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Tree Shrew assembly and gene annotation

Assembly

This is the first release of the low-coverage 2X assembly of the northern treeshrew(Tupaia belangeri). 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 88.86 kb and is 2.97 kb for contigs. The total number of bases in supercontigs is 3.66 Gb and in contigs is 2.14 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 6153 such gene-scaffolds which consist of 1.58 Gb , with identifiers of the form "GeneScaffold_1".

Mammalian Genome Project

Tupaia belangeri 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

AssemblytupBel1, Jun 2006
Base Pairs2,137,242,230
Golden Path Length3,670,341,392
Annotation providerEnsembl
Annotation methodProjection build
Genebuild startedOct 2006
Genebuild releasedFeb 2007
Genebuild last updated/patchedApr 2013
Database version94.1

Gene counts

Coding genes15,471
Non coding genes3,073
Small non coding genes2,926
Misc non coding genes147
Pseudogenes2,313
Gene transcripts20,861

Other

Genscan gene predictions101,619

About this species