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Pig-tailed macaque assembly and gene annotation

Assembly

The Mnem_1.0 assembly was submitted by Baylor College of Medicine on 2015/03/19 . The assembly is on the Scaffold level, consisting of 94,057 assembled into 9,733 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 106,897 while the scaffold N50 is 15,219,753.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000956065.1

Gene annotation

The southern pig-tailed macaque (Macaca nemestrina) is a medium-sized Old World monkey.

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

AssemblyMnem_1.0, INSDC Assembly GCA_000956065.1, Mar 2015
Base Pairs2,838,486,523
Golden Path Length2,948,703,511
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.1

Gene counts

Coding genes21,060
Non coding genes7,221
Small non coding genes4,584
Long non coding genes640
Misc non coding genes1,997
Pseudogenes584
Gene transcripts54,453

Other

Genscan gene predictions48,686

About this species