Danio rerio (NHGRI Press Photos)

The June 2004 zebrafish (Danio rerio) Zv4 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
ENSDART00000049940 |  | Displays region containing Ensembl gene prediction transcript ENSDART00000049940
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 entry authors -- even though GenBank searches require Amsterdam A format, GenBank entries themselves use Amsterdam,A. internally.

### Assembly details

The Zv4 assembly consists of 1,560,480,686 bp in 21,333 scaffolds with a sequence coverage of approximately 5.7x. 443 Mb of the assembly is from 2,828 finished clones and 121 Mb is from 1,272 unfinished clones.

This assembly was constructed 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 a fingerprint contig (FPC) map. From this map, a tiling path was calculated that covered 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.

75% of the sequence (1,260,930,206 bp) was tied to the FPC map, which provided a template for placing the unfinished sequence. The remaining sequence was filled with WGS contigs using a combination of sequence alignment and BAC end positions. The WGS contigs used in this assembly were identical to those used for the Zv3 assembly, but the FPC data and its integration with the WGS data has been considerably improved.

The Sanger Institute notes there is high level of misassembly present in this release due to the large amount of polymorphism in the DNA source. Highly variable regions within the genome posed assembly difficulties, most likely because the sequences originated from different 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.