Alignment is the Ground Truth

This news item is to update the community on the resources available on Echinobase.

It has come to our attention that some gene names and symbols in papers have not been updated to the new genome assembly versions. Authors using non-standard gene and reagent names results in their results being lost, rather than being linked in to Echinobase data and to results in other systems, such as human and model organisms. If your results cannot be found it reduces their impact and consistent nomenclature is the easiest way to ensure data is findable.

This raises two points, 1. authors should  update the names and symbols used and 2. reviewers need to insist on updated nomenclature (and encourage Echinobase citation). Most journals have guidelines stating this requirement, but it is up to reviewers to enforce.

On Echinobase, all curated morpholinos (and where available antibodies and guide RNAs) can be viewed at the bottom of the gene page.

If you are looking for a morpholino sequence be sure to check the gene page.

If you have an existing morpholino or are designing a new morpholino be sure to BLAST the sequence to check where it aligns.

Sequences that aligned to an old version of the genome will not necessarily align to the same gene model in a new assembly.

Equally unreliable is searching for an old name (synonym) and supposing that the old primer will align to the new gene model.

And remember that orthology to other model organisms is also available on the gene page.