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Karyotype

Click on a chromosome for a closer view

About the Medaka genome

Assembly

The Japanese medaka (Oryzias latipes) genome, which has been sequenced by whole-genome shotgun sequencing and by using 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.

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.

What's New in Ensembl 50

Oryzias latipes News

• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

• SSAHA
  From release 50 we will no longer be providing SSAHA sequence search. If you wish to run your own SSAHA sequence search you can download the files to generate the search hashes from our FTP site.
• Projections of gene names and GO terms
  These have been done as usual, between a variety of species.
• Stored peptide stats
  In order to improve efficiency on ProtView, peptide statistics are now calculated in advance and stored as translation attributes, instead of being calculated on the fly.

More news...

Statistics

How the statistics are calculated