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Japanese quail assembly and gene annotation

Assembly

The Coturnix japonica 2.0 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on March 2016. The assembly is on chromosome level, consisting of 9,642 contigs assembled into 2,531 scaffolds. From these sequences, 32 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 511,217 while the scaffold N50 is 2,975,000.

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

AssemblyCoturnix_japonica_2.0, INSDC Assembly GCA_001577835.1, Mar 2016
Base Pairs927,656,957
Golden Path Length927,656,957
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version100.2

Gene counts

Coding genes15,732
Non coding genes5,689
Small non coding genes478
Long non coding genes5,090
Misc non coding genes121
Pseudogenes140
Gene transcripts37,604

Other

Genscan gene predictions31,795

About this species

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