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American beaver assembly and gene annotation

Assembly

The C.can genome v1.0 assembly was submitted by Hospital for Sick Children on February 2017. The assembly is on scaffold level, consisting of 24,477 contigs assembled into 21,157 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 273,954 while the scaffold N50 is 317,708.

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

AssemblyC.can_genome_v1.0, INSDC Assembly GCA_001984765.1, Feb 2017
Base Pairs2,518,306,565
Golden Path Length2,518,306,565
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes20,637
Non coding genes7,387
Small non coding genes5,385
Long non coding genes648
Misc non coding genes1,354
Pseudogenes906
Gene transcripts38,514

Other

Genscan gene predictions61,256

About this species

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