Ciona intestinalis (photo courtesy Arjan Gittenberger, ascidians.com)

The Dec. 2002 Ciona intestinalis (sea squirt) draft assembly was obtained from the US DOE Joint Genome Institute (JGI) v.1.0.

### Sample position queries

A genome position can be specified by the accession number of a sequenced mRNA or EST, a scaffold coordinate range, a gene identifier, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the ciona genome. See the User's Guide for more information.

Request: | Genome Browser Response:
Scaffold_100 |  | Displays all of Scaffold_100 (on an unmapped genome assembly)
Scaffold_1000:1-10,000 |  | Displays the first 10,000 bases of Scaffold_1000 (on an unmapped genome assembly)
BW297212 |  | Displays region of EST with GenBank accession BW297212 on Scaffold_490
AK112180 |  | Displays region of mRNA with GenBank accession number AK112180
Scaffold_490-snap.1.1 |  | Displays region of genome with SNAP gene-finder identifier Scaffold_490-snap.1.1
ci0100131142 |  | Displays the region of genome with JGI predicted transcript ci0100131142
HOXA11 |  | Displays the region of genome corresponding to nTBLASTn aligment of HOXA11 from human Known Gene track
ephrin receptor |  | Lists ephrin receptor mNRAs
ievolella |  | Lists mRNAs deposited by scientist named Ievolella
Valle,G. |  | Lists mRNAs deposited by co-author G. Valle
Use this last format for author queries. Although GenBank requires the search format Valle G, internally it uses the format Valle,G..

### Assembly details

This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired-end sequencing reads at a coverage of 8.2X. The draft contains 116.7 million bp of nonrepetitive sequence in 2,501 scaffolds greater than 3 kb. 60 Mbp of this has been assembled into 117 scaffolds longer than 190 Kbp, and 85% of the assembly (104.1 Mbp) is found in 905 scaffolds longer than 20 kb. The assembly, gene modeling and analysis were performed at the JGI.

For more information about the ci1 assembly, see the JGI C. intestinalis project page. Additional information and an analysis of the euchromatic regions of this genome may be found in Dehal et al., The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins. Science. 2002 Dec 13;298(5601):2157-67.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The ci1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.