Data Submission

Q: How can I submit nucleotide sequence data?
You can submit your data using one of the followings:
       (A) Nucleotide Sequence Submission System via a WWW server
       (B) Mass Submission System (MSS)

(A) DDBJ recommend you to use Nucleotide Sequence Submission System.

(B) We recommend using MSS, when:

  • the submission consists of large number of sequences.
        When number of sequences is greater than 1024, you have to submit two or more times via Nucleotide Sequence Submission System
  • the complex submission containing many features (more than 30).
  • the submission with long sequences (greater than 500 kb).
  • the submission is not applicable for Nucleotide Sequence Submission System
       i.e. EST, STS, TSA, HTC, GSS, HTG, WGS or CON

You can see Mass Submission System for details.

Report of accession number

Q: How do I find out which accession number(s) correspond to my submitted sequence data ?
The accession number is notified to the Contact Person whose E-mail address is entered in the "Contact person E-mail address" field on Nucleotide Sequence Submission System by E-mail.

This notification is normally sent within five working days after receipt of data.
If you do not hear from us within this time period, please contact us.


Q: How can I request a databank to delay release of sequence data I am going to submit until the manuscript is published?
If you use Nucleotide Sequence Submission System, you can enter the release date in the "Submission Data Release Date" field.

Please remember to provide the release date if you want your data held until published.
Failure to do so will result in immediate release.

It is ideal to choose a date some months ahead if the publication date is not confirmed, because we can release your data immediately upon your request along with a copy of the published manuscript when your data becomes available for release earlier than the date you had specified at submission.
Extension of the holding period is also possible.

Release of "Hold-Until-Published" Data

Q: When are "Hold-Until-Published" data released?
In principle we release "Hold-Until-Published" data when one of the following three conditions is met:

  1. The Submitter requests to release the data.
  2. The publication of the Accession Number has been confirmed.
  3. Specified hold date has come.

In cases 2 and 3, data will be released with no exception and no permission from the submitter. Above three principles are applied to the data which were registered at DDBJ after January 1, 1998.

If you wish your data to be held for a while at DDBJ, be sure to specify the exact date on which the sequences should be released to the public.
If you want to postpone the hold-date of your data, please inform DDBJ of a new date and the accession number either by E-mail, FAX or postal mail before the hold-date.

Please contact DDBJ as soon as your data become available for release.

E-mail: ddbjsub
FAX: +81-55-981-6849
Postal Address: 1111 Yata, Mishima, Shizuoka
411-8540, JAPAN
DNA Data Bank of Japan (DDBJ)
National Institute of Genetics

Standards for issuing accession numbers

Q: Is it possible that the data submitted to DDBJ will be refused entry to the database after review?
As long as the sequence is experimentally determined and the submitters have ownership of it, we accept all the submitted data and assign an accession number to each entry as primary data or meets the standards.
If the submitted data fails to meet the standards, we ask the submitter to make corrections and resubmit the corrected data.
Moreover, if there are entries containing identical sequences, they still can be accepted as separate entries as long as the sequence was determined separately.
Also, we started to collect TPA (Third Party Annotation) data which is a complement to the existing DDBJ/EMBL/GenBank comprehensive database of primary data.
Please refer to TPA information in detail.

Submission of Amino Acid Sequence Data

Q: How can I submit amino acid sequence data?
When you wish to submit only amino acid sequence data, please submit it to UniProt using the SPIN which is a web based submission tool provided by UniProt through the EBI web page.
For the details of the SPIN, please see the SPIN help page.
If you need a contact, please mail to:

Submission of the Sequence Data containing an unknown site

Q: I have determined the DNA sequence of a gene, but some sites are still unknown. How can I submit the sequence data?
An accession number is issued to one contiguous DNA sequence.
You have to submit sequences in separate files excluding unknown sites.
For example, if there are four exons and three unknown introns between them, you have to make one submission file for each sequence and submit four files to the database.
Then, we will issue four accession numbers, one for each sequence.

Submission of Point Mutations and Polymorphism

Q: Should I submit Point Mutation and Polymorphism data as a new submission?
If the original sequence data was submitted by the same submitter, we will add Point Mutation or Polymorphism information to the "Features."
In this case, the new information is treated as an update; therefore, we will not issue another accession number.
However, if the journal publisher requires an accession number for the information, we will issue one for the sequence containing the mutation region.
In other cases, if the original sequence data was submitted by other researchers or groups, it is not an update to the original data and we will treat the data as a new entry and issue an accession number.

Submitted date

Q: Is the submitted date recorded in the database?
A: We add the accept date on which we received the submission to the flat file.


Q: Does submitting data to DDBJ secure priority or should I apply for a patent first?
A: You cannot get a patent by submitting your data to DDBJ.
If you really need to secure priority for your data, you must apply for a patent at the Patent Office; Japanese Patent Office

Submission while still working on a manuscript

Q: May I submit DNA sequence data to DDBJ, GenBank, or EMBL while I am still working on my manuscript?
A: Yes, you may.