Xenbase Data Downloads

Xenbase data downloads provide access to genomes, database content, and more. Most files are in a tab delimited format. Click the "readme" link to view information on the files, including the header row for these files. To download a file, click on the corresponding link on the far right side. More files are available on our data download site. If you have any questions about the content of the files, or would like a custom Data Report generated, please contact us. To submit your data to Xenbase, please contact us

Genomics

Genomes

X. laevis genome assemblies and gene models

• X. laevis v10.1 genome assembly [readme] FASTA
  
  Gene Model(s):
  • NCBI v10.1 [readme] NCBI-Xenbase gene models (gff3) NCBI-Xenbase gene models (gtf)NCBI gene models (gff3)
  • UCB gene models (gff3)transcripts (FASTA)peptides (FASTA)CDS (FASTA)
  • For the latest versions browse theXenbase data download site
• X. laevis v9.2 genome assembly [readme] FASTA
  
  Gene Model(s):
  • Xenbase v9.2 [readme] Xenbase gene models (gff3) Xenbase gene models (gtf)NCBI gene models (gff3) JGI gene models (gff3)
  • transcripts (FASTA) peptides (FASTA)CDS (FASTA)
• X. laevis v9.1 genome assembly[readme] FASTA
  
  Gene Model(s):
  • annot. v1.8.3.2 [readme] primary gene models (gff3) primary gene models (FASTA) gene models (gff3)
  • transcripts (FASTA)peptide (FASTA)CDS (FASTA)
  • For the latest versions browse theXenbase data download site
• X. laevis v8.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v8.0 [readme] gene models (gff3) transcripts (FASTA) peptide (FASTA)
• X. laevis v7.1 genome assembly[readme]FASTA
  
  Gene Model(s):
  • JGI v7.2 [readme] gene models - JGI (gff3) gene models - Xenbase (gff3) transcripts (FASTA) peptides (FASTA)
  • JGI v7.1 [readme] gene models (gff3) transcripts (FASTA) peptides (FASTA)
• X. laevis v6.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v6.0 [readme] gene models (gff3) gene models (FASTA) peptide (FASTA)
• X. laevis outbred v1.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • v1.0 [readme] gene models (gff3) transcripts (fasta) proteins (fasta)

X. tropicalis genome assemblies and gene models

• X. tropicalis v10.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • Xenbase v10.0 [readme] Xenbase gene models (gff3) Xenbase gene models (gtf) NCBI gene models (gff3)
  • UCB gene models (gff3) Ensembl gene models (gff3) transcripts (FASTA) peptides (FASTA) CDS (FASTA)
  • For the latest versions browse theXenbase data download site
• X. tropicalis v9.1 genome assembly[readme] FASTA
  
  Gene Model(s):
  • Xenbase v9.1 [readme] Xenbase gene models (gff3) Xenbase gene models (gtf) NCBI gene models (gff3)
  • JGI gene models (gff3) transcripts (FASTA) peptides (FASTA)CDS (FASTA)
• X. tropicalis v9.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v9.0 [readme] gene models (gff3) transcript (FASTA) peptide (FASTA)
• X. tropicalis v8.0 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v8.0 [readme] gene models (gff3) transcript (FASTA) peptide (FASTA)
• X. tropicalis v7.1 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v7.1 [readme] gene models (gff3) transcript (FASTA) peptide (FASTA)
• X. tropicalis v4.1 genome assembly[readme] FASTA
  
  Gene Model(s):
  • JGI v4.1[readme] gene models (gff3) transcript (FASTA) peptide (FASTA)

Sequences

X. laevis

• X. laevis mRNA (Xenbase)[readme]FASTA
• X. laevis protein (Xenbase)[readme]FASTA
• X. laevis EST (NCBI)[readme]FASTA
• X. laevis mRNA (NCBI)[readme]FASTA
• X. laevis protein (NCBI)[readme]FASTA

X. tropicalis

• X. tropicalis mRNA (Xenbase)[readme]FASTA
• X. tropicalis protein (Xenbase)[readme]FASTA
• X. tropicalis EST (NCBI)[readme]FASTA
• X. tropicalis mRNA (NCBI)[readme]FASTA
• X. tropicalis protein (NCBI)[readme]FASTA

BLAST databases

X. laevis

• X. laevis nucleotidesBLAST databases (Download)
• X. laevis proteinsBLAST databases (Download)

X. tropicalis

• X. tropicalis nucleotidesBLAST databases (Download)
• X. tropicalis proteinsBLAST databases (Download)

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Data Reports

Xenbase data reports are updated weekly.

Gene Information

• Xenbase Gene Information [readme]txt (tab separated)
• Xenbase Gene Product Information [readme]gzipped gpi (tab separated)
• Xenbase Genes to Genepages[readme]txt (tab separated)
• Genes Associated with Literature [readme]txt (tab separated)
• Gene Page Interactants [readme]txt (tab separated)
• OMIM Disease Associations[readme]txt (comma separated)
• Disease Ontology Associations[readme]txt (comma separated)

Expression Data

• X. laevis gene expression [readme]txt (tab separated)
• X. tropicalis gene expression [readme]txt (tab separated)
• Gene expression stage and tissue profile [readme] txt (tab separated)

Orthology

• Xenbase genes to Human Entrez Genes [readme] txt (tab separated)
• Xenbase genes to Mouse Entrez Genes [readme] txt (tab separated)
• Xenbase genes to Zebrafish Entrez Genes [readme] txt (tab separated)
• Xenbase genes to Non-Entrez OMIM, MGI, and ZFIN genes [readme] txt (tab separated)

Xenbase genes linked to other databases

Unigene

• Xenbase X. laevis genes mapped to Unigene [readme] txt (tab separated)
• Xenbase X. tropicalis genes mapped to Unigene [readme] txt (tab separated)

NCBI

• Xenbase X. laevis genes mapped to NCBI ESTs [readme] txt (tab separated)
• Xenbase X. laevis genes mapped to NCBI mRNA [readme] txt (tab separated)
• Xenbase X. laevis genes mapped to NCBI proteins [readme] txt (tab separated)
• Xenbase X. tropcalis genes mapped to NCBI ESTs [readme] txt (tab separated)
• Xenbase X. tropcalis genes mapped to NCBI mRNA [readme] txt (tab separated)
• Xenbase X. tropcalis genes mapped to NCBI proteins [readme] txt (tab separated)

Ensembl

• X. tropicalis 4.1 gene models to Human Ensembl Genes [readme] txt (tab separated)

GO Terms

• GO terms associated with Xenbase genepages [readme] txt (tab separated)
• GO annotations associated with Xenbase genes [readme] gzipped gpad (tab separated)
• gzipped gaf (tab separated)

Affymetrix

• X. laevis 1.0 probes [readme]txt (tab separated)
• X. laevis 2.0 probes [readme]txt (tab separated)
• X. tropicalis 1.0 probes [readme]txt (tab separated)

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Ontologies

Xenopus Anatomy Ontology (XAO)

The Xenopus Anatomy Ontology describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. Xenbase curators use XAO terms to describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.

XAO: Download latest version

Xenopus Phenotype Ontology (XPO)

The Xenopus Phenotype Ontology (XPO) is a structured controlled vocabulary for the curation of abnormal phenotypes in Xenopus species. The XPO covers anatomical, behavioral, molecular function and biological process phenotypes. The XPO has been developed using design patterns adhering to templates provided by uPheno (https://github.com/obophenotype/upheno). The XPO is built from logical axioms connecting terms from other ontologies and incorporates elements of the XAO, GO, NBO and PATO ontologies.

XPO: Download latest version

Xenopus Small Molecules Ontology (XSMO)

The Xenopus small molecule ontology (XSMO) is a controlled vocabulary of chemical entities, The XSMO is used in Xenbase curation of experimental details for phenotypes and metadata curation for GEO processing. Chemical entities in the XSMO have synonyms and cross references to PubChem IDs where available.

XSMO: Download latest version

Xenbase Experimental Data Ontology (XBED)

The Xenbase Experimental Data Ontology (XBED) is a structured controlled vocabulary covering many aspects of Xenbase curation. The XBED covers different classifications of article content, article copyright statuses, assay methods, experimental manipulation types and other factors required for curation.

XBED: Download latest version