Zebrafish assembly and gene annotation


After the previous zebrafish assembly (Zv9) was released in July 2010, the zebrafish genome sequence was given into the care of the GRC for future improvement and maintenance. The GRC have recently produced GRCz10, which is the tenth zebrafish reference assembly.

The previous assembly (Zv9), although of high quality, featured many gaps and suffered from sub-optimal long-range continuity. In order to overcome this, the GRC have sequenced more than 1500 additional BAC and fosmid clones and added them to the assembly.

The most notable changes in the chromosome landscape since the previous assembly can be found on chromosome 4, which has gained about 15 Mb in length. Also, 94 of 112 previously unplaced clone-contigs have now been placed on a chromosome. The current assembly contains a total sequence length of 1.37Gb with 2.09Mb of gaps. There are 26 chromosomes (including the mitochondrion) and 3,399 scaffolds, composed of 22,852 contigs with a scaffold N50 of 2.18Mb and a contig N50 of 1.232Mb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

More information about zebrafish research can be found at the Wellcome Trust Sanger Institute.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002035.3

Other assemblies

Gene annotation

The Ensembl GRCz10 assembly was annotated using Ensembl's automatic annotation 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 level 3 and above). Aligned zebrafish cDNAs and zebrafish RNASeq data have been used to add UTRs. RNASeq data from embryonic and olfactory epithelium tissues were also used to produce gene models. 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.

More information

General information about this species can be found in Wikipedia.



AssemblyGRCz10 (Genome Reference Consortium Zebrafish Build 10), INSDC Assembly GCA_000002035.3, Sep 2014
Base Pairs1,464,443,456
Golden Path Length1,371,719,383
Annotation providerEnsembl
Annotation methodMixed strategy build
Genebuild startedSep 2014
Genebuild releasedMay 2015
Genebuild last updated/patchedJun 2017
Database version90.10

Gene counts

Coding genes25,903 (incl 48 readthrough)
Non coding genes8,835
Small non coding genes3,655
Long non coding genes5,086 (incl 8 readthrough)
Misc non coding genes94
Gene transcripts62,895


Genscan gene predictions36,087
Short Variants17,502,082
Structural variants5,735

About this species