ArticleBioinformatics (Oxford, England)2015
GC3-biased gene domains in mammalian genomes.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Transgene sequence codon optimization and composition determines replication competence of self-amplifying RNA.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Decoding the general role of tRNA queuosine modification in eukaryotes.Scientific reports · 2025Article
- Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases.Annals of medicine and surgery (2012) · 2024Article
- Relative synonymous codon usage and codon pair analysis of depression associated genes.Scientific reports · 2024Article
- Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities.Frontiers in molecular neuroscience · 2023Article
- Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes.Frontiers in neuroscience · 2022Article
- Article
- Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution.Genes · 2021Article
- The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.BMC biology · 2019Article
- Codon Usage Pattern of Genes Involved in Central Nervous System.Molecular neurobiology · 2019Article
- Ras Suppresses TXNIP Expression by Restricting Ribosome Translocation.Molecular and cellular biology · 2018Article
- Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.Genetica · 2017Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationSynonymous codon usage bias has been shown to be correlated with many genomic features among different organisms. However, the biological significance of codon bias with respect to gene function and genome organization remains unclear.
resultsGuanine and cytosine content at the third codon position (GC3) could be used as a good indicator of codon bias. Here, we used relative GC3 bias values to compare the strength of GC3 bias of genes in human and mouse. We reported, for the first time, that GC3-rich and GC3-poor gene products might have distinct sub-cellular spatial distributions. Moreover, we extended the view of genomic gene domains and identified conserved GC3 biased gene domains along chromosomes. Our results indicated that similar GC3 biased genes might be co-translated in specific spatial regions to share local translational machineries, and that GC3 could be involved in the organization of genome architecture. AVAILABILITY AND IMPLEMENTATION: Source code is available upon request from the authors. CONTACT: zhaozh@nic.bmi.ac.cn or zany1983@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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