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Orange clownfish assembly and gene annotation

The orange clownfish (Amphiprion percula) is widely known as a popular aquarium fish. Like other clownfishes it often lives in symbiotic association with sea anemones; A. percula is associated specifically with Heteractis magnifica and Stichodactyla gigantea, and in its larval form uses chemical cues released by the anemone to identify and locate the appropriate host species.

The anemone helps the fish by giving it protection from predators, which include brittle stars, wrasses, and other damselfish, and the fish helps the anemone by feeding it, increasing oxygenation, and removing waste material from the host. The fish's ability to live within the anemone without being harmed has been shown to derive from a combination of two factors: immunity to the anemone's toxins, and secretion of a mucus that prevents the anemone from discharging its nematocysts.

Assembly

The Nemo_v1 assembly was submitted by King Abdullah University of Science and Technology on April 2018. The assembly is on chromosome level, consisting of 1,047 contigs assembled into 365 scaffolds. From these sequences, 24 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 3,123,421 while the scaffold N50 is 38,416,550.

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.

Statistics

Summary

AssemblyNemo_v1, INSDC Assembly GCA_003047355.1, Apr 2018
Base Pairs908,939,294
Golden Path Length908,939,294
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version100.1

Gene counts

Coding genes23,926
Non coding genes875
Small non coding genes849
Long non coding genes3
Misc non coding genes23
Pseudogenes39
Gene transcripts35,899

Other

Genscan gene predictions48,033

About this species

HASH(0x229a7580)