ArticleGenome research2003
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 212 papers.
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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
212 citing papers in PubMed, 424 citations in OpenAlex.
- Taxonomic context and genomic architecture jointly shape expression divergence across animals.Evolution; international journal of organic evolution · 2026Article
- Detection of endogenous LINE-1 ORF2p and its potent reverse transcriptase activity in the MCF-7 breast cancer cell line.The FEBS journal · 2026Article
- RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer's disease brain.Communications biology · 2026Article
- A perspective and demonstration of an approach to screening synthetic nucleic acid orders containing short nucleic acid sequences.Frontiers in bioengineering and biotechnology · 2026Article
- Taxonomic context and genomic architecture jointly shape expression divergence across animals.bioRxiv : the preprint server for biology · 2025Article
- Review
- RNA isoform diversity, splicing variants, and switching in single cells of the Alzheimer's disease brain.Research square · 2025Article
- Article
- L1-ORF1p nucleoprotein can rapidly assume distinct conformations and simultaneously bind more than one nucleic acid.Nucleic acids research · 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
- Exploring the enigma: history, present, and future of long non-coding RNAs in cancer.Discover oncology · 2024Review
- From the archives: evolutionary origins of Delphinieae flowers, pseudogenes, and the light-responsive localization of COP1.The Plant cell · 2024Article
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- Exploring the evolving roles and clinical significance of circRNAs in head and neck squamous cell carcinoma.Journal of Cancer · 2024Review
- Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.Molecular biology and evolution · 2023Article
- Ribosomal dysregulation: A conserved pathophysiological mechanism in human depression and mouse chronic stress.PNAS nexus · 2023Article
- Pseudogenes in Cancer: State of the Art.Cancers · 2023Review
- Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies.Plant communications · 2023Article
- Article
- Evolution of primate interferon-induced transmembrane proteins (IFITMs): a story of gain and loss with a differentiation into a canonical cluster and IFITM retrogenes.Frontiers in microbiology · 2023Article
152 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Processed pseudogenes were created by reverse-transcription of mRNAs; they provide snapshots of ancient genes existing millions of years ago in the genome. To find them in the present-day human, we developed a pipeline using features such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts approximately 8000 processed pseudogenes (distributed from http://pseudogene.org). Overall, processed pseudogenes are very similar to their closest corresponding human gene, being 94% complete in coding regions, with sequence similarity of 75% for amino acids and 86% for nucleotides. Their chromosomal distribution appears random and dispersed, with the numbers on chromosomes proportional to length, suggesting sustained "bombardment" over evolution. However, it does vary with GC-content: Processed pseudogenes occur mostly in intermediate GC-content regions. This is similar to Alus but contrasts with functional genes and L1-repeats. Pseudogenes, moreover, have age profiles similar to Alus. The number of pseudogenes associated with a given gene follows a power-law relationship, with a few genes giving rise to many pseudogenes and most giving rise to few. The prevalence of processed pseudogenes agrees well with germ-line gene expression. Highly expressed ribosomal proteins account for approximately 20% of the total. Other notables include cyclophilin-A, keratin, GAPDH, and cytochrome c.
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Registered trials
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