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 located at our FTP File Browser. If you have any questions about the content of the files, or would like a custom Data Report generated, please contact us. To upload your data to Xenbase, please visit the Data Submission page

Genomics

Genomes

X. laevis genome assemblies and gene models

• X. laevis v9.1 genome assembly[readme]FASTA
  
  Gene Model(s):
  • 1.8.3.2 [readme] primary gene models (gff3) primary gene models (FASTA) gene models (gff3) peptide(FASTA)
  • For the latest versions browse theXenbase FTP site
• X. laevis v8.0 genome assembly[readme]FASTA
  
  Gene Model(s):
  • JGI v8.0 [readme] gene models (gff3) gene models (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) transcript (FASTA) peptide (FASTA)
  • JGI v7.1 [readme] gene models (gff3) transcript (FASTA) peptide (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 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

Xenbase Data Reports

Xenbase data reports are updated weekly.

Gene Information

• Xenbase Gene Information [readme]txt (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 (tab 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)

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)

Anatomy

The Xenopus Anatomical Ontology, aka the XAO, 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

• XAO v4.0 [readme] Download as: obo owl
• XAO v3.1 [readme] Download as: obo owl
• XAO v2.1 [readme] Download as: obo
• XAO v2.0.8 [readme] Download as: obo owl
• XAO v2.0.7 [readme] Download as: obo owl