Hedgehog assembly and gene annotation

Assembly

This is the first release of the low-coverage 1.86X assembly of the western European hedgehog (Erinaceus europaeus). The genome sequencing and assembly is provided by the Broad Institute.

The total number of bases in scaffolds is 3.37 Gb and in contigs it is 2.13 Gb.

Gene 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 9036 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".

Mammalian Genome Project

Erinaceus europaeus is one of 24 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyeriEur1, Jun 2006
Database version75.1
Base Pairs2,133,134,836
Golden Path Length3,377,541,562
Genebuild byEnsembl
Genebuild methodProjection build
Genebuild startedOct 2006
Genebuild releasedFeb 2007
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes

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

14,601
Short non coding genes

Short 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 short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

6,456
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.

1,391
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.22,452

Other

Genscan gene predictions138,561

InterPro Hits