ArticleBMC genomics2008
Retrocopy contributions to the evolution of the human genome.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed, 118 citations in OpenAlex.
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- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.Genome research · 2025Article
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- Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.Molecular biology and evolution · 2024Article
- The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of "retrobiome" in naked mole rat.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.bioRxiv : the preprint server for biology · 2024Article
- An immune-suppressing protein in human endogenous retroviruses.Bioinformatics advances · 2023Article
- CRISPR/Cas9-induced gene conversion betweenHGG advances · 2022Article
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- Architecture and evolution of theeLife · 2022Article
- Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse.Molecular biology and evolution · 2022Article
- PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.BMC bioinformatics · 2022Article
- Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals.Computational and structural biotechnology journal · 2022Article
- βIII-Tubulin Gene Regulation in Health and Disease.Frontiers in cell and developmental biology · 2022Review
- Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.Genome biology · 2021Article
- Cancer, Retrogenes, and Evolution.Life (Basel, Switzerland) · 2021Review
- SARS-CoV-2-Host Chimeric RNA-Sequencing Reads Do Not Necessarily Arise From Virus Integration Into the Host DNA.Frontiers in microbiology · 2021Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundEvolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. By contrast, 45% of the human genome is composed of retroposed elements, many of which were inserted in the primate lineage. A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes.
resultsTo identify and analyze the relatively recently evolved retrogenes, we carried out BLASTZ alignments of all human mRNAs against the human genome and scored a set of features indicative of retroposition. Of over 12,000 putative retrocopy-derived genes that arose mainly in the primate lineage, 726 with strong evidence of transcript expression were examined in detail. These mRNA retroposition events fall into three categories: I) 34 retrocopies and antisense retrocopies that added potential protein coding space and UTRs to existing genes; II) 682 complete retrocopy duplications inserted into new loci; and III) an unexpected set of 13 retrocopies that contributed out-of-frame, or antisense sequences in combination with other types of transposed elements (SINEs, LINEs, LTRs), even unannotated sequence to form potentially novel genes with no homologs outside primates. In addition to their presence in human, several of the gene candidates also had potentially viable ORFs in chimpanzee, orangutan, and rhesus macaque, underscoring their potential of function.
conclusionmRNA-derived retrocopies provide raw material for the evolution of genes in a wide variety of ways, duplicating and amending the protein coding region of existing genes as well as generating the potential for new protein coding space, or non-protein coding RNAs, by unexpected contributions out of frame, in reverse orientation, or from previously non-protein coding sequence.
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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.