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Common carp assembly and gene annotation

Assembly

The common carp genome assembly was submitted by Chinese Academy Of Fishery Science on November 2016. The assembly is on chromosome level, consisting of 53,088 contigs assembled into 9,378 scaffolds. From these sequences, 50 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 75,080 while the scaffold N50 is 7,828,959.

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

Assemblycommon_carp_genome, INSDC Assembly GCA_000951615.2, Nov 2014
Base Pairs1,713,658,011
Golden Path Length1,713,658,011
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedNov 2019
Database version100.2

Gene counts

Coding genes46,322
Non coding genes5,341
Small non coding genes1,531
Long non coding genes3,761
Misc non coding genes49
Pseudogenes1,114
Gene transcripts106,504

Other

Genscan gene predictions83,196

About this species

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