SelenoDB statistics

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Protocols

SelenoDB specifications

Information


Unique identifier OMICS_06166
Name SelenoDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Frederic Romagne

Additional information


Primary version of the database still available at http://www1.selenodb.org/ http://www.selenodb.org/leipzig/faq/

Publications for SelenoDB

SelenoDB citations

 (4)
library_books

The selenium content of SEPP1 versus selenium requirements in vertebrates

2015
PeerJ
PMCID: 4699779
PMID: 26734501
DOI: 10.7717/peerj.1244

[…] The in silico predicted species specific Sec content of SEPP1 (SEPP1a in fish) were obtained from , the open access selenoprotein database (selenodb.org; ) or by analysing genomic Sepp1 sequences (NCBI) for Sec content (http://seblastian.crg.es/), an open access online software for this purpose (). The SEPP1 Sec content of five bony fish […]

library_books

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

2013
eLife
PMCID: 3840789
PMID: 24302569
DOI: 10.7554/eLife.01179.026

[…] a selenocysteine insertion (SECIS) element. However, UGA stop codons represent only 25% of the readthrough events we report, and none of these are annotated as selenoproteins in either FlyBase () or SelenoDB (). Furthermore, we were unable to detect SECIS elements in any of their 3′ UTRs using SeciSearch 2.19 (). Thus, at most, even unannotated selenocysteine insertion events could only account f […]

library_books

Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees

2009
PLoS Pathog
PMCID: 2685015
PMID: 19503607
DOI: 10.1371/journal.ppat.1000466

[…] e of mammals and bacteria (reviewed in ). We did not find a homolog of the SelU family , the most broadly distributed selenoprotein family across eukaryotes. Of the six selenoproteins reported by the SelenoDB database to be present in yeast, we found only two clear homologs in N. ceranae, NcORF-01193 and NcORF-01194, both of which are glutathione peroxidases. These genes do not appear to be selen […]

call_split

Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

2007
BMC Genomics
PMCID: 2194788
PMID: 17937804
DOI: 10.1186/1471-2164-8-371
call_split See protocol

[…] dataset, since these are a known example of a re-coding phenomenon []. This was achieved through protein-level BLAST comparisons (e ≤ 10-4) to the determined human selenoproteome, downloaded from the SelenoDB database [].To insure that we are not considering spurious frameshifts arising from bad protein annotations, we used an additional filter to insure that the protein reading frames in question […]

Citations

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SelenoDB institution(s)
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Department of Medicine, Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
SelenoDB funding source(s)
Supported by The Max Planck Society; the Plan Nacional and the Instituto Nacional de BIoinformatica (Spain); and National Institutes of Health grants.

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