The July 2005 Ciona savignyi draft assembly was obtained from the Arend Sidow lab at Stanford University.

### Sample position queries

A genome position can be specified by the accession number of a sequenced mRNA, a reftig 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 C. savignyi genome. See the User's Guide for more information.

Request: | Genome Browser Response:
reftig_15 |  | Displays all of reftig_15
reftig_15:1-1,000,000 |  | Displays the first 1,000,000 bases of reftig_15
AV952451 |  | Displays alignment of EST with GenBank accession AV952451
AK174221 |  | Displays alignment of mRNA with GenBank accession AK174221
NM_001032538 |  | Displays alignment of mRNA with RefSeq identifier NM_001032538
CTM1 |  | Displays region of genome associated with gene symbol CTM1
HOXA1 |  | Displays nTBLASTn aligments of HOXA1 from the human Known Gene track
ephrin receptor |  | Lists Blat alignments of non-C.savignyi ephrin receptor RefSeq mRNAs
schultz |  | Lists mRNAs deposited by scientist named schultz
Smith,W.C. |  | Lists mRNAs deposited by co-author W.C. Smith
Use this last format for author queries. Although GenBank requires the search format Smith WC, internally it uses the format Smith,W.C.

### Assembly details

The Broad Institute Arachne2 assembly was used as a starting point by the Sidow Lab to generate a nonredundant reference assembly of "reftigs". The cioSav2 assembly contains 374 reftigs and has a total size of 174 Mb. See the Sidow Lab C. savignyi Reference Genome web page for more information about the assembly methods.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or through the Sidow Lab Ciona downloads. The cioSav2 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.