ArticleGenome biology2011
Hundreds of putatively functional small open reading frames in Drosophila.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
What it found
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Who cites it
98 citing papers in PubMed, 171 citations in OpenAlex.
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- Identification of Potentially Coding Small ORFs in Plant Transcriptomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structure and Disorder Predictions of Microproteins: Usage, Applications, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Pharmaceutical perspectives on oligonucleotide therapeutics and delivery systems.Pharmacological reviews · 2025Review
- Pervasiveness of Microprotein Function AmongstCells · 2024Article
- De Novo Genes.Annual review of genetics · 2024Review
- Small ORFs, Big Insights:Cells · 2024Review
- Microproteins unveiling new dimensions in cancer.Functional & integrative genomics · 2024Review
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
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- A survey of experimental and computational identification of small proteins.Briefings in bioinformatics · 2024Review
- Updating mRNA variants of the human RSK4 gene and their expression in different stressed situations.Heliyon · 2024Article
- Molecular and functional characterization of the Drosophila melanogaster conserved smORFome.Cell reports · 2023Article
- A novel protein encoded by circUBE4B promotes progression of esophageal squamous cell carcinoma by augmenting MAPK/ERK signaling.Cell death & disease · 2023Article
- Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.Molecular cell · 2023Article
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38 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundThe relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization.
resultsUsing bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data.
conclusionsThe combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist.
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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.