Takifugu rubripes Photo courtesy of (Byrappa Venkatesh, all rights reserved.)

The Takifugu rubripes v4.0 (Oct. 2004) whole genome shotgun assembly was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium, led by JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).

### Sample position queries

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

Request: |  | Genome Browser Response:
--- | --- | ---
chrUn |  | Displays all of virtual chromosome Un
chrUn:1-1000000 |  | Displays first million bases of chr Un
chrUn:1000000+2000 |  | Displays a region of chr Un that spans 2000 bases, starting with position 1000000
AY617120 |  | Displays region of mRNA with GenBank accession number AY617120
CA846300 |  | Displays region of EST with GenBank accession CA846300
pseudogene mRNA |  | Lists transcribed pseudogenes, but not cDNAs
homeobox caudal |  | Lists mRNAs for caudal homeobox genes
zinc finger |  | Lists many zinc finger mRNAs
kruppel zinc finger |  | Lists only kruppel-like zinc fingers
zhang |  | Lists mRNAs deposited by scientist named Zhang
Begemann,G. |  | Lists mRNAs deposited by co-author G. Begemann
Use this last format for author queries. Although GenBank requires the search format Begemann G, internally it uses the format Begemann,G..

### Assembly details

The v4.0 Fugu genome has been sequenced to approximately 8.5X coverage. The assembly contains 7,213 scaffolds covering 393,312,790 bp. The UCSC browser displays the scaffolds on a virtual chromosome chrUn with gaps of 1,000 bp between scaffolds. The scaffolds range in size from 2,223 bp to 7,245,445 bp. Fifty percent of the sequence (196,648,171 bp) is contained within 125 scaffolds of size 858,115 or greater (N50). The Fugu mitochondrial sequence is also available as the virtual chromosome "chrM" (GenBank accession: NC_004299.1).

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have been freely provided by the JGI for use in the UCSC Genome Browser.

The Fugu browser 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.