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Welcome to Echinobase
Echinobase has many new features including:
· new S. purpuratus v5.0 genome
· gene pages including updated gene symbols and names
· orthology to A. planci,
· partial hosting of the new A. japonica genome
· citations involving the genes and
· the Echinoderm Anatomical Ontology (ECAO) of anatomical features and developmental stages.
Read More...
The previous site is available at legacy.echinobase.org. -
Data Exploration
Echinobase has data available for download through the FTP site.
Links to other echinoderm datasets are collected.
Tutorial video here.
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FAQs - Gene Names and IDs
Discovery of new genes, or analysis of current genes sometimes leads to gene nomenclature questions.
Genome-wide studies involving transcripts and proteins require related IDs.
Here we have listed a few of the more common questions.
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CRISPR/Cas Resources
Echinobase curators have collected the gRNA sequences that have been used to date.
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Echinobase Identifiers
Echinobase identifiers have been updated.
Suggestions for finding your gene of interest and using the new identifiers are available in this
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The Echinoderm Anatomical Ontology (ECAO)
An ontology has been developed for echinoderms using standardized terms to describe anatomical cell types and structures and developmental stages.
These spatiotemporal terms will be used by curators to link to gene expression data.
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New crinoid genome
Echinobase is providing partial support for the newly released feather star, Anneissia japonica, genome.
The genome can be viewed in JBrowse and BLAST is supported.
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Resources, Community, Literature and Genomics
Echinobase has resources and community support content in addition to collected and curated literature and extensive genomic content.
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A short tutorial video. -
DBSUMI meeting postponed until 2021
The DBSUMI meeting has been rescheduled for April 14-18, 2021 due to the COVID-19 pandemic.
This international conference has occurred every 18 months since 1981.
Check back for updates about the 26th meeting of echinoderm scientists.
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The new Echinobase
Echinobase – The Echinoderm resource for the research community
Echinobase supports the international echinoderm research community with a centralized, comprehensive, integrated and easy to use web based resource that provides access to the diverse and rich genomic, expression and functional data.
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Echinobase - a resource for studies of evolution and development
Come to Echinobase for currently available molecular data on eleutherozoan echinoderms including genomes, genes, and annotations.
Molecular data will be collected and curated and made available to the community.
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Echinoderms are Deuterostomes
The superphylum
Deuterostomia includes
Chordata,
Echinodermata and
Hemichordata phyla.
Echinodermata includes
marine only species,
7,000 extant and
13,000 extinct.
.
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Welcome to Echinobase
Echinobase has many new features including:
· new S. purpuratus v5.0 genome
· gene pages including updated gene symbols and names
· orthology to A. planci,
· partial hosting of the new A. japonica genome
· citations involving the genes and
· the Echinoderm Anatomical Ontology (ECAO) of anatomical features and developmental stages.
Read More...
The previous site is available at legacy.echinobase.org.
The New Echinobase
Latest Echinobase Content
Visit the previous echinobase.org
Announcements
Gene nomenclature and related ID questions.
The wiki page has gRNA sequences that have been used in Echinoderms.
Previous site legacy.echinobase.org. Please provide feedback.
A brief overview of Echinobase content and a video.
Echinobase has data available for download through the FTP site with a tutorial video.
Finding your gene and using new identifiers, a brief video tutorial.
Anneissia japonica (feather star)
Genes & Expressions
Search transcriptome and RNA-seq data
Search for genes expressed during embryo development
View Echinoderm Embryo Anatomy Ontology
Genome Browsers
Browse the past and present versions of genomes and community contributed datasets. If you find a dataset missing or have a new dataset to contribute for one of our supported genomes please contact us!
Deuterostomia (superphylum) includes Chordata, Echinodermata and Hemichordata phylum, Echinodermata emerged in the Lower Cambrian (> 540 million years ago, MYA) and split from Chordata 400-500 MYA, Echinodermata includes 7,000 extant and 13,000 extinct, marine only species. Echinodermata has 5 Classes:
the basal branching Crinoidea (crinoids), and the 4 motile Eleutherozoa Classes including Asterozoa, the Ophiuroidea (brittle stars) and Asteroidea (starfish) and the Echinozoa, the Echinoidea (sea urchins and sand dollars) and Holotheroidea (sea cucumber).
Echinoderms are model organisms for studying embryo development and regeneration due to many unique features including:
- the ability to synchronize fertilization of millions of eggs
- transparent embryos and larvae
- varied development within and between a genus
Echinobase is organized around the genepage which collects and displays information about genes, orthology, and links to research papers and gene models of echinoderm species are associated with the genome sequence using JBrowse. Temporal developmental gene expression data will be displayed when available, and spatial cell type information will be associated using the Echinoderm Anatomical Ontology (ECAO).
Echinobase provides a critical data sharing infrastructure for other NIH-funded projects, and is a focal point for the echinoderm community. In addition to our primary goal of supporting echinoderm researchers, Echinobase enhances the availability and visibility of Echinoderm data to the broader biomedical research community.
The substantially improved current release of the purple sea urchin genome assembly (Spur5.0) is sixth in the series.
Learn more about the genomics of the crown-of-thorns seastar.
The development of echinoderm embryos and larvae has been studied for over 100 years. Echinoderm eggs are fertilized externally and embryos and larvae are transparent, enabling detailed descriptions of the structure and timing of the development of multiple species. The variation in developmental patterns is used to improve understanding of these vital processes in echinoderms and deuterostomes.
Skeletogenesis in echinoderms is diverse and well documented and an area of active research.
Regeneration capability makes echinoderms ideal organisms for the study of these processes at the anatomical and genetic levels.
Animal suppliers and protocols
Protocols and reagents for studying gene expression:Microinjection, morpholinos and BACs
Genomics methods:RNA-seq and scRNA-seq
ChIP-seq and ATAC-seq
The Echinoderm Community is able to submit new genomes for partial support when assembly and annotation are publicly available through Genbank. The assemblies, annotations, and functional data tracks (GFF files) will be available on JBrowse and can be searched via BLAST.
The Echinobase PIs and SAB members will decide the new species for full support and integration into the database as gene pages with complete functionality, including gene names and symbols, synonyms, literature, orthology, and developmental gene expression display. This process will only be possible when the genome has been fully processed by the NCBI annotation pipeline. Suggestions for priority species are always welcome.
Useful links: