Search Archive EnsEMBL Zebrafish
e.g. gene SLC24A5 or 22:23684022-23844244 or kinesin
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Description
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Zebrafish (Danio rerio)
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.
Assembly
Zv8 is the eighth integrated Whole Genome Shotgun (WGS) assembly of the zebrafish genome at a coverage of 6.5-7x. The project coordination and genome sequencing and assembly is provided by the Wellcome Trust Sanger Institute.
The N50 size is the length such that 50% of the assembled genome lies in blocks of N50 size or longer. The N50 size of the 247,928 contigs is 20,629bp. There are 105,987 supercontigs in the WGS assembly with an N50 size of 687,451bp. ( More information about the assembling process, and further statistics ).
Please note: This is still a preliminary assembly. The regions of the assembly covered by WGS contigs are of lower quality. The assembly will still contain misjoins, misassemblies and artificial duplications due to retention of haplotypic sequences are likely to occur. During the generation of Zv8, particular attention has been paid to improving the order of the clone path.
Annotation
The zebrafish Zv8 assembly was annotated using a modified Ensembl pipeline. Predictions from zebrafish proteins have been given priority over predictions from other non-mammalian vertebrate species. Aligned zebrafish cDNAs have been used to add UTR regions. 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 final gene-set comprises 24,147 protein-coding genes, 80 genes that have been identified as pseudogenes, and 6 retrotransposed gene predictions. The prediction of ncRNA genes will added for the ensembl 55 release.
Additional manual annotation of this genome can be found in
Vega
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