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Chimpanzee assembly and gene annotation


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_000001515.5

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.



AssemblyPan_tro_3.0, INSDC Assembly GCA_000001515.5, May 2016
Base Pairs3,385,800,935
Golden Path Length3,231,170,666
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.3

Gene counts

Coding genes23,534
Non coding genes9,710
Small non coding genes5,640
Long non coding genes1,786
Misc non coding genes2,284
Gene transcripts61,457


Genscan gene predictions59,841
Short Variants1,569,627

About this species