Photo courtesy of (Shinichi Morishita)
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Oryzias latipes Photo courtesy of (Shinichi Morishita) |
The Oct. 2005 version 1.0 draft assembly of Oryzias latipes was produced by the National Institute of Genetics (NIG) and the University of Tokyo, Japan. This assembly is equivalent to the Ensembl Oct. 2005 MEDAKA1 assembly.
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 medaka genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chr23 | Displays all of chromosome 23 | |
| chr3:1-1,000,000 | Displays first million bases of chr 3 | |
| chr3:19,840,000+100,000 | Displays a region of chr 3 that spans 100,000 bases, starting with position 19,840,000 | |
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| AY158893 | Displays region of mRNA with GenBank accession number AY158893 | |
| BJ733542 | Displays region of EST with GenBank accession BJ733542 on chr 6 | |
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| 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 | |
| Takeda,H. | Lists mRNAs deposited by co-author H. Takeda | |
| Use this last format for author queries. Although GenBank requires the search format Takeda H, internally it uses the format Takeda,H.. | ||
The Medaka genome has been sequenced to 10.6X coverage. It consists of approximately 690.7 Mb of sequence, including gaps, on 24 chromosomes (chr1 - chr24). In addition to the sequence placed on chromosomes, the assembly contains approximately 118.2 Mb of unplaced sequence in 36,494 contigs comprising 7,164 ultracontigs and scaffolds. Note that within this assembly not all scaffolds are assembled into ultracontigs, and not all ultracontigs are assembled into chromosomes. The medaka mitochondrial sequence is also available as the virtual chromosome "chrM" (GenBank accession: GI:25057156, NC_004387).
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. Please refer to the University of Tokyo Genome Browser Medaka webpage for more information about the v1.0 assembly and data use guidelines.
The Medaka 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.