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Example Data Points

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

A few example data points :

• Gene Scaffold: GeneScaffold_6570
• Scaffold: scaffold_314284

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About the Echinops telfairi genome

Assembly

This is the first release of the low-coverage 2X assembly of the small Madagascar hedgehog (Echinops telfairi). 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 length for supercontigs is 48 kb and is 3.1 kb for contigs. The total number of bases in supercontigs is 3.81 Gb and in contigs is 2.11 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 9150 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".

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

Mammalian Genome Project

Echinops telfairi is one of 16 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). The 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 50

Echinops telfairi News

• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.
• Multiple alignments
  

  The multiple alignments are being extended with new species and 2X genomes.
  Read more...

• Blastz-net alignments
  

  The Blastz-net alignments have been updated for the following species.
  Read more...

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

• SSAHA
  From release 50 we will no longer be providing SSAHA sequence search. If you wish to run your own SSAHA sequence search you can download the files to generate the search hashes from our FTP site.

More news...

Statistics

Assembly:	TENREC, July 2005
Genebuild:	Ensembl, Aug 2006
Database version:	50.1f
Known protein-coding genes:	10
Projected protein-coding genes:	13,454
Novel protein-coding genes:	3,098
Pseudogenes:	3,824
RNA genes:	3,052
Genscan gene predictions:	162,490
Gene exons:	251,481
Gene transcripts:	20,386
Base Pairs:	2,111,581,369
Golden Path Length:	3,833,568,392
Most common InterPro domains:	Top 40 Top 500

How the statistics are calculated