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Japanese Medaka HSOK assembly and gene annotation

Assembly

The ASM223469v1 assembly was submitted by The University of Tokyo on July 2017. The assembly is on chromosome level, consisting of 342 contigs assembled into 24 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 3,516,609 while the scaffold N50 is 32,853,055.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002234695.1

Gene annotation

The Japanese rice fish (Oryzias latipes) also known as the medaka, is a member of genus Oryzias (ricefish), the only genus in the subfamily Oryziinae. This small (up to about 3.6 cm or 1.4 in) native of East Asia is a denizen of rice paddies, marshes, ponds, slow-moving streams and tide pools. It is euryhaline, occurring in both brackish and freshwater. It became popular as an aquarium fish because of its hardiness and pleasant coloration: its coloration varies from creamy-white to yellowish in the wild to white, creamy-yellow, or orange in aquarium-bred individuals. Bright yellow, red or green transgenic populations, similar to GloFish, have also been developed, but are banned from sale in the EU. The medaka has been a popular pet since the 17th century in Japan. After fertilization, the female carries her eggs attached between her anal fins for a period before depositing them on plants or alike.

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

AssemblyASM223469v1, INSDC Assembly GCA_002234695.1, Jul 2017
Base Pairs744,414,398
Golden Path Length744,414,398
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes22,785
Non coding genes499
Small non coding genes460
Long non coding genes2
Misc non coding genes37
Pseudogenes32
Gene transcripts36,575

Other

Genscan gene predictions43,879

About this species