Strongylocentrotus purpuratus (Spur_3.1)

Strongylocentrotus purpuratus Assembly and Gene Annotation

About Strongylocentrotus purpuratus

The purple sea urchin, Strongylocentrotus purpuratus, belongs to the echinoderma, a sister phylum to the chordates. As well as having an important phylogenetic placement, it also has an invaluable ecological role in the marine system and is a model organism for cell and development biology.

Picture credit (Creative Commons BY 3.0): Kirt L. Onthank 2008


The genome sequencing project is a joint effort between the Sea Urchin Genome Facility at the Center for Computational Regulatory Genomics, Beckman Institute, Caltech, and the National Human Genome Research Institute of the National Institutes of Health (NHGRI - NIH). The sequencing was done at the Baylor College of Medicine, Houston, Texas.

Ensembl Metazoa uses assembly version 3.1.


The annotations in Ensembl Metazoa were imported from SpBase. SPBase provide a mapping of the original GLEAN gene set to the latest assembly, version 3.1. Extensive manual curation has been conducted since the GLEAN data was generated, but the revised transcript sequences have not been mapped back to modify the gene models. In Ensembl Metazoa the transcript co-ordinates and visualisations use the original GLEAN data, but the cDNA and protein sequences represent the manual annotations (which exist for approximately half of the genes). This situation means that it is not possible to produce meaningful GTF files, so these are unavailable for download from Ensembl Metazoa. RNA-seq transcript data from SpBase has been imported and is displayed as a separate 'predicted transcript' track.

Protein domains were annotated with the Ensembl Genomes protein feature pipeline.


  1. The genome of the sea urchin Strongylocentrotus purpuratus.
    Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR et al. 2006. Science. 314:941-952.
  2. Shedding genomic light on Aristotle's lantern.
    Sodergren E, Shen Y, Song X, Zhang L, Gibbs RA, Weinstock GM. 2006. Developmental Biology. 300:2-8.
  3. SpBase: the sea urchin genome database and web site.
    Cameron RA, Samanta M, Yuan A, He D, Davidson E. 2009. Nucleic Acids Research. 37:D750-4.

More information

General information about this species can be found in Wikipedia.



AssemblySpur_3.1, INSDC Assembly GCA_000002235.2, Dec 2012
Database version100.3
Base Pairs815,995,273
Golden Path Length936,564,995
Genebuild bySpBase
Genebuild methodImport
Data sourceSpBase

Gene counts

Coding genes28,987
Non coding genes1,253
Small non coding genes1,246
Long non coding genes7
Gene transcripts30,284


RNA-seq transcripts29,089

About this species