Danio rerio (NHGRI Press Photos)

The November 2003 zebrafish (Danio rerio) Zv3 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.

### Sample position queries

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 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 Guide for more help.

Request: | Genome Browser Response:
chr1 |  | Displays all of chromosome 1
chr1:1-200000 |  | Displays first two hundred thousand bases of chromosome 1
U30710 |  | Displays region containing zebrafish mRNA with GenBank accession number U30710
AA658622 |  | Displays region containing zebrafish EST with GenBank accession AA658622
ENSDART00000021228 |  | Displays region containing Ensembl gene prediction transcript ENSDART00000021228
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 scientist 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

This assembly was constructed by using two different strategies. In the first, a whole genome shotgun (WGS) approach was used. DNA from 1000 five-day-old Tuebingen embryos was used to generate plasmid and fosmid libraries. The libraries were sequenced and the resulting traces were assembled with the Sanger Institute assembler, Phusion. The second approach used traditional clone mapping and sequencing techniques to produce a higher quality genome sequence. BAC libraries were selected and fingerprinted to generate an FPC map. From this map, a tiling path was calculated that covers the genome sequence clone-by-clone. Clones from this path were selected for high quality sequencing and then pieced together to form the genome sequence.

The Zv3 assembly consists of 1,459,115,486 bp in 58,339 supercontigs, with a sequence coverage of approximately 5.7X. This zebrafish assembly is the first to be tied to the FPC map: 1,083,447,588 bp (74%) of the sequence were mapped in this way.

The Sanger Institute notes that this is a preliminary assembly; a high level of misassembly is present due to polymorphisms in the DNA source. Highly variable regions of the assembly are difficult to assemble, most likely due to differing haplotypes. For more information about this assembly, see the Sanger Institute page for the Danio rerio Sequencing Project.

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 danRer1 annotation tracks were generated by UCSC and collaborators worldwide. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston, MA, USA for their collaboration on this release. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.