ArticleNucleic acids research2002
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 136 citations in OpenAlex.
- Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.Genome biology · 2002Pooled it
- Polyglycine Strands Within a Collagen Triple Helix.Biopolymers · 2026Article
- Phosphorylation-Dependent Charge Transport in Biomolecular Junctions of Major Histocompatibility Complex Phosphopeptides.The journal of physical chemistry. B · 2026Article
- Attempts to Achieve Targeted Covalent Inhibition of Hsp90β.Chemical biology & drug design · 2026Article
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- Peptide/Protein Functionalization and Macrocyclization via Alkyne Umpolung with Hypervalent Iodine Reagents.Accounts of chemical research · 2025Article
- A selenoxide for single-atom protein modification of tyrosine residues enabled by water-resistant chalcogen and hydrogen bonding.Nature chemistry · 2025Article
- Chemoselective Reagents for the Traceless Bioreversible Modification of Native Proteins.Bioconjugate chemistry · 2024Article
- Facile Access to Branched Multispecific Proteins.Bioconjugate chemistry · 2024Article
- An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases.International journal of molecular sciences · 2023Review
- Use of pyridazinediones for tuneable and reversible covalent cysteine modification applied to peptides, proteins and hydrogels.Chemical science · 2023Article
- Methodology of stable peptide based on propargylated sulfonium.Biochemistry and biophysics reports · 2023Article
- Structural characterization of protein-material interfacial interactions using lysine reactivity profiling-mass spectrometry.Nature protocols · 2023Review
- Predicting small molecule binding pockets on diacylglycerol kinases using chemoproteomics and AlphaFold.RSC chemical biology · 2023Article
- Modular Diazo Compound for the Bioreversible Late-Stage Modification of Proteins.Journal of the American Chemical Society · 2023Article
- Tyrosine bioconjugation with hypervalent iodine.Chemical science · 2022Article
- Context-Dependence of the Reactivity of Cysteine and Lysine Residues.Chembiochem : a European journal of chemical biology · 2022Article
- Reactive chemistry for covalent probe and therapeutic development.Trends in pharmacological sciences · 2022Review
- CBRPP: a new RNA-centric method to study RNA-protein interactions.RNA biology · 2021Article
- Site-selective tyrosine bioconjugation via photoredox catalysis for native-to-bioorthogonal protein transformation.Nature chemistry · 2021Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes-the worm, yeast, fly and human (chromosomes 21 and 22 only). Each of our nearly 2500 pseudogenes is characterized by one or more disablements mid-domain, such as premature stops and frameshifts. Here, we perform a comprehensive survey of the amino acid and nucleotide composition of these pseudogenes in comparison to that of functional genes and intergenic DNA. We show that pseudogenes invariably have an amino acid composition intermediate between genes and translated intergenic DNA. Although the degree of intermediacy varies among the four organisms, in all cases, it is most evident for amino acid types that differ most in occurrence between genes and intergenic regions. The same intermediacy also applies to codon frequencies, especially in the worm and human. Moreover, the intermediate composition of pseudogenes applies even though the composition of the genes in the four organisms is markedly different, showing a strong correlation with the overall A/T content of the genomic sequence. Pseudogenes can be divided into 'ancient' and 'modern' subsets, based on the level of sequence identity with their closest matching homolog (within the same genome). Modern pseudogenes usually have a much closer sequence composition to genes than ancient pseudogenes. Collectively, our results indicate that the composition of pseudogenes that are under no selective constraints progressively drifts from that of coding DNA towards non-coding DNA. Therefore, we propose that the degree to which pseudogenes approach a random sequence composition may be useful in dating different sets of pseudogenes, as well as to assess the rate at which intergenic DNA accumulates mutations. Our compositional analyses with the interactive viewer are available over the web at http://genecensus.org/pseudogene.
Indexed as
Identifiers
What OpenQuestion holds
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.