs) can base-pair with introns, suggesting a role in splicing regulation.

Conclusions:

  • IRBIS facilitates large-scale RNA structure analysis, revealing insights into gene regulation.
  • Conserved sequences on both DNA strands can inflate false discovery rates, necessitating careful analysis.
  • The open-source IRBIS software is available for broader research applications.