Medaka assembly and gene annotation


The Japanese medaka (Oryzias latipes) genome, which has been sequenced by whole-genome shotgun sequencing and by using the Ramen assembler, is approximately 700Mb in length and comprises 24 pairs of chromosomes; 2 metacentric, 8 submetacentric, 1 subtelocentric and 13 acrocentric chromosomes in haploid condition. The genome sequencing and assembly for MEDAKA1 (October 2005) were provided by the National Institute of Genetics (NIG) and the University of Tokyo.

This Ensembl website presents sequence data provided by the two institutes. It also displays their gene set together with the Ensembl gene set and related analysis. See the data release policy for the medaka genome.

Gene annotation

The gene set for Medaka was built using a modified version of the standard Ensembl genebuild pipeline. The species-specific sequence resources (medaka cDNA and protein) are very limited, so the majority of gene models are based on genewise alignments of proteins from other species that are genetically distant to medaka. To improve accuracy, genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Medaka cDNAs were aligned and used to add UTRs to the genewise predictions where possible. The gene models were then assessed by generating sets of potential orthologs to genes from other species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs and used to improve the gene models. Finally, additional genes were predicted using medaka EST evidence, and medaka ESTs were used to add UTRs to the gene set where possible.

More information

General information about this species can be found in Wikipedia.



AssemblyHdrR, Oct 2005
Database version82.1
Base Pairs700,386,597
Golden Path Length869,000,216
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedMay 2006
Genebuild releasedOct 2006
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes19,699
Non coding genes759
Small non coding genes748
Misc non coding genes11
Gene transcripts25,434


Genscan gene predictions123,380