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Explore the Gasterosteus aculeatus genome

Search Ensembl Gasterosteus aculeatus

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e.g. chromosome groupXVI or groupXIX:10000..200000 or Q59FM4.1

Karyotype

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chromosome I chromosome II chromosome III chromosome IV chromosome V chromosome VI chromosome VII chromosome VIII chromosome IX chromosome X chromosome XI chromosome XII chromosome XIII chromosome XIV chromosome XV chromosome XVI chromosome XVII chromosome XVIII chromosome XIX chromosome XX chromosome XXI chromosome MT Stickleback karyotype selector

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About the Gasterosteus aculeatus genome

Assembly

Stickleback This is the first release of the Stickleback genome (Gasterosteus aculeatus). The genome sequencing and assembly are provided by the Broad Institute, with cDNAs and ESTs being provided by the Stanford Human Genome Center. The assembly has been sequenced by whole-genome shotgun sequencing with a base coverage of approximately 11x. The stickleback genome is approximately 460 Mb in length and comprises 22 pairs of chromosomes (groups) including a mitochondrial chromosome and an additional 1,822 unplaced supercontigs.

Annotation

The gene set for stickleback was built using a modified version of the standard Ensembl genebuild pipeline. The majority of gene models are based on genewise alignments of proteins from species genetically distant from stickleback. To improve accuracy, genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. cDNA and EST sequences were used to add UTR to genes with 3' and 5' ESTs from the same clone being paired where possible.

The quality of the gene models was assessed by generating sets of potential orthologs to genes from other species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs and used to improve the gene models. 2,208 cDNAs from Stanford Human Genome Center were used to further assess quality before being incorporated into the final gene set.

What's New in Ensembl 50

Gasterosteus aculeatus News

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

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.
  • Stored peptide stats
    In order to improve efficiency on ProtView, peptide statistics are now calculated in advance and stored as translation attributes, instead of being calculated on the fly.

More news...

Statistics

Assembly: BROAD S1, Feb 2006
Genebuild: Ensembl, Jun 2006
Database version: 50.1g
Known protein-coding genes: 71
Projected protein-coding genes: 15,143
Novel protein-coding genes: 5,573
Pseudogenes: 52
RNA genes: 1,468
Genscan gene predictions: 44,884
Gene exons: 245,824
Gene transcripts: 27,629
Base Pairs: 446,627,861
Golden Path Length: 461,533,448
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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