Fugu assembly and gene annotation


This site presents version 4 of the Fugu genome, released in June 2005 by the International Fugu Genome Consortium. Takifugu rubripes has a very compact genome, with less than 15% consisting of dispersed repetitive sequence, which makes it ideal for gene discovery.

The latest assembly includes 7,213 scaffolds, constituting 390 Mb of the genome, and the mitochondrion. 90% of the genome is on 1118 scaffolds. 74 scaffolds are larger than 1 Mb each and the largest scaffold is 7 Mb. Please refer to the Fugu Project webpage for more details of the sequencing effort.

Other assemblies

Gene annotation

This is the first full Ensembl genebuild of this genome. It was carried out in an incremental fashion, using fugu proteins initially then adding in other fish, mammal, vertebrate and finally non-vertebrate protein sequences.

More information

General information about this species can be found in Wikipedia.



AssemblyFUGU 4.0, Jun 2005
Database version82.4
Base Pairs393,312,790
Golden Path Length393,312,790
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedNov 2007
Genebuild releasedMar 2008
Genebuild last updated/patchedMay 2010

Gene counts

Coding genes18,523
Non coding genes703
Small non coding genes693
Misc non coding genes10
Gene transcripts48,706


Genscan gene predictions29,699