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

The March 2005 Ciona intestinalis (sea squirt) draft assembly was obtained from the US DOE Joint Genome Institute (JGI) v2.0.

### 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:
chr04q |  | Displays all of chr04q
chr04q:1-1,000,000 |  | Displays the first 1,000,000 bases of chr04q
scaffold_63:1-500,000 |  | Displays the first 500,000 bases of scaffold_63:1-727,480
BW297212 |  | Displays region of EST with GenBank accession BW297212 on Scaffold_106
AK115528 |  | Displays region of mRNA with GenBank accession number AK115528
NM_001011659 |  | Displays region of genome with RefSeq accession NM_001011659
ephrin receptor |  | Lists ephrin receptor mRNAs
mochizuki |  | Lists mRNAs deposited by scientist named Mochizuki
Satou,Y. |  | Lists mRNAs deposited by co-author Y. Satou
Use this last format for author queries. Although GenBank requires the search format Satou Y, internally it uses the format Satou,Y..

### Assembly details

The v2.0 whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, 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 size of this assembly, including unmapped scaffolds, is 173 Mb, with 94 Mb of the sequence mapped to chromosome arms.

For more information about the ci2 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, P. et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298(5601), 2157-67 (2002).

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The ci2 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 this release.