ArticleBioinformatics (Oxford, England)2015
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.Cell reports methods · 2024Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.BMC bioinformatics · 2022Article
- Computational Detection of MicroRNA Targets.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts.Briefings in bioinformatics · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Alternative Polyadenylation: a new frontier in post transcriptional regulation.Biomarker research · 2020Review
- tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.Genome biology · 2020Article
- Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma.Genome research · 2020Article
- Aire Gene Influences the Length of the 3' UTR of mRNAs in Medullary Thymic Epithelial Cells.Frontiers in immunology · 2020Article
- Discovery of alternative polyadenylation dynamics from single cell types.Computational and structural biotechnology journal · 2020Review
- Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.Frontiers in genetics · 2020Article
- Alternative polyadenylation produces multiple 3' untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons.BMC genomics · 2019Article
- Alternative polyadenylation of single cells delineates cell types and serves as a prognostic marker in early stage breast cancer.PloS one · 2019Article
- Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.Frontiers in genetics · 2019Article
- TAPAS: tool for alternative polyadenylation site analysis.Bioinformatics (Oxford, England) · 2018Article
- An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response.Nucleic acids research · 2018Article
- ExUTR: a novel pipeline for large-scale prediction of 3'-UTR sequences from NGS data.BMC genomics · 2017Article
- Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies.BMB reports · 2017Review
- Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledProtein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 ': UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3 ': UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3 ': UTRs are identified and reported by the server. AVAILABILITY AND IMPLEMENTATION: 3USS is freely available at http://www.biocomputing.it/3uss_server.
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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.