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Related Concept Videos

Alternative RNA Splicing02:18

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 Splicing02:18

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.
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Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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...
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...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Related Experiment Video

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Refining orthologue groups at the transcript level.

Yizhen Jia1, Thomas K F Wong, You-Qiang Song

  • 1Department of Biochemistry, The University of Hong Kong, Hong Kong. jiayizhen1986@gmail.com

BMC Genomics
|December 15, 2010
PubMed
Summary
This summary is machine-generated.

This study refines gene orthologue groupings by considering alternative splicing and its functional impact. Analyzing transcript-level sub-clusters improves the accuracy of functionally equivalent gene sets.

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Last Updated: Jun 6, 2026

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09:58

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

Published on: June 27, 2020

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Orthologous genes, originating from a common ancestor, are typically assumed to have similar functions across species.
  • Current orthologue databases often overlook alternative splicing, a process where genes can produce multiple protein isoforms with distinct functions.
  • The functional and disease-related implications of alternative splicing are frequently disregarded in standard orthologue definitions.

Purpose of the Study:

  • To investigate the impact of alternative splicing on the functional definition of orthologue groups.
  • To develop a method for sub-clustering orthologue groups at the transcript level to account for isoform diversity.
  • To assess the functional similarity within and between these transcript-based sub-clusters.

Main Methods:

  • Selected human and mouse orthologue groups from the InParanoid database.
  • Developed a sequence similarity-based method to divide orthologue groups into transcript-level sub-clusters.
  • Verified sub-clusters using functional signatures from the InterPro database and analyzed protein intrinsic disorder predictions.

Main Results:

  • Functional similarity was significantly higher within transcript-based sub-clusters compared to between them.
  • Identified distinct, potentially cancer-related, protein isoforms within specific orthologue groups.
  • Correlated predictions of intrinsic protein disorder with isoform sub-clusters.

Conclusions:

  • Sub-clustering orthologue groups at the transcript level enhances the accuracy of functionally equivalent gene definitions.
  • This study pioneers the refinement of orthologous groupings by incorporating the functional consequences of alternative splicing.
  • Further methodological development is required for broader application, especially across more distantly related species.