Echinobase Data Downloads

Echinobase 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 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

Genomics

Genomes

S. purpuratus genome assemblies and gene models

• S. purpuratus v5.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • S. purpuratus v5.0[readme] gene models (gff3)gene models (gtf)transcripts (FASTA)

    peptides (FASTA)CDS (FASTA)

  • For the latest versions browse theEchinobase data download site
• S. purpuratus v3.1 genome assembly [readme] FASTA
  
  Gene Model(s):
  • S. purpuratus v3.1 [readme] gene models (gff3)transcripts (FASTA)peptides (FASTA)CDS (FASTA)

L. variegatus genome assemblies and gene models

• L. variegatus v3.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • L. variegatus v3.0 [readme] gene models (gff3)gene models (gtf)

    transcripts (FASTA) peptides (FASTA) CDS (FASTA)

P. miniata genome assemblies and gene models

• P. miniata v3.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • P. miniata v3.0 [readme] gene models (gff3)gene models (gtf)

    transcripts (FASTA)peptides (FASTA)CDS (FASTA)

A. planci genome assemblies and gene models

• A. planci v1.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • A. planci v1.0 [readme] gene models (gff3)gene models (gtf)

    transcripts (FASTA)peptides (FASTA)CDS (FASTA)

  • For the latest versions browse theEchinobase data download site

L. pictus genome assemblies and gene models

• L. pictus v3.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • L. pictus v3.0 [readme] gene models (gff3) transcripts (FASTA) peptides (FASTA)
• L. pictus v2.1 genome assembly [readme] FASTA
  
  Gene Model(s):
  • L. pictus v2.1 [readme] gene models (gff3) transcripts (FASTA) peptides (FASTA)

A. rubens genome assemblies and gene models

• A. rubens v1.3 genome assembly [readme] FASTA
  
  Gene Model(s):
  • A. rubens v1.3 [readme] gene models (gff3) transcripts (FASTA) peptides (FASTA) CDS (FASTA)

A. japonica genome assemblies and gene models

• A. japonica v1.0 genome assembly [readme] FASTA
  
  Gene Model(s):
  • A. japonica v1.0 [readme] gene models (gff3) transcripts (FASTA) peptides (FASTA) CDS (FASTA)

Sequences

Echinoderms

• Echinoderm mRNA [readme] FASTA
• Echinoderm CDS [readme] FASTA
• Echinoderm protein [readme] FASTA

BLAST databases

S. purpuratus

• S. purpuratus 5.0 genomeBLAST DB files (tar.gz)
• S. purpuratus 5.0 mRNABLAST DB files (tar.gz)
• S. purpuratus 5.0 CDSBLAST DB files (tar.gz)
• S. purpuratus 5.0 proteinBLAST DB files (tar.gz)
• S. purpuratus 3.1 genomeBLAST DB files (tar.gz)
• S. purpuratus 3.1 mRNABLAST DB files (tar.gz)
• S. purpuratus 3.1 CDSBLAST DB files (tar.gz)
• S. purpuratus 3.1 proteinBLAST DB files (tar.gz)

L. variegatus

• L. variegatus 3.0 genomeBLAST DB files (tar.gz)
• L. variegatus 3.0 mRNABLAST DB files (tar.gz)
• L. variegatus 3.0 CDSBLAST DB files (tar.gz)
• L. variegatus 3.0 proteinBLAST DB files (tar.gz)

P. miniata

• P. miniata 3.0 genomeBLAST DB files (tar.gz)
• P. miniata 3.0 mRNABLAST DB files (tar.gz)
• P. miniata 3.0 CDSBLAST DB files (tar.gz)
• P. miniata 3.0 proteinBLAST DB files (tar.gz)

A. planci

• A. planci 1.0 genomeBLAST DB files (tar.gz)
• A. planci 1.0 mRNABLAST DB files (tar.gz)
• A. planci 1.0 CDSBLAST DB files (tar.gz)
• A. planci 1.0 proteinBLAST DB files (tar.gz)

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Echinobase Data Reports

Echinobase data reports are updated weekly.

Gene Information

• Echinobase Gene Information [readme] txt (tab separated)
• Echinobase Genes to Genepages [readme] txt (tab separated)
• Genes Associated with Literature [readme] txt (tab separated)

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Ontologies

Echinoderm Anatomical and Development Ontology (ECAO)

The Echinoderm Anatomical and Development Ontology (ECAO) describes echinoderm anatomy and embryological development using a controlled vocabulary of anatomy terms and developmental stages that are organized in a hierarchy with a graphical structure. Echinobase curators use ECAO terms to describe the spatiotemporal expression patterns of endogenous gene products, the transcriptional activity of cis-regulatory modules, the effects of morpholinos, and other types of biological information. The ECAO is constantly being updated in response to the latest published echinoderm research.

ECAO: 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