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Clown anemonefish assembly and gene annotation

The clown anemonefish (Amphiprion ocellaris), also known as the false percula clownfish or common clownfish, is a marine fish belonging to the family Pomacentridae, which includes clownfishes and damselfishes. A. ocellaris is the most basal species in the genus Amphiprion which is closely related to the genus Premnas. The species' most closely related ancestor is Amphiprion percula, the Orange clownfish. It is thought that A. ocellaris specialized after diverging from the genus Premnas, and scientific evidence confirms that all clownfish belonging to the genus Amphiprion initially could withstand the stings of only one type of anemone; after further speciation the 28 different species of clownfish including A. ocellaris have specialized to be able to resist the poisonous stings of many different anemone species.


The AmpOce1.0 assembly was submitted by Deakin University on November 2017. The assembly is on scaffold level, consisting of 7,803 contigs assembled into 6,405 scaffolds. 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 324,210 while the scaffold N50 is 401,715.

Gene annotation

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.



AssemblyAmpOce1.0, INSDC Assembly GCA_002776465.1, Nov 2017
Base Pairs880,720,895
Golden Path Length880,720,895
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version104.1

Gene counts

Coding genes23,592
Non coding genes1,144
Small non coding genes1,124
Long non coding genes3
Misc non coding genes17
Gene transcripts33,631


Genscan gene predictions51,225

About this species