ArticleBMC genomics2010
In silico identification of the sea squirt selenoproteome.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- Selenoproteins: Minute yet vital players governing cellular fate.Genes & diseases · 2026Review
- Tracing the vertebrate selenoproteome evolution reveals expansions in ray-finned fishes and convergent depletions in tetrapods.BMC genomics · 2026Article
- The algal selenoproteomes.BMC genomics · 2020Article
- Bioinformatics of Selenoproteins.Antioxidants & redox signaling · 2020Review
- Computational identification of the selenocysteine tRNA (tRNASec) in genomes.PLoS computational biology · 2017Article
- Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation.PLoS genetics · 2015Article
- SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans.Nucleic acids research · 2014Article
- SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.Nucleic acids research · 2013Article
- Selenoprotein-transgenic Chlamydomonas reinhardtii.Nutrients · 2013Article
- Probing a coral genome for components of the photoprotective scytonemin biosynthetic pathway and the 2-aminoethylphosphonate pathway.Marine drugs · 2013Article
- Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes.PeerJ · 2013Article
- Evolution of selenoproteins in the metazoan.BMC genomics · 2012Article
- Article
- A 4-selenocysteine, 2-selenocysteine insertion sequence (SECIS) element methionine sulfoxide reductase from Metridium senile reveals a non-catalytic function of selenocysteines.The Journal of biological chemistry · 2011Article
- Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.Bioinformatics (Oxford, England) · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComputational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins.
resultsA gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA) was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before.
conclusionThe method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.
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