ArticleFrontiers in genetics2018
UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Trypanosoma cruzi cell atlas as a single-cell resource for understanding parasite population heterogeneity and differentiation.Nature communications · 2026Article
- Specialized RNA decay fine-tunes monogenic antigen expression in Trypanosoma brucei.Nature microbiology · 2026Article
- Article
- Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms.Molecular biology and evolution · 2025Article
- Exploring a gene co-expression network throughout the trypanosoma cruzi life cycle.BMC genomics · 2025Article
- Exploring the genomic landscape of the GP63 family in Trypanosoma cruzi: Evolutionary dynamics and functional peculiarities.PLoS neglected tropical diseases · 2025Article
- SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.Nucleic acids research · 2025Article
- Transcriptomic analysis of N-terminal mutated Trypanosoma cruzi UBP1 knockdown underlines the importance of this RNA-binding protein in parasite development.PLoS neglected tropical diseases · 2024Article
- Genome-wide chromatin interaction map for Trypanosoma cruzi.Nature microbiology · 2023Article
- peaks2utr: a robust Python tool for the annotation of 3' UTRs.Bioinformatics (Oxford, England) · 2023Article
- Article
- Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci.Epigenetics & chromatin · 2022Article
- A novel family of secreted insect proteins linked to plant gall development.Current biology : CB · 2021Article
- SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data.BMC bioinformatics · 2021Article
- SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem.BMC bioinformatics · 2020Article
- Upstream ORFs Influence Translation Efficiency in the ParasiteFrontiers in genetics · 2020Article
- Conserved motifs in nuclear genes encoding predicted mitochondrial proteins in Trypanosoma cruzi.PloS one · 2019Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Most signals involved in post-transcriptional regulatory networks are located in the untranslated regions (UTRs) of the mRNAs. Therefore, to deepen our understanding of gene expression regulation, delimitation of these regions with high accuracy is needed. The trypanosomatid lineage includes a variety of parasitic protozoans causing a significant worldwide burden on human health. Given their peculiar mechanisms of gene expression, these organisms depend on post-transcriptional regulation as the main level of gene expression control. In this context, the definition of the UTR regions becomes of key importance. We have developed UTR-mini-exon (UTRme), a graphical user interface (GUI) stand-alone application to identify and annotate 5' and 3' UTR regions in a highly accurate way. UTRme implements a multiple scoring system tailored to address the issue of false positive UTR assignment that frequently arise because of the characteristics of the intergenic regions. Even though it was developed for trypanosomatids, the tool can be used to predict 3' sites in any eukaryote and 5' UTRs in any organism where trans-splicing occurs (such as the model organism
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