Danio rerio Photo courtesy of NHGRI (Press Photos)

The Jul. 2010 zebrafish (Danio rerio) Zv9 assembly (GCA_000002035.2) was produced by The Wellcome Trust Sanger Institute, UK.

### 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 zebrafish 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 zebrafish. See the User's Guide for more information.

Request: | Genome Browser Response:
chr1 |  | Displays all of chromosome 1
chr1:1-200000 |  | Displays first two hundred thousand bases of chromosome 1
chr1:100000+2000 |  | Displays a region of chr 1 that spans 2000 bases, starting with position 100000
U30710 |  | Displays region containing zebrafish mRNA with GenBank accession number U30710
AA658622 |  | Displays region containing zebrafish EST with GenBank accession AA658622
ENSDART00000025573 |  | Displays region containing Ensembl gene prediction transcript ENSDART00000025573
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
porter |  | Lists mRNAs deposited by scientists named Porter
Amsterdam,A. |  | Lists mRNAs deposited by co-author A. Amsterdam
Use this last format for author queries. Although GenBank requires the search format Amsterdam A, internally it uses the format Amsterdam,A. ### Assembly details The Zv9 assembly comprises a sequence length of 1.4 Gb in 26 chromosomes and 1,107 scaffolds. This assembly is based on a clone path sorted with the high-density meiotic map SATMAP (Clark et al., in preparation). The data freeze was taken on 1 April 2010. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involved sequence alignemnts as well as cDNA, marker and BAC/Fosmid end sequence placements. For more details about the Zv9 assembly, see the Sanger Institute page for the Danio rerio Sequencing Project. In this assembly, scaffolds that are based on clone contigs or could be associated with chromosome placements through marker information are named Zv9_scaffoldn. WGS contigs that could not be placed on chromosomes are named Zv9_NAn. Linkage group numbers were translated directly into chromosome numbers (e.g. linkage group 1 = chromosome 1). The zebrafish mitochondrial sequence is also available as the virtual chromosome, chrM (GenBank accession NC_002333.2) The Sanger Institute notes that this assembly release is still preliminary. The regions of the assembly covered by WGS contigs are of lower quality. Downloads of the zebrafish data and annotations can be obtained from the UCSC FTP site or Downloads page. This data set has specific conditions for use. The danRer7 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.