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 49

Ciona savignyi News

There is no Ciona savignyi-specific news this release.

General News

• Release schedule
  

  Ensembl release 50 will occur in July (rather than in April as originally scheduled).
  Read more...

• API changes - regulatory features
  Regulatory feature support has been moved from the core API to the functional genomics API. More information about using the new code...
• Removal of viral genes
  We have removed a total of about 1200 viral genes from the following species.
  Read more...
• Mart updates
  RGD and SGD Symbol+ID combinations have been introduced, similar to HGNC, MGI and ZFIN. The issue with subsets of homologs being returned has been resolved.
• Compara updates
  

  Multiple alignments

  We are now using the new enredo-pecan-ortheus (EPO) pipeline for 7-way alignments (placental mammals).
  Read more...

More news...

Statistics

How the statistics are calculated