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Fugu assembly and gene annotation


The FUGU5 assembly was submitted by The Fugu Genome Sequencing Consortium on October 2011. The assembly is on chromosome level, consisting of 30,861 contigs assembled into 7,091 scaffolds. From these sequences, 22 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 52,883 while the scaffold N50 is 928,938.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000180615.2

Gene annotation

Takifugu rubripes, commonly known as the Japanese puffer, Tiger puffer, or torafugu (Japanese: 虎河豚), is a pufferfish in the genus Takifugu. It is distinguished by a very small genome that has been fully sequenced because of its use as a model species and is in widespread use as a reference in genomics.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.



AssemblyFUGU5, INSDC Assembly GCA_000180615.2, Oct 2011
Base Pairs391,484,725
Golden Path Length391,484,725
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.5

Gene counts

Coding genes20,545
Non coding genes529
Small non coding genes504
Long non coding genes2
Misc non coding genes23
Gene transcripts29,243


Genscan gene predictions29,880

About this species