ArticleGenome research2007
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed, 173 citations in OpenAlex.
- Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum.BMC biology · 2026Article
- Plant non-canonical peptides: From identification to mechanisms.Plant communications · 2026Review
- Identification of Potentially Coding Small ORFs in Plant Transcriptomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Mitochondrial Microproteins: Emerging Regulators in Neurodevelopment and Neurodegeneration.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
- LncRNA-encoded peptides in cancer.Journal of hematology & oncology · 2024Review
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- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- Review
- Small secreted peptides (SSPs) in tomato and their potential roles in drought stress response.Molecular horticulture · 2023Article
- Genome-wide identification and functional prediction ofMolecular breeding : new strategies in plant improvement · 2023Article
- Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.International journal of molecular sciences · 2023Review
- Peptidomics Methods Applied to the Study of Flower Development.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identification of salt stress-tolerant candidate genes in the BCFrontiers in plant science · 2023Article
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- Identification of short open reading frames in plant genomes.Frontiers in plant science · 2023Review
32 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale cDNA sequencing projects and tiling array studies have revealed the presence of many unannotated genes. For protein coding genes, small coding sequences may not be identified by gene finders because of the conservative nature of prediction algorithms. In this study, we identified small open reading frames (sORFs) with high coding potential by a simple gene finding method (Coding Index, CI) based on the nucleotide composition bias found in most coding sequences. Applying this method to 18 Arabidopsis thaliana and 84 yeast sORF genes with evidence of expression at the protein level gives 100% accurate prediction. In the A. thaliana genome, we identified 7159 sORFs that are likely coding sequences (coding sORFs) with the CI measure at the 1% false-positive rate. To determine if these coding sORFs are parts of functional genes, we evaluated each coding sORF for evidence of transcription or evolutionary conservation. At the 5% false-positive rate, we found that 2996 coding sORFs are likely expressed in at least one experimental condition of the A. thaliana tiling array data. In addition, the evolutionary conservation of each A. thaliana sORF was examined within A. thaliana or between A. thaliana and five plants with complete or partial genome sequences. In 3997 coding sORFs with readily identifiable homologous sequences, 2376 are subject to purifying selection at the 1% false-positive rate. After eliminating coding sORFs with similarity to known transposable elements and those that are likely missing exons of known genes, the remaining 3241 coding sORFs with either evidence of transcription or purifying selection likely belong to novel coding genes in the A. thaliana genome.
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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.