ArticleGenome research2006
A genome-wide study of dual coding regions in human alternatively spliced genes.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 43 citations in OpenAlex.
- Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region.Genome biology · 2026Article
- Pervasive non-triplet alternative splicing drives functional isoform diversity.Nature communications · 2026Article
- Alternatively Spliced Dual-Coding Regions Contribute to the Human Gene Regulatory Program.bioRxiv : the preprint server for biology · 2026Article
- Novel Players in the Aging Synapse: Impact on Cognition.Journal of caffeine and adenosine research · 2019Review
- Mitochondrial dual-coding genes in Trypanosoma brucei.PLoS neglected tropical diseases · 2017Article
- The A2A adenosine receptor is a dual coding gene: a novel mechanism of gene usage and signal transduction.The Journal of biological chemistry · 2014Article
- Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses.PLoS computational biology · 2013Article
- Observation of dually decoded regions of the human genome using ribosome profiling data.Genome research · 2012Article
- Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences.Journal of molecular evolution · 2011Article
- Detection of functional overlapping genes: simulation and case studies.Journal of molecular evolution · 2010Article
- Dual coding in alternative reading frames correlates with intrinsic protein disorder.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Divergence of exonic splicing elements after gene duplication and the impact on gene structures.Genome biology · 2009Article
- Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans.Nature genetics · 2008Article
- Retrocopy contributions to the evolution of the human genome.BMC genomics · 2008Article
- Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts.BMC genomics · 2008Article
- Systematic analysis of alternative first exons in plant genomes.BMC plant biology · 2007Article
- Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures.BMC genomics · 2007Article
- Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- A first look at ARFome: dual-coding genes in mammalian genomes.PLoS computational biology · 2007Article
- The implications of alternative splicing in the ENCODE protein complement.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcripts and show that approximately 7% of alternatively spliced genes contain dual (multiple) coding regions. By using a conservative criterion, we found that in these regions most secondary reading frames evolved recently in mammals, and a significant proportion of them may be specific to primates. Based on the presence of in-frame stop codons in orthologous sequences in other animals, we further classified ancestral and derived reading frames in these regions. Our results indicated that ancestral reading frames are usually under stronger selection than are derived reading frames. Ancestral reading frames mainly influence the coding properties of these dual coding regions. Compared with coding regions of the whole genome, ancestral reading frames largely maintain similar nucleotide composition at each codon position and amino acid usage, while derived reading frames are significantly different. Our results also indicated that prior to acquisition of a new reading frame, the suppression of in-frame stop codons in the ancestral state is mainly achieved by one-step transition substitutions at the first or second codon position. Finally, the selective forces imposed on these dual coding regions will also be discussed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.