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Northern pike assembly and gene annotation

Assembly

The Eluc_V3 assembly was submitted by Ben F Koop, Jong S Leong on January 2017. The assembly is on chromosome level, consisting of 18,750 contigs assembled into 1,211 scaffolds. From these sequences, 25 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 125,635 while the scaffold N50 is 7,945,253.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000721915.3

Gene annotation

The northern pike (Esox lucius), known simply as a pike in Britain, Ireland, most of Canada, and most parts of the United States (once called luce when fully grown; also called jackfish or simply "northern" in the U.S. Upper Midwest and in Manitoba), is a species of carnivorous fish of the genus Esox (the pikes). They are typical of brackish and fresh waters of the Northern Hemisphere (i.e. holarctic in distribution).Pike can grow to a relatively large size: the average length is about 40–55 cm (16–22 in), with maximum recorded lengths of up to 150 cm (59 in) and published weights of 28.4 kg (63 lb). The IGFA currently recognizes a 25 kg (55 lb) pike caught by Lothar Louis in Lake on Grefeern, Germany, on 16 October 1986, as the all-tackle world-record northern pike.

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

AssemblyEluc_V3, INSDC Assembly GCA_000721915.3, Jan 2017
Base Pairs904,497,253
Golden Path Length904,497,253
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.3

Gene counts

Coding genes23,954
Non coding genes646
Small non coding genes623
Long non coding genes2
Misc non coding genes21
Pseudogenes32
Gene transcripts43,821

Other

Genscan gene predictions33,560

About this species