ReviewNucleic acids research2020
Alternative ORFs and small ORFs: shedding light on the dark proteome.
Review in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 186 papers.
What it found
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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.
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.
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Who cites it
186 citing papers in PubMed, 338 citations in OpenAlex.
- DetectNAR genomics and bioinformatics · 2026Article
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Decoding the Transcriptional Complexity of the Human BRCA2 DNA Repair Gene Using Hybrid-seq.Biochemical genetics · 2026Article
- Metabolic and transcriptional plasticity supports CD8Immunity · 2026Article
- Whole-genome characterization and analysis of Pantoea agglomerans R6: a genomic insight into its pathogenicity and resistance as a potential opportunistic plant pathogen.BMC genomics · 2026Article
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The birth, death, and evolutionary compensation of uORFs in Drosophila.Nucleic acids research · 2026Article
- Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus.Nature communications · 2026Article
- Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes.Journal of molecular evolution · 2026Article
- S-phase PARylation of microprotein RSMC enhances the function of Sororin in sister chromatid cohesion.The EMBO journal · 2026Article
- Antimicrobial Resistant Factors inInternational journal of genomics · 2026Article
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- Recent Characterization of Key Proteins to Combat Tuberculosis.Advances in experimental medicine and biology · 2026Review
- Protein Architecture and Composition in Mycobacterium tuberculosis.Advances in experimental medicine and biology · 2026Review
- Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A 5'-UTR cis-acting RNA element targeted by RNase III is essential for DNA simple sequence repeat-dependent phase variation in Haemophilus influenzae.Nucleic acids research · 2025Article
126 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
4 authors at 2 institutions in 1 country.
Funding
Abstract
Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored 'dark proteome' is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.
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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.