Ensembl C.savignyi

Example Data Points

This release of Ciona_savignyi data is assembled into scaffolds, so there are no chromosomes available to browse.

A few example data points :

• Transcript: SNAP00000081384
• Region: reftig_35:1-16756
• Region: reftig_2291

About the C.savignyi genome

Assembly

The genome of a single Ciona savignyi from San Francisco Bay was shotgun-sequenced by the Broad Institute and assembled using Arachne2. The Sidow lab at Stanford used this as a basis for the assembly [details].

The assembly consists of 374 Reftigs, totalling 174 Megabases, with a Contig N50 of 141Kb and Reftig N50 size of 1800Kb.

Annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona savignyi genome, owing to the lack of genomic information from closely-related species. Thus, in addition to aligning known Ciona proteins to the sequence (as per the standard pipeline), we aligned Ciona-specific cDNA and EST sequences against the genome, and then used these in conjunction with protein data from other species to build additional gene models.

What's New in Ensembl 40

Ciona savignyi News

• Patch for C. savignyi database
  The transcript_biotypes for pseudogenes have been patched in the Ciona savignyi database.

General News

• New orthologue display - GeneTreeView
  A new Ensembl view page, GeneTreeView, displays gene orthologies as tree diagrams (example).
  Read more...
• Core data patches
  

  The following non-schema changes have been made to the core database.
  Read more...

• API changes
  The API has been updated to reflect changes to the schema, including setting xref versions to 0 if undefined, and supporting ditag tables.
  Read more...
• Compara updates
  

  Protein/Protein

  Updates of orthologues/paralogues and families to include the new species and gene sets announced.
  Read more...

More news...

Statistics