e.g. SLC24A5 or 10:10138322-10349251 or kinesin

The zebrafish genome project is a collaboration between the Sanger Institute and the zebrafish community, announced during the Sanger Institute Zebrafish Workshop 2000 and was started in February 2001.


Danio rerio

Zv9 (GCA_000002035.2) is the ninth integrated assembly of the zebrafish genome. This assembly is used by UCSC to create their danRer7 database. It is based on nearly 90% clone sequence (data freeze April 2010), with remaining gaps being filled using sequence from a novel whole genome shotgun assembly, WGS31. The project coordination, genome sequencing and assembly is provided by the Wellcome Trust Sanger Institute.

An overview of the assembly is available here, and frequently asked questions about the assembly process and terminology are addressed here.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002035.2

Download Zebrafish genome sequence (FASTA)

Previous assemblies


The zebrafish Zv9 assembly was annotated using a modified Ensembl pipeline. Predictions from zebrafish proteins have been given priority over predictions from other non-mammalian vertebrate species. All Uniprot proteins were filtered to remove predictions ( PE levels 3 and above ). Aligned zebrafish cDNAs have been used to add UTR regions.8,374 RNASeq models made from a range of zebrafish developmental stages and tissues were added into the gene build where they added a novel model or splice variant.Genes are named based on the alignment of their coding regions to known entries in public databases; ZFIN genes have priority in this process.

The Ensembl annotations were then merged with Vega annotations at the transcript level. Transcripts were merged if they shared the same internal exon-intron boundaries (i.e. had identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Vega source transcripts (regardless of merge status) were included in the final merged gene set.

Vega logo Additional manual annotation of this genome can be found in Vega