Ensembl C.intestinalis

Karyotype

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About the Ciona intestinalis genome

Assembly

Ciona intestinalis version 2.0 [details] is a whole genome shotgun assembly released by the JGI. The Ciona intestinalis genome is the smallest of any experimentally manipulable chordate, and thus provides a good system for exploring vertebrate evolutionary origins. This Ensembl website presents the sequence data provided by the JGI, with additional Ensembl genebuild (see below).

The assembly release version 2.0 of the whole genome shotgun reads was constructed with the JAZZ assembly, using paired end sequencing reads. Starting with a coverage of 11x, additional data--including BAC and FISH markers--were used to map scaffolds to chromosome arms. The current size of the assembly which includes unmapped scaffolds is 173Mb with 94Mb of the assembly mapped to chromosome arms.

Annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona 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 the large quantities of Ciona-specific cDNA and EST sequences against the genome, and then used protein data from other species to build additional gene models.

Photo: www.ascidians.com

What's New in Ensembl 41

Ciona intestinalis News

• RNA updates
  

  Ensembl RNA data has been updated as follows:

  • New ncRNAs for Zebrafish, Chimp, Medaka, Elephant, Rabbit, Armadillo and Tenrec
  • Updated miRNAs for all chordates.

General News

• New animated tutorials
  A selection of Ensembl tutorials are now available online as Flash-animated presentations (with popup notes instead of a soundtrack).
  Read more...
• Compara updates
  

  Homologies

  Gene trees have been updated to include the 2X genomes and use a multifurcating species tree, and homologues added based on gene trees.
  Read more...

• Minor schema changes
  

  analysis_description

  Now has a 'displayable' flag to control whether or not it is usually displayed in the web pages

  xref

  One column has been changed and one added

  • the info_type column has addition ENUM values to give more details about xref provenance
  • A new column 'priority' supports the fetching of xrefs of the same type

  The API has of course been updated to reflect these changes

  .
  Read more...

More news...

Statistics

Assembly:	JGI 2, Mar 2005
Genebuild:	Ensembl, Feb 2006
Database version:	41.2c
Known genes:	666
Novel genes:	13,612
RNA genes:	251
Genscan gene predictions:	14,192
Genefinder gene predictions:	12,384
Gene exons:	134,008
Gene transcripts:	20,000
Base Pairs*:	173,499,994
Golden Path Length**:	173,499,994
Most common InterPro domains:	Top 40 Top 500

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

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