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).
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.
|| 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.|
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.