How to Submit Targeted Sequences


The information on this page pertains to the submission of targeted sequences, typically short assembled and annotated sequences representing interesting features or gene regions. This is unrelated to the submission of full chromosome or genome assemblies, which is described in our Assembly Submission Pages.


All submissions of this type are subitted as ‘analysis’ objects, but the accessions of these analyses are not exposed. Instead, specific sequence accessions are assigned later, and these are what should be used to reference the sequences.

Sequence submission requires that a study be registered first. Please do this before attempting any of the guides shown below:


This submission route is for sets of stand-alone targeted assembled and annotated sequences only. If you intend to submit an annotated assembly such as a genome, please follow the assembly submission guidelines and submit your assembly in EMBL flat file format.


As all sequences in ENA are submitted as ‘analyses’, for each sequence set submission, Webin will report a unique accession number that starts with ERZ. This accession number is for internal processing only and will not be visible in the browser. Furthermore, if your submission includes multiple sequences, the ERZ accession will not be unique to any one of them. Instead, you will receive additional post-processing accession numbers for your sequences via email, each of which will be unique to one of your sequences.

Always make a note of any accessions you receive as these are the unique identifiers for each of your submissions to ENA.

Submission Options

Many types of sequence can be submitted using a checklist. These define a set of metadata whicih should be provided for a given type of sequence and streamline the submission process for these sequence types. Checklist submission allows you to avoid having to create the flatfile record manually.

Therefore, please check the list of available checklists to determine whether one of them meets the needs of your submission:

If There Is A Suitable Checklist Available

You can use the Webin Interactive service to submit your checklist sequences through web forms. You also have the option of preparing a spreadsheet and submitting it through our Webin-CLI tool.

If No Suitable Checklist Exists

You will need to prepare your sequence in the EMBL Flat File Format and submit it using Webin-CLI as described in the below link. Webin-CLI will validate the file for you before accepting its submission, and will advise you of any formatting errors.