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 version80.1
Base Pairs700,386,597
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedMay 2006
Genebuild releasedOct 2006
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes759
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes11

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.25,434


Genscan gene predictions123,380