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.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001905.1

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

AssemblyLoxafr3.0, INSDC Assembly GCA_000001905.1, Jul 2009
Database version76.3
Base Pairs3,118,565,340
Golden Path Length3,196,760,833
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJul 2009
Genebuild releasedMar 2010
Genebuild last updated/patchedDec 2011

Gene counts

Coding genes

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

20,033
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, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, 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.

2,644
Pseudogenes

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.

568
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.28,847

Other

Genscan gene predictions57,537