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Elephant assembly and gene annotation


loxAfr3 is an assembly of the genome of the African Elephant (Loxodonta africana), sequenced to 7x coverage. The genome sequencing and assembly are provided by the Broad Institute.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of the scaffolds is 48Mb. The N50 size of the contigs is 69kb. The total length of all contigs is 3.12 Gb, and the total length of all supercontigs is 3.2 Gb.

Gene annotation

The gene set for elephant was built using the Ensembl pipeline. Gene models are based on genewise alignments of rodent proteins as well are genetically distant proteins from other species, including most vertebrate proteins from Uniprot. Additionally, mouse proteins were aligned using exonerate. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.

More information

General information about this species can be found in Wikipedia.



AssemblyLoxafr3.0, INSDC Assembly GCA_000001905.1, Jul 2009
Base Pairs3,196,760,833
Golden Path Length3,196,760,833
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2009
Genebuild releasedMar 2010
Genebuild last updated/patchedDec 2011
Database version104.3

Gene counts

Coding genes20,033
Non coding genes2,644
Small non coding genes2,391
Misc non coding genes253
Gene transcripts28,847


Genscan gene predictions57,537

About this species