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European seabass assembly and gene annotation

Assembly

The seabass_V1.0 assembly was submitted by MPI-PZ on May 2014. The assembly is on scaffold level, consisting of 37,781 contigs assembled into 25 scaffolds. 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 54,134 while the scaffold N50 is 26,439,989.

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

Assemblyseabass_V1.0, INSDC Assembly GCA_000689215.1, Apr 2014
Base Pairs675,917,103
Golden Path Length675,917,103
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedOct 2019
Database version100.1

Gene counts

Coding genes23,382
Non coding genes2,767
Small non coding genes1,144
Long non coding genes1,614
Misc non coding genes9
Pseudogenes171
Gene transcripts66,948

Other

Genscan gene predictions35,707

About this species

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