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Chimpanzee assembly and gene annotation

The common chimpanzee (Pan troglodytes) is a great ape found almost exclusively in the heavily forested regions of Central and West Africa. Along with the bonobo, the chimpanzee is humanity's closest living relative, with almost 99% of DNA in common between the species.


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.

Gene annotation

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 Pairs3,231,170,666
Golden Path Length3,231,170,666
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedMar 2020
Database version104.3

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