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

The Takifugu rubripes v.3.0 (Aug. 2002) 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 an mRNA or EST, a scaffold range, an Ensembl transcript ID, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the Fugu genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in Fugu. See the User Guide for more help.

Request:
    Genome Browser Response:

scaffold_407 Displays all of scaffold 407
scaffold_1:1-200000 Displays first two hundred thousand bases of scaffold 1
scaffold_1:100000+2000 Displays a region of scaffold 1 that spans 2000 bases, starting with position 100000

AF083811 Displays region containing fugu mRNA with GenBank accession number AJ310911
BU805870 Displays region containing fugu EST with GenBank accession BU805870
SINFRUT00000127009 Displays region containing Ensembl gene prediction transcript SINFRUT00000127009

p53 Lists mRNAs related to the p53 tumor suppressor
pseudogene mRNA Lists transcribed pseudogenes but not cDNAs, in GenBank
homeobox caudal Lists mRNAs for caudal homeobox genes in GenBank
zinc finger Lists many zinc finger mRNAs
kruppel zinc finger Lists only kruppel-like zinc fingers
huntington Lists mRNAs associated with Huntington's disease

zahler Lists mRNAs deposited by scientist named Zahler
Evans,J.E. Lists mRNAs deposited by co-author J.E. Evans

Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format Evans,J.E.

Assembly details

This assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced by JGI and IMCB at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are plasmid, cosmid, or BAC end sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 20,379 scaffolds totaling 319 million base pairs. The largest 679 scaffolds total 160 million base pairs. Note: IMCB and Ensembl refer to this release of the Fugu genome as Version 2 rather than Version 3, because it is the second annotated release.

Downloads of the Fugu data and annotations may be obtained from the UCSC FTP site or Downloads page. These data have been freely provided by the JGI for use in the UCSC Genome Browser.

Note: the genus name Fugu was recently changed to Takifugu. GenBank files for this organism are named with the Takifugu genus, but NCBI includes Fugu as a synonym in the database for searches. Both genus names are currently in use.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: low-coverage.