Chimpanzee assembly and gene annotation

Assembly

The Pan_tro 3.0 assembly was submitted by Chimpanzee Sequencing and Analysis Consortium on 2016/05/03 . The assembly is on the Chromosome level, consisting of 72,226 assembled into 45,511 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 384,816 while the scaffold N50 is 26,972,556.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001515.4

Other assemblies

Gene annotation

The taxonomical genus Pan (often referred to as "Chimpanzees" or "chimps") consists of two extant species: the common chimpanzee and the bonobo. Together with humans, gorillas and orangutans they are part of the family Hominidae (the great apes). Bonobos and common chimpanzees are the only species of great apes that are currently restricted in their range to Africa. Native to sub-Saharan Africa, common chimpanzees and bonobos are currently both found in the Congo jungle, while only the common chimpanzee is also found further north in West Africa. In 2017, the UN backed Convention of Migratory Species held in The Philippines selected chimpanzee for protection .

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

AssemblyCHIMP2.1.4, INSDC Assembly GCA_000001515.4, Feb 2011
Base Pairs2,995,917,117
Golden Path Length3,309,577,922
Annotation methodFull genebuild
Genebuild startedMay 2011
Genebuild releasedDec 2011
Genebuild last updated/patchedNov 2012
Database version94.214

Gene counts

Coding genes18,759
Pseudogenes572
Gene transcripts29,160

Other

Genscan gene predictions56,687
Short Variants1,729,238

About this species