ArticleNucleic acids research2009
Transterm: a database to aid the analysis of regulatory sequences in mRNAs.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 65 citations in OpenAlex.
- A meta-analysis of single base-pair substitutions in translational termination codons ('nonstop' mutations) that cause human inherited disease.Human genomics · 2011Pooled it
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- Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogenbioRxiv : the preprint server for biology · 2023Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression.Nucleic acids research · 2020Article
- Identification of promoter elements in the Dolichospermum circinale AWQC131C saxitoxin gene cluster and the experimental analysis of their use for heterologous expression.BMC microbiology · 2020Article
- Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel.Nucleic acids research · 2018Article
- Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection.PloS one · 2018Article
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- Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli.Nucleic acids research · 2017Article
- ImiRP: a computational approach to microRNA target site mutation.BMC bioinformatics · 2016Article
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- Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.Plant molecular biology · 2015Article
- Nonsense codon suppression in fission yeast due to mutations of tRNA(Ser.11) and translation release factor Sup35 (eRF3).Current genetics · 2015Article
- Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals.PLoS genetics · 2014Article
- Optimization of mRNA design for protein expression in the crustacean Daphnia magna.Molecular genetics and genomics : MGG · 2014Article
- Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus.World journal of gastroenterology · 2014Review
- The folding of 5'-UTR human G-quadruplexes possessing a long central loop.RNA (New York, N.Y.) · 2014Article
- Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs.BMC bioinformatics · 2014Article
- SeqDepot: streamlined database of biological sequences and precomputed features.Bioinformatics (Oxford, England) · 2014Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3'-untranslated regions (3'-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses.
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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.