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

The Takifugu rubripes v5.0 (Oct. 2011) whole genome shotgun assembly was provided by the International Fugu Genome Sequencing Consortium, led by JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).

The Oct. 2011 Takifugu Rubripes assembly (Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2)) was produced by the International Fugu Genome Sequencing Consortium See also: Genome Biol Evol (2011) 3 424-442.

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:
chrM   Displays the complete mitochondrial chromosome chrM
chr1:1-1000000   Displays first million bases of chr1
chr1:1000000+2000 Displays a region of chr1 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
homeobox caudal   Lists mRNAs for caudal homeobox genes
kruppel zinc finger   Lists only kruppel-like zinc fingers
zahler   Lists mRNAs deposited by scientist named Zahler
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 v5 assembly was generated by filling some gaps in the v4 assembly and by organizing scaffolds into chromosomes based on a genetic map of fugu. About 72% of the assembly (281,572,362 bases) is organized into 22 chromosomes. Approximately 28% of the assembly (109,895,906 bases) has not been ordered in the assembly and is included in the genome browser as 6,812 scaffolds with their genbank identifier as their name, for example: HE591497 The fugu mitochondrial sequence is also available as the virtual chromosome "chrM"(NC_004299).

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 the success of this release.

GenBank Pipeline Details

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