Photo courtesy of (Shinichi Morishita)
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Oryzias latipes Photo courtesy of (Shinichi Morishita) |
The Apr. 2006 Oryzias latipes Version 1.0 draft assembly 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.
NOTICE OF ERROR: We have determined that UCSC's assembly of the chrUn sequence for oryLat1 is incorrect: the gap relationships between contigs within their ultracontigs are broken. We are in the process of correcting this error, and plan to post a corrected data set in late July. We apologize for the inconvenience.
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.. | ||
This assembly has been sequenced to 10.6X coverage. It consists of approximately 700.4 Mb (excluding gaps) on 24 chromosomes, chr1 - chr24. There are also 7,299 scaffolds comprised of 36,494 contigs of unplaced sequence (118,243,491 bp plus 1,021,750 N of gaps) displayed on the virtual chromosome "chrUn". The contigs on chrUn are spaced with a 10 bp gap; scaffold gaps are 100 bp in size. The medaka mitochondrial sequence is also available as the virtual chromosome "chrM" (GenBank accession: NC_004387).
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.
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.