Echinobase Identifiers

Many identifiers on Echinobase have changed.

You can find a gene of interest directly from the search bar. 

Search gene name or symbol or XM or XP numbers or original SPU identifiers. 

Autofill can provide options to help identify the gene of interest.

From the gene page you have access to the database content.

When you arrive at the GENEPAGE you will see, 

Gene symbol is a short concise identifier.

Gene name is a longer and more descriptive identifier.

The Echinobase Gene Nomenclature Guidelines provide details on these identifiers.

The symbol and name conform to the Human Genome Organisation Gene Nomenclature Committee - the HGNC - guidelines as closely as possible.

HUGO - Human Genome Organisation 

HGNC - HUGO Gene Nomenclature Committee 

The HGNC sets the standards for human gene nomenclature and approves a unique and meaningful name for every known human gene.

Note that status is indicated next to names and symbols as curated, partially curated or provisional.

The Curated status of gene symbols and names is assigned when the protein sequence coded for by the human gene model has orthology, determined using multiple tools, to the S. purpuratus protein sequence.

Partially curated status indicates that the gene symbols and names have been manually considered.

Provisional status of the symbols and names indicates that they were automatically generated by the NCBI pipeline.

Some genes still have the NCBI LOC# assigned as the gene symbol, which means that we have not as yet assigned a gene symbol through orthology.  The LOC_IDs are unique identifiers that we will be curating to provide more descriptive identifiers, and then the LOC_ID would become a synonym and can be searched. This work is still in progress. 

Synonyms are the place to look for all past identifiers of the gene models including historical IDs, descriptive IDs, SPU_IDs, and LOC IDs if the species specific symbol has been updated.

The synonyms are included in searches so if you have an SPU_ID you can find the 5.0 gene model.

92% of all SPU_IDs have mapped directly to a new 5.0 gene model.

There are cases where many SPU_IDs are now collapsed to one 5.0 gene model.

For the instances of one SPU_ID mapping to multiple 5.0 gene models we are working on identifying these. If you encounter an example please email echinobase@andrew.cmu.edu