Locus Tag Prefixes

What Are Locus Tags?

Locus tags are identifiers applied systematically to every gene in a sequencing project. If two submitters of different genomes use the same systematic names to describe different genes, this can be a source of confusion. Therefore, INSDC maintains a registry of locus tag prefixes to avoid overlap between genome annotation projects. The prefix is then used systematically to give a new unambiguous name to every gene.

How Do I Register A Locus Tag Prefix?

A locus tag prefix can be registered when a project is registered. Advice on doing this can be found at our study registration page. You can allow automatic assignment of a prefix, or you can specify your own.

If you did not add a prefix when you registered your project, it is possible to update the project with a prefix later on. See our advice on updating studies.

Please note that after you register the prefix, it will not be usable until 24 hours later. Therefore, you will not immediately be able to submit your annotated assembly.

A study can have multiple prefixes registered to it, but each prefix can only be registered to a single study.

What Rules Should The Prefix Conform To?

The prefix you register must follow the listed conventions or it will not be accepted:
  • Must begin with a letter

  • All letters must be upper case

  • Must from 3 to 12 characters in length

  • All characters must be alphanumeric with no diacritics and none such as -_*

Each prefix can only be registered to a single study; you cannot reuse a prefix from another study, or one which another user has registered.

How Do I Use Locus Tags?

Locus tags should be assigned to all genes, including both protein-coding and non-protein coding genes (e.g. structural RNAs). Within your flat file, you should include the /locus_tag qualifier in every gene, mRNA, CDS, 5’UTR, 3’UTR, intron, exon, tRNA, rRNA, misc_RNA, etc. We discourage the use of this qualifier on repeat_region and misc_features.

You should include the qualifier in each component of a gene, and it should have the same value for all components of a single gene. The feature itself should resemble the following in the format <prefix>_<id>:

FT      /locus_tag="BN5_00001"

Locus tags should be added systematically to every gene within a genome, generally in sequential order. When updating an assembly with additional annotation, you may either add new genes onto the end, or leave gaps when initially assigning /locus_tags and fill new genes into these gaps.

It is possible to encode information after the underscore but before the number. For example, the following tags might indicate the first genes of chromosomes I and II:


The following tags could indicate an rRNA gene and a tRNA gene: