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Sooty mangabey assembly and gene annotation

Assembly

The Caty_1.0 assembly was submitted by Human Genome Sequencing Center - BCM on 2015/03/19 . The assembly is on the Scaffold level, consisting of 76,752 assembled into 11,433 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 112,942 while the scaffold N50 is 12,849,131.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000955945.1

Gene annotation

The sooty mangabey (Cercocebus atys) is an Old World monkey found in forests from Senegal in a margin along the coast down to Ghana. While overall rated as Near Threatened, the eastern race lunulatus, also known as the white-crowned, white-naped, or white-collared mangabey (leading to confusion with the collared mangabey), is considered Endangered by the IUCN. The White-collared mangabey was declared its own species by the IUCN in 2016, but it retains the endangered conservation status.

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

AssemblyCaty_1.0, INSDC Assembly GCA_000955945.1, Mar 2015
Base Pairs2,787,272,854
Golden Path Length2,848,246,356
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.1

Gene counts

Coding genes20,926
Non coding genes6,993
Small non coding genes4,525
Long non coding genes545
Misc non coding genes1,923
Pseudogenes540
Gene transcripts53,925

Other

Genscan gene predictions47,942

About this species