ArticleNucleic acids research2023
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- Characterizing highly conserved fragments in 3'UTRs via statistical and transfer learning approaches.NAR genomics and bioinformatics · 2026Article
- Enhancement of Therapeutic mRNA Translation in Cellular Stress Conditions.International journal of molecular sciences · 2026Review
- Genome-wide association mapping, phylogenetic study, and multivariate analysis of component traits of grain yield in wheat under heat stress conditions.Plant molecular biology · 2026Article
- TEDD: a comprehensive database for translation efficiency dynamics.Nucleic acids research · 2026Article
- Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics.Frontiers in genetics · 2026Article
- Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- mRNAdesigner: an integrated web server for optimizing mRNA design and protein translation in eukaryotes.Nucleic acids research · 2025Article
- Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.Circulation research · 2025Review
- Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors.BMC genomics · 2025Article
- UTRGAN: learning to generate 5' UTR sequences for optimized translation efficiency and gene expression.Bioinformatics advances · 2025Article
- Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.PloS one · 2025Article
- Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber.Marine biotechnology (New York, N.Y.) · 2024Article
- Dissecting non-B DNA structural motifs in untranslated regions of eukaryotic genomes.Genomics & informatics · 2024Article
- Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome.Genome biology and evolution · 2024Article
- Unravelling the Complexity of the +33 C>G [HBB:c.-18C>G] Variant in Beta Thalassemia.Biomedicines · 2024Article
- Characterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model.Microbial cell factories · 2024Article
- The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.Nucleic acids research · 2023Article
- Impact of the Diversity in the 5' UTR on Translation Regulation.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Since 1996, we have developed and maintained UTRdb, a specialized database of UTR sequences. Here we present UTRdb 2.0, a major update of UTRdb featuring an extensive collection of eukaryotic 5' and 3' UTR sequences, including over 26 million entries from over 6 million genes and 573 species, enriched with a curated set of functional annotations. Annotations include CAGE tags and polyA signals to label the completeness of 5' and 3'UTRs, respectively. In addition, uORFs and IRES are annotated in 5'UTRs as well as experimentally validated miRNA targets in 3'UTRs. Further annotations include evolutionarily conserved blocks, Rfam motifs, ADAR-mediated RNA editing events, and m6A modifications. A web interface allowing a flexible selection and retrieval of specific subsets of UTRs, selected according to a combination of criteria, has been implemented which also provides comprehensive download facilities. UTRdb 2.0 is accessible at http://utrdb.cloud.ba.infn.it/utrdb/.
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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.