ArticleDatabase : the journal of biological databases and curation2014
APADB: a database for alternative polyadenylation and microRNA regulation events.
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63 citing papers in PubMed, 100 citations in OpenAlex.
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- mScience advances · 2026Article
- A flexible and unified framework for single- and multi-outcome Mendelian randomization using summary statistics.American journal of human genetics · 2026Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
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- LUBAC-mediated M1 Ub regulates necroptosis by segregating the cellular distribution of active MLKL.Cell death & disease · 2024Article
- Genome-wide identification of dominant polyadenylation hexamers for use in variant classification.Human molecular genetics · 2023Article
- Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease.Nature communications · 2023Article
- Extension of mRNA poly(A) tails and 3'UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics.Nucleic acids research · 2023Article
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions.Nucleic acids research · 2023Article
- Deciphering the impact of genetic variation on human polyadenylation using APARENT2.Genome biology · 2022Article
- Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to the Frataxin transcriptional deficit in Friedreich's ataxia.Human molecular genetics · 2022Article
- Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients.NPJ genomic medicine · 2022Article
- Review
- Cardiac SARS-CoV-2 infection is associated with pro-inflammatory transcriptomic alterations within the heart.Cardiovascular research · 2022Article
- scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse.Nucleic acids research · 2022Article
- scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution.Nucleic acids research · 2022Article
- Inferring microRNA regulation: A proteome perspective.Frontiers in molecular biosciences · 2022Article
- Characterization of the 3'UTR of the BTD gene and identification of regulatory elements and microRNAs.Genetics and molecular biology · 2022Article
3 more citing papers are in PubMed but not listed here.
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11 authors at 1 institution in 1 country.
Sören MüllerPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, GermanyPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany
Lukas RycakPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Fabian Afonso-GrunzPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, GermanyPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany
Peter WinterPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Adam M ZawadaPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Ewa DamrathPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Jessica ScheiderPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Juliane SchmähPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Ina KochPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Günter KahlPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Björn RotterPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
Goethe University Frankfurt · DE
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/.
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Databases, GeneticMicroRNAsPolyadenylationAnimalsChickensComputational BiologyDatabase Management SystemsHumansMiceUser-Computer InterfaceMicroRNAs
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