Orangutan assembly and gene annotation


This site presents the 6X whole genome shotgun assembly from a female Sumatran orangutan (Pongo pygmaeus abelii) named Susie, housed at the Gladys Porter Zoo (Brownsville, TX). The primary donor-derived reads were assembled using PCAP (Huang, 2006) using stringent parameters; by aligning the orangutan genome against the human genome, it was possible to identify interchromosomal cross-overs and thus eliminate global mis-assemblies larger than 50kb.

Of the 3.09Gb of total sequence, 3.08Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum allowed gap size of 30kb.

The genome assembly represented here corresponds to GCA_000001545.1

Gene annotation

Due to the high sequence similarity to the human genome, the Orangutan genebuild was based on a projection of human gene structures. The projections were made through chained whole genome BLASTz alignments. These projected genes were combined with orangutan-specific proteins, and additional human genes were added using exonerate where the projection was unable to make satisfactory gene models. UTRs were added using orangutan-specific ESTs and cDNAs as well as human cDNAs.

More information

General information about this species can be found in Wikipedia.



AssemblyPPYG2, INSDC Assembly GCA_000001545.1, Sep 2007
Database version80.1
Base Pairs3,109,347,532
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodProjection build
Genebuild startedOct 2007
Genebuild releasedMar 2008
Genebuild last updated/patchedAug 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes6,996
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes1,200

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.29,447


Genscan gene predictions53,999
Short Variants10,004,323