Ensembl Elephant

Example Data Points

This release of Loxodonta africana data is assembled into scaffolds, so there are no chromosomes available to browse.

A few example data points :

• Gene Scaffold: GeneScaffold 4163
• Scaffold: scaffold 373

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About the Loxodonta africana genome

Assembly

This is the first release of the low-coverage 2X assembly of the Elephant (Loxodonta africana). The genome sequencing and assembly is 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 length for supercontigs is 41 kb and is 2.8 kb for contigs. The total number of bases in supercontigs is 3.69 Gb and in contigs is 2.30 Gb.

Annotation

Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures, in order to present complete genes. There are 7883 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".

• Details of the gene-scaffold construction and subsequent gene-build

Mammalian Genome Project

Loxodonta africana is one of 16 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.

What's New in Ensembl 49

Loxodonta africana News

There is no Loxodonta africana-specific news this release.

General News

• Release schedule
  

  Ensembl release 50 will occur in July (rather than in April as originally scheduled).
  Read more...

• API changes - regulatory features
  Regulatory feature support has been moved from the core API to the functional genomics API. More information about using the new code...
• Removal of viral genes
  We have removed a total of about 1200 viral genes from the following species.
  Read more...
• Mart updates
  RGD and SGD Symbol+ID combinations have been introduced, similar to HGNC, MGI and ZFIN. The issue with subsets of homologs being returned has been resolved.
• Compara updates
  

  Multiple alignments

  We are now using the new enredo-pecan-ortheus (EPO) pipeline for 7-way alignments (placental mammals).
  Read more...

More news...

Statistics

Assembly:	BROAD E1, May 2005
Genebuild:	Ensembl, Aug 2006
Database version:	49.1d
Known protein-coding genes:	17
Projected protein-coding genes:	12,750
Novel protein-coding genes:	2,950
Pseudogenes:	3,030
RNA genes:	1,498
Genscan gene predictions:	107,250
Gene exons:	216,909
Gene transcripts:	18,747
Base Pairs:	2,295,548,473
Golden Path Length:	3,717,990,240
Most common InterPro domains:	Top 40 Top 500

How the statistics are calculated