ArticleBioinformatics (Oxford, England)2009
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
Article in Bioinformatics (Oxford, England), 2009. 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.
- Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals.Scientific reports · 2023Article
- Molecular characterization and expression analysis of selenoprotein W gene in rainbow trout (Oncorhynchus mykiss) with dietary selenium levels.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2022Article
- Human Disorders Affecting the Selenocysteine Incorporation Pathway Cause Systemic Selenoprotein Deficiency.Antioxidants & redox signaling · 2020Article
- Bioinformatics of Selenoproteins.Antioxidants & redox signaling · 2020Review
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- Article
- Processive incorporation of multiple selenocysteine residues is driven by a novel feature of the selenocysteine insertion sequence.The Journal of biological chemistry · 2018Article
- Identification, characterization of selenoprotein W and its mRNA expression patterns in response to somatostatin 14, cysteamine hydrochloride, 17β-estradiol and a binary mixture of 17β-estradiol and cysteamine hydrochloride in topmouth culter (Erythroculter ilishaeformis).Fish physiology and biochemistry · 2017Article
- Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.Molecular biology and evolution · 2016Article
- Structural polymorphism in the promoter of pfmrp2 confers Plasmodium falciparum tolerance to quinoline drugs.Molecular microbiology · 2014Article
- SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.Nucleic acids research · 2013Article
- Reconstitution of selenocysteine incorporation reveals intrinsic regulation by SECIS elements.Journal of molecular biology · 2013Article
- The selenocysteine-specific elongation factor contains a novel and multi-functional domain.The Journal of biological chemistry · 2012Article
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- Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.Bioinformatics (Oxford, England) · 2010Article
- Threading the needle: getting selenocysteine into proteins.Antioxidants & redox signaling · 2010Review
- Eukaryotic selenoproteins and selenoproteomes.Biochimica et biophysica acta · 2009Review
- Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine.Nucleic acids research · 2009Article
- A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.Nucleic acids research · 2009Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summarySelenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem-loop structure, the SECIS element in the 3 untranslated region of (UTR) selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web-based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities. AVAILABILITY: SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/.
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