Archive Ensembl Home Ensembl Ciona The Wellcome Trust Sanger Institute The European Bioinformatics Institute
Ciona intestinalis Genome Browser
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About Ciona Ensembl

Ciona intestinalis larvae Ciona intestinalis version 1.95 [details] is a whole genome shotgun assembly released by the JGI. The Ciona 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 1.95 of the whole genome shotgun reads was constructed with the JAZZ assembly, using paired end sequencing reads at a coverage of 11X. After trimming for vector and quality, 3.9 million reads assembled into 2242 scaffolds, totaling 117 Mb. Roughly half the genome is contained in 136 scaffolds at least 234 kb in length.

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. More details of the genebuild process...

Photo: www.ascidians.com
Current Release 31.195
Last Update:  29-04-2005
Ensembl gene predictions:  10988
Genscan gene predictions:  11724
Ensembl gene exons:  142682
Ensembl gene transcripts:  21574
Scaffolds:  2242
Base Pairs:  117112364
Golden Path Length:  117112364
Ensembl What's new
Example data points

This release of Ciona data is assembled into scaffolds, so there are no chromosomes available to browse. Use the BLAST and SSAHA buttons in the Entry Points section above to locate data.

A few example data points :
o   Scaffold: Scaffold_1
o   Gene: ENSCING00000000875
o   Peptide: ENSCINP00000006340
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