Danio rerio

Genome assembly: GRCz10 (GCA 000002035.3)

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 (corresponding to GenBank Assembly ID GCA_000002035.3), 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, comprised 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.

The full gene build of an older Zebrafish assembly, Zv9, can be found on our main website.

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Gene annotation

What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.


This preliminary gene annotation was generated through a combination of nucleotide and protein sequence alignments, obtained from a number of different sources. We aligned 26,459 zebrafish and 20,318 human translations from Ensembl release 77, providing us with 25,696 and 7,259 gene models, respectively. Predictions were also made using vertebrate proteins, giving predictions from zebrafish proteins priority over those from other vertebrate species. Ab initio gene predictions and alignments of sequences from UniProt, UniGene and the ENA vertebrate RNA collection are also provided.



Assembly: GRCz10, Sep 2014
Database version: 78
Base Pairs: 1,464,443,456
Golden Path Length: 1,371,719,383
Genscan gene predictions: 36,087