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Goldfish assembly and gene annotation


The ASM336829v1 assembly was submitted by National Institutes of Health on August 2018. The assembly is on chromosome level, consisting of 8,463 contigs assembled into 6,216 scaffolds. From these sequences, 59 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 821,153 while the scaffold N50 is 22,763,433.

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.



AssemblyASM336829v1, INSDC Assembly GCA_003368295.1, Aug 2018
Base Pairs1,820,635,050
Golden Path Length1,820,635,050
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedOct 2019
Database version104.1

Gene counts

Coding genes54,774
Non coding genes6,442
Small non coding genes3,572
Long non coding genes2,806
Misc non coding genes64
Gene transcripts144,639


Genscan gene predictions91,956

About this species