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Protocols

Xenbase specifications

Information


Unique identifier OMICS_01665
Name Xenbase
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Xenbase

Taxon


  • Vertebrates
    • Xenopus laevis
    • Xenopus tropicalis

Maintainer


  • person_outline Peter D. Vize

Publication for Xenbase

Xenbase citations

 (53)
library_books

NCX DB: a unified resource for integrative analysis of the sodium calcium exchanger super family

2018
BMC Neurosci
PMCID: 5898058
PMID: 29649983
DOI: 10.1186/s12868-018-0423-2

[…] d from UniProt (ver. June 2017) [] as well as the animal model organism databases that comprise the Alliance of Genome Resources (http://www.alliancegenome.org/). These are: WormBase (ver. WS260) [], XenBase (ver. 4.5.0) [], FlyBase (FB2017_04) [], the Zebrafish Information Network (ZFIN: https://zfin.org/), Mouse Genomics Informatics (http://www.informatics.jax.org/), and the Rat Genome Database […]

library_books

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

2018
BMC Genomics
PMCID: 5896114
PMID: 29642853
DOI: 10.1186/s12864-018-4647-4

[…] so manually verified each genome-specific gene according to ZFIN (Zebrafish International Resource Center database, http://zfin.org/), MGI (Mouse Genome Informatics, http://www.informatics.jax.org/), Xenbase (Xenopus model organism database, http://www.xenbase.org/entry/), HGNC (HUGO Gene Nomenclature Committee, http://www.genenames.org/) and HCOP (HGNC Comparison of Orthology Predictions, http:// […]

library_books

Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

2018
Genome Biol Evol
PMCID: 5841384
PMID: 29608717
DOI: 10.1093/gbe/evy045

[…] that are within and flank genes, because these areas contain less repetitive DNA (at least in X. tropicalis; ). We used the X. laevis genome annotation (version 9.1 primary gene models gff file; www.xenbase.org) to separately calculate nucleotide diversity (π) in each parent for coding sequence of genes (hereafter CDS), introns, 5′ and 3′ untranslated regions (hereafter UTR), 5,000-bp upstream of […]

call_split

Reference gene identification and validation for quantitative real time PCR studies in developing Xenopus laevis

2018
Sci Rep
PMCID: 5764961
PMID: 29323148
DOI: 10.1038/s41598-017-18684-1
call_split See protocol

[…] e used from previously published data,. The primers were designed to target the exon-exon region where possible to avoid genomic DNA amplification. The specificity of each primer set was checked used Xenbase Blast and by manual alignment of the small and large copy of both genes. Transcript information of genes was based on Xenopus laevis 9.1 genome primary transcripts by JGI. Primers were ordered […]

library_books

Role of the visual experience dependent nascent proteome in neuronal plasticity

2018
eLife
PMCID: 5815848
PMID: 29412139
DOI: 10.7554/eLife.33420.040

[…] sciences-publications/rawconverter). MS2 spectra remaining after filtering were searched with the Prolucid Software () separately against three different databases: UniProt_Xenopus_laevis_01-23-2015, Xenbase_Xenopus_laevis_05-29-2014 (http://www.xenbase.org/, RRID:SCR_003280), and PHROG_07-01-2014 (). Each database was concatenated to a decoy database in which the sequence for each entry in the or […]

library_books

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader

2017
GigaScience
PMCID: 5765561
PMID: 29186423
DOI: 10.1093/gigascience/gix114

[…] er, yet higher (∼20 million bp) than that produced from muscle tissue. Additionally, our assembly exhibits comparable lengths of mRNAs and CDS to those from X. tropicalis (gene build v9.0, downloaded Xenbase.org, Aug. 2017) (), albeit with a greater frequency of shorter features. This is not unexpected given that we are comparing a de novo transcriptome assembly to gene models from a genome assemb […]

Citations

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Xenbase institution(s)
University of Calgary-Computer Science, Calgary, AB, Canada; Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA; University of Calgary-Biological Sciences, Calgary, AB, Canada
Xenbase funding source(s)
Eunice Kennedy Shriver National Institute of Child Health and Human Development [R01HD045776 and P41HD064556].

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