Elephant assembly and gene annotation
Assembly
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.
Other assemblies
- BROADE1 (Ensembl release 54)
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.
Statistics
Summary
| Assembly | Loxafr3.0, INSDC Assembly GCA_000001905.1, Jul 2009 |
| Base Pairs | 3,196,760,833 |
| Golden Path Length | 3,196,760,833 |
| Annotation provider | Ensembl |
| Annotation method | Full genebuild |
| Genebuild started | Jul 2009 |
| Genebuild released | Mar 2010 |
| Genebuild last updated/patched | Dec 2011 |
| Database version | 111.3 |
Gene counts
| Coding genes | 20,033 |
| Non coding genes | 2,644 |
| Small non coding genes | 2,391 |
| Misc non coding genes | 253 |
| Pseudogenes | 568 |
| Gene transcripts | 28,847 |
Other
| Genscan gene predictions | 57,537 |