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 49

Ciona intestinalis News

There is no Ciona intestinalis-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

Assembly:	JGI 2, Mar 2005
Genebuild:	Ensembl, Feb 2006
Database version:	49.2i
Known protein-coding genes:	666
Novel protein-coding genes:	13,514
RNA genes:	256
Genscan gene predictions:	14,192
Genefinder gene predictions:	12,384
Gene exons:	133,519
Gene transcripts:	19,858
Base Pairs:	173,499,994
Golden Path Length:	173,499,994
Most common InterPro domains:	Top 40 Top 500

How the statistics are calculated