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Japanese medaka HNI assembly and gene annotation

The medaka or Japanese rice fish (Oryzias latipes) is a native of East Asia, found in denizen of rice paddies, marshes, ponds, slow-moving streams and tide pools. The medaka is a model organism and is extensively used in many areas of biological research, most notably in toxicology.

Assembly

The ASM223471v1 assembly was submitted by The University of Tokyo on July 2017. The assembly is on chromosome level, consisting of 741 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 1,450,098 while the scaffold N50 is 28,873,095.

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

AssemblyASM223471v1, INSDC Assembly GCA_002234715.1, Jul 2017
Base Pairs677,633,405
Golden Path Length677,633,405
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version100.1

Gene counts

Coding genes22,127
Non coding genes528
Small non coding genes491
Long non coding genes3
Misc non coding genes34
Pseudogenes26
Gene transcripts36,005

Other

Genscan gene predictions39,710

About this species

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