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Tetraodon assembly and gene annotation

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.

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.

Statistics

Summary

AssemblyTETRAODON 8.0, Mar 2007
Base Pairs342,419,788
Golden Path Length358,618,246
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2007
Genebuild releasedJul 2008
Genebuild last updated/patchedMay 2010
Database version94.8

Gene counts

Coding genes19,602
Non coding genes813
Small non coding genes806
Misc non coding genes7
Pseudogenes147
Gene transcripts24,078

Other

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

About this species