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

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 41

Loxodonta africana News

• RNA updates
  

  Ensembl RNA data has been updated as follows:

  • New ncRNAs for Zebrafish, Chimp, Medaka, Elephant, Rabbit, Armadillo and Tenrec
  • Updated miRNAs for all chordates.

General News

• New animated tutorials
  A selection of Ensembl tutorials are now available online as Flash-animated presentations (with popup notes instead of a soundtrack).
  Read more...
• Compara updates
  

  Homologies

  Gene trees have been updated to include the 2X genomes and use a multifurcating species tree, and homologues added based on gene trees.
  Read more...

• Minor schema changes
  

  analysis_description

  Now has a 'displayable' flag to control whether or not it is usually displayed in the web pages

  xref

  One column has been changed and one added

  • the info_type column has addition ENUM values to give more details about xref provenance
  • A new column 'priority' supports the fetching of xrefs of the same type

  The API has of course been updated to reflect these changes

  .
  Read more...

More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions