Tetraodon assembly and gene annotation


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.

Gene 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.

More information

General information about this species can be found in Wikipedia.



AssemblyTETRAODON 8.0, Mar 2007
Database version80.8
Base Pairs342,419,788
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedNov 2007
Genebuild releasedJul 2008
Genebuild last updated/patchedMay 2010

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes813
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes7

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.24,078


GSC gene prediction24,558
Genscan gene predictions23,832
Short Variants911,017