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Capuchin assembly and gene annotation

Assembly

The Cebus capucinus Cebus_imitator-1.0 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on 2016/04/04 . The assembly is on the Scaffold level, consisting of 140,597 assembled into 7,156 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 41,196 while the scaffold N50 is 5,274,112.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001604975.1

Gene annotation

The capuchin monkeys are New World monkeys of the subfamily Cebinae. They are readily identified as the "organ grinder" monkey, and have been used in several movies and television shows. The range of capuchin monkeys includes Central America and South America as far south as northern Argentina. In Central America, they usually occupy the wet lowland forests on Caribbean coast of Costa Rica and Panama and deciduous dry forest on the Pacific coast.

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.

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

AssemblyCebus_imitator-1.0, INSDC Assembly GCA_001604975.1, Apr 2016
Base Pairs2,610,518,382
Golden Path Length2,717,703,182
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.1

Gene counts

Coding genes20,317
Non coding genes7,121
Small non coding genes4,080
Long non coding genes155
Misc non coding genes2,886
Pseudogenes550
Gene transcripts48,384

Other

Genscan gene predictions47,761

About this species