Stacks Image 5

Welcome to the threespine stickleback genome browser.

  • This site contains genome assembly version 5 (2020), version 4 (2017), and the Y chromosome assembly.

  • The Genes, Pseudogenes, and Non-coding RNAs tracks contain annotations lifted over from Ensembl (release 95) as well as newly predicted annotations derived from the MAKER gene annotation pipeline.

  • The browsers are built using the JBrowse platform, which allows for easy visualization of annotation tracks. Supported track formats are detailed here.


December 1, 2020: liftOver chain files between the v. 5 genome and previous assemblies (v. 1, v. 2, v. 3, and v. 4) have been added to the data download page.

December 1, 2020: Full-length isoform sequencing was conducted on eight different tissues (Naftaly et al. 2020) and added as gene annotation tracks.

November 18, 2020: SNP variants from Puget Sound and Lake Washington (Shanfelter et al. 2019) have been integrated as browsable VCF annotation tracks.

July 6, 2020: The Stn microsatellite markers (Peichel et al. 2001) have been integrated as a searchable annotation track.

July 6, 2020: The v. 5 annotation files on the download page have been updated to a GFF3 file format.

July 6, 2020: The unplaced contigs in chromosome Un. have been updated in the browser and on the download page.

June 23, 2020: Annotations will be added regularly to the genome browser. Check back for updates.

June 23, 2020: LiftOver files are coming soon. Stay tuned to the download page.