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 43

Ciona savignyi News

There is no Ciona savignyi-specific news this release.

General News

• A faster ContigView
  ContigView now displays information faster. Each open panel in ContigView is prepared in parallel, and then returned to the page when complete. This results in faster page loads.
• New - Table view
  In ContigView you can now click on the name of a feature alignment track and select 'DAS Table View' (or for DAS tracks 'view DAS reponse') from the zmenu.
  Read more...
• New search option
  It is now possible to select whether to search either the Ensembl website or the EBI site when using Ensembl search.
• Changes to Xrefs
  The following changes have been made to xrefs for Release 43:
  • We have made improvements to EntrezGene xrefs, to allow for better handling of names and synonyms
  • Incorporation of new Illumina probe data as xrefs.
    Read more...
  • API changes to ensembl-functgenomics
    A new DataSet API has been developed aimed at making web display much easier.

  More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions