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Explore the Spermophilus tridecemlineatus genome

Search Ensembl Spermophilus tridecemlineatus

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e.g. GeneScaffold_5367 or ENSSTOG00000000033 or Q59FM4.1

Example Data Points

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

A few example data points :

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About the Spermophilus tridecemlineatus genome

Assembly

Thirteen-lined Ground Squirrel This is the first release of the low-coverage 1.90X assembly of the thirteen-lined ground squirrel (Spermophilus tridecemlineatus ). 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 53.23 kb and is 2.75 kb for contigs. The total number of bases in supercontigs is 3.42 Gb and in contigs is 1.91 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 6247 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".

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

Mammalian Genome Project

Spermophilus tridecemlineatus 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 50

Spermophilus tridecemlineatus 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...

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.
  • Projections of gene names and GO terms
    These have been done as usual, between a variety of species.

More news...

Statistics

Assembly: speTri1, Jun 2006
Genebuild: Ensembl, Oct 2006
Database version: 50.1f
Known protein-coding genes: 14
Projected protein-coding genes: 12,912
Novel protein-coding genes: 1,901
Pseudogenes: 1,742
RNA genes: 1,551
Genscan gene predictions: 64,104
Gene exons: 218,590
Gene transcripts: 16,572
Base Pairs: 1,913,367,893
Golden Path Length: 3,499,049,606
Most common InterPro domains: Top 40 Top 500

How the statistics are calculated


 

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GermOnline based on Ensembl release 50 - Jul 2008
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