Ensembl Zebrafish

Karyotype

Click on a chromosome for a closer view

About the Zebrafish genome

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

This Ensembl website features the zebrafish assembly version 5 (Zv5), as released on the 27th May 2005. This assembly was produced by integrating the whole genome shotgun assembly with data from the physical map (more information).

Datasets used for the analyses that were provided by collaborators are acknowledged here.

The zebrafish sequencing project is funded by the Wellcome Trust.

You may export data from this site. Please see the Conditions of use for these data.

Annotation

This site provides a full Ensembl gene set for Zv5. This release is based on a strategy where transcripts are generated based on protein evidence and clustered in genes. Aligned zebrafish cDNA are used to add UTR regions. Genes are named based on the alignment of their coding regions to known entries in public databases, in this process ZFIN genes have priority.

A number of Zebrafish clones have also been manually annotated in Vega, these genes are currently accessible in zebrafish Ensembl through a DAS track.

What's New in Ensembl 37

Danio rerio News

• New ZFIN data
  Ensembl Zebrafish expression pattern xrefs and dna align features have been updated with new data from the ZFIN Project.
• SSAHA2
  Transcript-based SSAHA2 servers are now available for all species. Go to BlastView and select SSAHA2 from the Search Tool box.
• UniProt updates
  Support has been added for variable splice UniProt records by adding an external db with a display label of "UniprotKB/SpliceVariant" to the external_db table on all databases.
  Read more...
• GeneSeqalignView
  This new view is based on GeneSeqView, with the added ability to align the given sequence with one or more species.
  Read more...
• Bug fix to Transcript.pm
  Transcript.pm; is_known() was returning true if the transcript had a display_xref set, which is both incorrect and inconsistent with the is_known() method in Gene.pm. The new behaviour is to return true if the transcript's status is KNOWN.

More news...

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