Ensembl Tetraodon

Karyotype

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About the Tetraodon genome

Assembly

The Tetraodon genome project is a collaboration between Genoscope and the Broad Institute (MIT). This Ensembl website presents sequence data and analyses provided by the two institutes.

The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.

The genome assembly was performed using Arachne (Jaffe D.B. et. al. 2003. Gen. Res. 13, 91-96). This site presents version 7 of the assembly.

Annotation

Genes were annotated by Genoscope, combining evidence from Geneid, Genscan, Genewise and Exofish predictions with alignments of Tetraodon cDNAs to the genome. This was done automatically using GAZE (Howe K., Chothia T. and Durbin R. 2002. Gen. Res. 12, 1418-27) with a custom-designed configuration and gene structure model.

The annotation also includes 87 manually curated structures of a number of HOX and Cytokine genes.

What's New in Ensembl 49

Tetraodon nigroviridis News

• Variation updates
  New variation databases have been released for human, mouse, chicken and zebrafish (dbSNP 128) and rat (dbSNP 126). Transcript variation has been rerun for dog, platypus, chimp, and tetraodon due to gene set changes.

General News

• Release schedule
  

  Ensembl release 50 will occur in July (rather than in April as originally scheduled).
  Read more...

• API changes - regulatory features
  Regulatory feature support has been moved from the core API to the functional genomics API. More information about using the new code...
• Removal of viral genes
  We have removed a total of about 1200 viral genes from the following species.
  Read more...
• Mart updates
  RGD and SGD Symbol+ID combinations have been introduced, similar to HGNC, MGI and ZFIN. The issue with subsets of homologs being returned has been resolved.

More news...

Statistics

Assembly:	TETRAODON 7, Apr 2003
Genebuild:	Genoscope, Sep 2004
Database version:	49.1k
Known protein-coding genes:	27,991
RNA genes:	648
Gene exons:	197,248
Gene transcripts:	27,991
SNPs:	914,456
Base Pairs:	342,403,326
Golden Path Length:	402,240,326
Most common InterPro domains:	Top 40 Top 500

How the statistics are calculated