Last updated:2014.7.7.

FAQ

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Tag Search(NSSS:DDBJ Nucleotide Sequence Submission System , MSS:Mass Submission System)

FAQs 71 : Tag = submission
Can we update submitted data with DDBJ Nucleotide Sequence Submission System? NSSS update

Since DDBJ Nucleotide Sequence Submission System can be only used for new submissions, you can not update submitted data with the system.
For update, see Data Updates/Corrections.

Last Updated:June 9, 2014
How to delete my data? submission update

In principle, we can delete only the sequence data that have not yet been publicized.
See the relevant item in Data Updates/Corrections and mail to us with data.
Just for information, we can restrict access to your sequence data that have been publicized, if the conditions are right. See also the following item.

Reference
How to restore the released data to private?
Why is the retracted data still available?
Last Updated:July 18, 2014
What kinds of data are acceptable at DDBJ? category submission

See Categories for Sequence Data.

If you are not sure to which category your sequence data should be submitted, see followings;

If you still have any question, please contact us from contact form by selecting the item, "Data Submission".

Last Updated:July 3, 2014
How to submit only annotation for previously reported sequences? format submission

If your annotation meets the requirements of TPA Submission Guidelines, DDBJ can accept it as TPA (Third Party Data).

Last Updated:August 27, 2014
How to submit sequence data with annotation to DDBJ? category format MSS NSSS submission

Select from following two ways.

In general, we recommend to use DDBJ Nucleotide Sequence Submission System
In cases of, large number of sequences, many features, and/or long sequences, MSS is more useful.

Last Updated:June 16, 2014
How to submit amino acid sequences? category submission

In general, you can submit amino acid sequences by describing CDS feature for your nucleotide sequences.
However, DDBJ does not accept amino acid sequences only, i.e. without any nucleotide sequences.
In that case, please submit to UniProt, directly.
You can submit amino acid sequences to UniProt through SPIN.
Please contact to datasubs@ebi.ac.uk.

Last Updated:November 26, 2014
How can I get protein_id? submission

The protein_id will be automatically assigned at DDBJ during release of your nucleotide sequence with CDS feature.

Last Updated:July 3, 2014
How to submit assembled EST sequences? category submission

DDBJ can not accept only assembled EST sequences. However, DDBJ can accept EST assembled sequences as TSA with original (i.e. before assemble) sequence data. See also Data Submission form Transcriptome Project.
When original sequence data (primary entries) are generated from Next Generation Sequencers, submit to DDBJ sequence Read Archive (DRA), from traditional sequencers, submit as EST via Mass Submission System (MSS).
Then, DDBJ can accept assembled sequences (both de novo and reference mapping) as TSA through MSS.

Last Updated:June 16, 2014
How to describe organism name, if the species is not identified or not defined? format MSS NSSS submission
Last Updated:June 16, 2014
How to submit sequence data directly obtained from soil or sea water? format MSS NSSS submission

In cases of sequences derived by direct molecular isolation from soil, sea water, etc. i.e. a bulk environmental DNA sample by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods, see What is ENV ? – environmental samples.
For description of organism qualifier, see 3. Environmental samples.

Though frequently confused, the term, 'environmental samples', does NOT mean "wild type". If sequences are derived from isolated or cultured organisms, the sequence data are not classified into environmental samples.

Last Updated:June 16, 2014
How to describe organism name for artificially constructed sequence? format MSS NSSS submission
Last Updated:June 16, 2014
How to descrbe the evidence of speculation for the feature? format MSS NSSS submission

You can use experiment or inference qualifier to describe evidence of speculation in each feature.

Last Updated:June 16, 2014
How to submit sequence data determined by Next Generation Sequencers? category submission

See Categories for Sequence Data.
Please submit raw reads generated from Next Generation Sequencers to DDBJ sequence Read Archive.
See also Data Submission from Genome Project or Data Submission from Transcriptome Project.
Please submit assembled sequences through Mass Submission System, if necessary.

Last Updated:June 16, 2014
How to submit sequence-based expression data like as RNA seq? category submission

Please submit raw reads of sequence-based expression data to DDBJ Sequence Read Archive.

Last Updated:June 16, 2014
How to submit sequence data related to Barcode of Life (BoL)? format submission

For sequence data related to Barcode of Life project, please submit via DDBJ Nucleotide Sequence Submission System or Mass Submission System.
For chromatograms (traces), please submit to DDBJ Trace Archive

Last Updated:June 18, 2014
Should we send offprint related to our sequence data? submission update

Generally, DDBJ do not need any offprint to process your data.
Occasionally, DDBJ may contact the submitter of sequence data to ask sending an offprint, if necessary.

Last Updated:June 18, 2014
Should we submit both genomic and mRNA sequences of the same gene to DDBJ? submission

Basically, please submit every sequence that you have experimentally determined, whatever the resource of genome, mRNA or any others.
In principle, DDBJ accepts submission of experimentally determined sequence in its contiguous structure.
You can describe mRNA feature, CDS feature and so on as annotation for genomic sequence, however, descriptions of mRNA features do not mean "the mRNA sequence is experimentally determined.", in general.
If you have read mRNA sequences, please submit mRNA sequences to DDBJ. See also Acceptable data for DDBJ.

Last Updated:June 19, 2014
Can I submit seuqence data without any published paper, during writing or in press? MSS NSSS submission

Yes you can. It ought to be required at 'instructions to authors' of most of journals to submit sequence data to DDBJ (, EMBL-Bank or GanBank) before the paper submission.
During submission of sequence data, select status for your REFERENCE as follows.

  • "Unpublished"; In cases of preparing paper, during paper submission, or you do not prepare any publication.
  • "In Press"; When your paper is accepted and in press.

Your citations will be appeared at REFERENCE 2 or after on DDBJ flat file.

Last Updated:June 19, 2014
When we have no plan to paper publication, how to describe REFERENCE? format MSS NSSS submission

Regardless you are to publish academic paper or not, DDBJ accepts your submission of sequence data.
If you have no plan to paper publication, you have to fill following items of REFERENCE.

  • status: [Unpublished]
  • year: tentative year (this year), i.e. 2014
  • title: tentative title to explain your data
  • ab_name (authors): abbreviation of tentative author(s) (often the same as ab_name of SUBMITTER)

When you change your plan after sequence data submission, i.e. if you publish a paper, see When our paper was published, what should I do? on Data Updates/Corrections and contact us from this form to send request with subject "Our paper was published".

Last Updated:June 19, 2014
Do we have to submit sequence data to DDBJ, when the journal has no requirement to do so? submission

Though there is no requirement to submit sequence data to DDBJ (, EMBL-Bank or GenBank) on the journal, we strongly recommend to submit sequence data to DDBJ for improvement of data availability for readers of your paper.

References
Last Updated:June 19, 2014
Is it OK to submit sequence data by only one submitter? format MSS NSSS submission

DDBJ accepts updating requests only from the original submitter of the entry.
Basically, we strongly recommend to describe joint submitters more than two persons, e.g. at least a true worker and an adviser, to avoid lost communication in future.

See Required items for nucleotide sequence submission.

Last Updated:June 19, 2014
Is FAX number required to submit sequence data? MSS NSSS submission

Generally, DDBJ contacts submitters via E-mail.
However, in case of breakdown of communication via E-mail by any reason, DDBJ would contact submitters via fax.
So, please let us know your fax number, if possible.

Last Updated:June 19, 2014
Should I submit sequence data to GenBank? submission

When sequence data are published, the data will be shared among DDBJ, EMBL-Bank and GenBank. So, it is necessary and sufficient to submit sequence data to either of three data banks only once.
If you submit sequence data to GenBank after submission of the same data to DDBJ, the data will be duplicated. So, do not submit the same data to two or more data banks.

Though some journals instruct to authors to submit sequence data to GenBank, Accession Number is commonly used by all of DDBJ, EMBL-Bank and GenBank to construct INSD.

Last Updated:July 3, 2014
Can we submit sequence data related to patent application? submission

Nucleotide sequence data related to patent applications are transferred from Japan Patent Office to DDBJ.
So, usually, you do not have to submit such sequence data to DDBJ.

However, if you apply to any other Patent Office, or if you need to publish a paper during patent application, confirm at Patent Office whether you can submit the data to DDBJ or not.

Note that when the sequence data is published from DDBJ, the data becomes a part of the public domain, as "official notice".

References
Sequence data included in patent applications
Patent, Intellectual Property and Priority
Patent column from DDBJ
Last Updated:May 26, 2015
If I submit sequence data to DDBJ, can I get priorities for the data? submission

If you submit nucleotide sequence data to DDBJ, you can get NO priority for the data.
DDBJ takes no responsibility for any property or priority issues for patenting. For patent application, you should confirm JPO or some other Patent Offices.

References
Last Updated:May 26, 2015
If I submit sequence data with gene and protein names, will the names become official? submission

DDBJ does not have any right for the gene nomenclature. Also, DDBJ does not make any official collaboration with any committee of gene nomenclature. If there is no particular incident, the descriptions related to gene nomenclature are described as provided by submitter.
Even if you name a gene during your sequence data submission to DDBJ, there is no guarantee that the gene name is accepted at research communities.

References

You should confirm each gene nomenclature committee, i.e. HUGO Gene Nomenclature Committee (HGNC) for human, MGI - Mouse Nomenclature for mouse, and so on.

Last Updated:May 26, 2015
How to describe a base substitution that causes an amino acid substitution? format NSSS submission

In general, you can describe base substitutions by using variation feature with replace and note qualifiers.
In case of using DDBJ Nucleotide Sequence Submission System, select 'other' for template.
About format of feature annotation, see F01) polymorphism and variation at Example of Submission.

Last Updated:June 26, 2014
After submission of SNP data to DDBJ, will it automatically reflect to dbSNP? format submission

Though you can submit sequence data including SNP (Single Nucleotide Polymorphisms) to DDBJ, the data will not automatically reflect to dbSNP.
dbSNP is an independent database from INSDC, operated by NCBI.
For SNP data, we recommend you to submit to dbSNP.

In case of submission to DDBJ, see format of feature annotation at B13) polymorphism and variation on Example of Submission.

References
Where to submit variation data, such as single nucleotide variations, structural variations, copy number variations (CNVs) and so on?
How to submit sequence data related to DNA polymorphism?
Last Updated:February 26, 2016
In a circular genome, when a feature is located in the base range joined from the last base to the first base, how to describe the location of the feature? format MSS NSSS submission

For instance, when the length of sequence is 199035 bp and a CDS feature is located in the range from 199001 to 100, you should describe the location of CDS feature as
join(199001..199035,1..100)
See also Description of Location in detail.

Last Updated:June 30, 2014
To submit a complete sequence of a genome, are annotation data for the genome required? format MSS submission

As feature annotation, we strongly recommend you to describe CDS (protein-coding sequence)rRNAtRNA and so on.
Please inform us in detail, when you apply to Mass Submission System.
When it is difficult for you to annotate your genome sequence, we recommend to use some public services, for example, MiGAP.

Last Updated:June 30, 2014
When the correspondences between nucleotides and amino acids are different from the standard genetic code, how to describe CDS feature? format submission

At first, please confirm whether The Genetic Code is appropriately selected or not.
Generally, if /transl_table qualifier is appropriately described with a number of the genetic code, the nucleotide sequence is automatically translated to amino acid sequence according to the genetic code.

In exceptional cases of specific codons (selenocysteine etc.) that is not followed the genetic codes, describe /transl_except qualifier, appropriately.

In cases of RNA editing,ribosomal frameshiftmitochondrial TAA stop codon, see Example of submission and describe with /exception and /translation, /ribosomal_slippage, /transl_except, respectively.

In case of rare initiation of translation, staring with an amino acid other than methionine, describe the location of CDS feature with starting from "<", operatively indicating 5'end not complete. And describe brief explanation about the translation mechanism in /note qualifier.

Last Updated:June 30, 2014
Who should be the Contact person? format submission

See Contact person.
If your affiliation was changed after sequencing or when you belong two or more institutes, please describe the most responsible one as a representative.

Last Updated:June 30, 2014
How to describe a submiter or an author who has first name only? format MSS NSSS submission
In case of Mass Submission System
Describe first name, only.
Though some warning will be outputted, please ignore them.
In case of Nucleotide Sequence Submission System
Please enter first name with some dummy initial.
Please inform us about the person with "Submission Information" on Final confirmation screen.
Last Updated:June 30, 2014
I have not yet received accession number, how many days does it take to get accession number? NSSS submission

In principle, accession numbers will be acknowledged to contact person via e-mail (with Subject: "[DDBJ] Assigned Accession No.") within 5 working days (i.e. except holidays) after DDBJ accepting submitted data.
See DDBJ Calendar about working days of DDBJ Center.
When you do not receive accession numbers or inquiry about your data from DDBJ within 5 working days after your data submission, please contact us from contact form by selecting the item, "Data Submission".

To make sure, Do not block E-mails from DDBJ.

In case of using DDBJ Nucleotide Sequence Submission System, please confirm if you have received a mail from DDBJ with "DDBJ: Web submission completed" in its subject or not. This mail is automatically sent to contact person, when DDBJ accepts your sequence data via Nucleotide Sequence Submission System.

If you have NOT received the mail,
Your submission is not yet finished, so, please complete your submission.
If you have received the mail,
please contact us from contact form with contact person E-mail address and EntryID of your data by selecting the item, "Data Submission".
Last Updated:July 3, 2014
Is there any case to reject submission to DDBJ? submission

See Acceptable data for DDBJ.
If you have any question, please contact us from contact form.

Reference
Is there any restriction of sequence length to submit to DDBJ?
Last Updated:February 26, 2016
I lost my accession number submission update

If you have specific ID for your data other than accession number, such as EntryID or any, contact us from contact form by selecting the item, "Updating Submitted Data", with ID and E-mail address of contact person.
In case of uncertain, tell us following items as far as you know, then we will search your data.

  • Your name
  • Your affiliation at the time of submission
  • Your current affiliation
  • Your mail address at the time of submission
  • Your current mail address
  • The date, month and/or year, when you submit your data
  • Tool that you used to submit your sequence
  • Your sequence(s) (if many, just a few representatives)
  • Biological feature of your sequence

When we can not find your data, we will ask you to submit your data as new one.

Last Updated:July 3, 2014
How to describe accession numbers on the academic paper? search submission

In general, see the rule of the journal (i.e. Instructions to Authors), and follow it.
At INSDC, we recommend you to describe accession numbers in the footnote on the title page of your paper as following;
Note: Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number(s)----'.

Last Updated:July 2, 2014
What is "Direct Submission" in TITLE of REFERENCE 1? search submission

It indicates that this data is directly submitted from the submitter. The term is the antonym to "journal scan".
REFERENCE 1 is the information of submitter(s), not general reference.
So, do not describe "Direct Submission" in the title for literature in REFERENCE 2 or after.

Last Updated:July 1, 2014
Is there any reference for Feature/Qualifier? format search submission
I would like to know the date when the data was submitted. format search submission

In general, you can find accept date in JOURNAL line of REFERENCE 1 on DDBJ flat file.
Please note that some old data do not have the description of accept date.

Last Updated:July 1, 2014
Tell us conditions to release unpublished data. search submission
I like to hold my sequence data until related paper publication, shoud l specify the hold date? submission update

The hold date is required if you hold the data until your paper publication. So, please specify the date.
Though DDBJ does not restrict the date, we strongly recommend to specify the date within two years.
If not specified, the data will be published, immediately.

After data submission, you can change the hold date as needed.
See the relevant item in Data Updates/Corrections and contact us from this form by selecting "Change the hold-date" in [Subject].

How to postpone the hold date?

Last Updated:July 3, 2014
When the data submitted with hold date is published, is there any announcement from DDBJ? submission update

If you set the hold date for your data, the data will be published according to Principle of “Hold-Until-Published” data release.
After setting to publish the data, the mail with "[DDBJ] Publicized your data" in its subject is sent to contact person.
So, Do not block E-mails from DDBJ.

If the information of contact person is old or invalid, we may be unable to acknowledge publication of your data or any other important announcement.
See the relevant item in Data Updates/Corrections and contact us from this form to send request by selecting the subject, "Change the contact person, belonging, institution, etc..".

Last Updated:July 3, 2014
Why is the retracted data still available? search submission

For once published entries, we can restrict to use the data, if the conditions are right.
In case of the restriction, DDBJ will not include the data in its periodical release and remove from all services under DDBJ.
However, the data is permanently available on getentry queried with its accession number.
# The rule is not applied, when the data is published by any mistake of INSD.
This policy is written in the document prepared by International Advisory Committee of INSD on Overview of International Nucleotide Sequence Databases Policies as follows;


All database records submitted to the INSD will remain an entry accessible as part of the scientific record. Corrections of errors and update of the records by authors are welcome and erroneous records may be removed from the next database release, but all will remain permanently accessible by accession number.


In addition, there are a number of databases constructed by occasionally using data from INSD.
DDBJ can not support to delete data from such databases. If you are to delete the cited data on other databases, you have to contact managing staff of each database, directly.

Last Updated:August 4, 2016
Can not find appropriate feature key MSS NSSS submission

See Definition of Feature Key and Feature Table Definition.
When you can not find any accommodated feature, use misc_feature and enter information in value of /note qualifier.

For instance, since DDBJ is a database for nucleotide sequences, we do not prepare any specific item for amino acid sequence motifs.
However, you can describe such kind of information by using misc_feature with /note qualifier.

Last Updated:June 9, 2014
How can I input amino acid sequence (/translation qualifier) for CDS feature? format MSS NSSS submission

The amino acid sequence for CDS feature will be automatically translated from nucleotide sequence according to location and other items, and reflected into /translation qualifier. So, in general, do not enter it.

References
[Nucleotide Sequence Submission System] How to confirm translated amino acid sequences (i.e. /translation qualifier) for CDS features?
The amino acid sequence in the value of /translation qualifier seems to be incorrect.
Last Updated:July 7, 2014
The amino acid sequence in the value of /translation qualifier seems to be incorrect. format search submission

The rule to translate nucleotide sequence into amino acid sequence is specified in accordance with agreements of International Nucleotide Sequence Database Collaboration.
The codon table using a CDS feature is specified in the value of /transl_table qualifier as a number of The Genetic Codes.

There are three points frequently misunderstood.

  • You should specify /organelle qualifier to assign correct genetic code for mitochondrion or chloroplast.
  • The initiation codon is M, Met, methyonine, not G or V.
        See Start codon and N-Formylmethionine
  • When an amino acid can be specified by two bases (i.e. degeneracy of codons), it will be outputted.

There are some exceptional cases, represented by RNA editing and so on.

Last Updated:July 3, 2014
Which should I use to submit to DDBJ, Nucleotide Sequence Submission System or Mass Submission System? MSS NSSS submission

Nucleotide Sequence Submission System is an interactive application to enter all of items required for your submission on step by step basis.
To use Mass Submission System (MSS), submitters have to make submission files by themselves. So, DDBJ will review and consult for submitters on the process of making files.
Some submitters use Nucleotide Sequence Submission System to submit a lot of sequences, while some submitter use MSS to submit a few sequences.
Based on above information, select either of them as needed.

Last Updated:July 3, 2014
How many data can I submit by using Mass Submission System? MSS submission

There is no limit of the number of entries to use Mass Submission System.
You can use it not only for many sequences but also for one long sequence with many features (i.e. complete genome with annotation).
See Mass Submission System

Last Updated:July 3, 2014
How to restore the released data to private? submission update

In principle, you cannot remove your sequence data from DDBJ retrieval system, if it has already been open to the public.

See the relevant item in Data Updates/Corrections and "Why is the retracted data still available?".

Last Updated:July 3, 2014
How can I check my sequence to exclude vector contamination? MSS NSSS submission
Last Updated:July 3, 2014
[Nucleotide Sequence Submission System] How to suspend and resume my submission? NSSS submission
Last Updated:July 3, 2014
[Nucleotide Sequence Submission System] How to entetr two or more features for a sequence? NSSS submission

At 6. template, a) select 'other' and click [Input annotation] or b) Click [Upload annotation file].
Then, you can describe two or more features for each sequence as follows.
In case of a), see 7.Annotation (when “other” was selected at template).
In case of b), see 7. Annotation: upload an annotation file.

Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] How can I describe DEFINITION? NSSS submission

Since DEFINITION is constructed by DDBJ according to rules, there is no field to enter it.

Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] Can not find input field for some qualifier NSSS submission

Click [Select Qualifier], check qualifiers in the dialog as needed and click [Save] button.
Then, you can find input fields for qualifiers on 7.Annotation.

Related to this issue, in case of selecting "other" on 6. template, you have to specify some features other than source. So, click [Add feature] and select some feature on the list.

Reference
7.Annotation (when “other” was selected at template)
Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] How to fix error message: "First codon [***] is not a start codon." / "Final codon [***] is not a stop codon."? NSSS submission

These errors mean amino acid translation for CDS (protein coding sequence) feature is not appropriate in the 5' or 3' end, respectively.
When the CDS feature is not complete (i.e. partial) at 5' and/or 3' ends, its location is required to include flag for 'not complete'.
According to rules on Description of Location, partial sequences should be appropriately specified with flags for 5' end not complete, "<", and/or for 3' end not complete, ">" on its feature location.

For example: partial CDS feature in the range, 1..295
location condition
<1..295 [not start with initiation codon] and [stop with termination codon]
1.. >295 [start with initiation codon] and [not stop with termination codon]
<1.. >295 [not start with initiation codon] and [not stop with termination codon]
References
[Nucleotide Sequence Submission System] How to fix error message: “Stop codon ‘*’ is found in the range.”?
[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."?
Offset of the frame at translation initiation by codon_start
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "To use [translation] qualifier, [exception] qualifier is required in the [CDS] feature." ? NSSS submission

This error message is outputted, because you select /translation for CDS feature by dialog of [Select Qualifier] button.
Generally, since /translation qualifier is automatically created according to items under CDS feature, do not enter any amino acid sequence.
So, you can fix the error by removing /translation qualifier.

For your information, /translation qualifier is required only in case describing with /exception qualifier.
Typically, /exception qualifier indicates "RNA editing" is occurred on mRNA. In that case, conceptual amino acid translation of genome sequence is different from protein product of real mRNA molecules.

References
Example of Submission: B09) RNA editing
How can I input amino acid sequence (/translation qualifier) for CDS feature?
[Nucleotide Sequence Submission System] How to confirm translated amino acid sequences (i.e. /translation qualifier) for CDS features?
The amino acid sequence in the value of /translation qualifier seems to be incorrect.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Invalid value [***] for [transl_table] qualifier."? NSSS submission

The error is occurred because you do not enter correct genetic code.
See 7.Annotation -- How to input an organism name.
To specify genetic code, enter digit in the input field.
The value will be automatically applied for /transl_table qualifier for CDS feature.

For your information, in case of a previously reported organism, the genetic code is automatically specified, by describing Scientific name (/organism qualifier) and /organelle qualifier. If your sequence is derived from an organelle other than nuclei, you have to specify /organelle qualifier to set the genetic code for mitochondrion, chloroplast or some, appropriately.

References
7.Annotation
7.Annotation – How to input an organism name
The Genetic Codes
About /transl_table qualifier
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] browser still waiting for response on the process of data input NSSS submission

At first, please save the URL of the page on Nucleotide Sequence Submission System.
Then, shutdown the browser and reopen the saved URL.
When your sequences are relatively many, it is likely to resolve the condition.

If not resolved, confirm if you use either of browsers Firefox or Chrome that we recommend to use.
If not, change to Firefox or Chrome and reopen the URL.

If you still have any problem, please contact us with followings from contact form by selecting the item, "DDBJ Nucleotide Sequence Submission System".

  • URL
  • Number of your sequences
  • OS: Windows, MacOSX, or Linux, and its version
  • Browser: software and its version
Last Updated:July 6, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."? NSSS submission

You may enter incorrect values for Location and/or /codon_start of CDS feature.
If the value of /codon_start is either of "2" or "3", the location of CDS feature should be 5' end not complete.

See Description of Location and modify the location with flag for "5' end not complete", for an example, from "1..300" to "<1..300".
When the CDS feature is started with an initiation codon, correct /codon_start with "1".

References:
Offset of the frame at translation initiation by codon_start
[Nucleotide Sequence Submission System] How to fix error message: "First codon [***] is not a start codon." / "Final codon [***] is not a stop codon."?
[Nucleotide Sequence Submission System] How to fix error message: "Stop codon ‘*’ is found in the range."?
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] Can I modify descriptions on a previous page? NSSS submission

You can modify your inputs on any pages before finishing your submission.
You can go back to each page by clicking either of 1.Contact person, 2.Hold date, 3.Submitter, 4.Reference, 5.Sequence, 6.Template or 7.Annotation in progress bar at upside of pages.


※Caution
After inputting feature annotation on 7.Annotation, if you do either of followings, feature annotation will be removed.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] I can not upload my annotation file NSSS submission

Confirm following points.

  • You have to input the same entry names for both sequences and in annotation file.
  • The format of annotation file must be tab delimited text consisting with 5 columns.
  • The line feed code of annotation file must be in LF (unix format) or CR-LF (windows format).
  • You have to use correct names for feature and qualifier keys.

If you still have any problem, contact us from contact form by selecting the item, "Data Submission".

Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to submit more than one sequence at once? NSSS submission

On 5.Sequence, input all of your sequences in multi-FASTA format. We will assign consequent accession numbers for your sequences.
Moving to 7.Annotation, you can enter feature annotation for each sequence at once.

Caution
※ All of following items must be unified for all sequences. You can not specify thenm for each sequence.
  • Contact person
  • Hold date
  • Submitter
  • Reference
※ You can select only one template on 6.Template for all sequences. You can not select a template for each sequence.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Stop codon ‘*’ is found in the range."? NSSS submission

In general, see How to describe CDS feature, when termination codon is found in the range.
You can also see Protein Coding Sequence; CDS feature to describe CDS feature.
Following items are case study for the error.

1. Did you correctly specify /codon_start qualifier to indicate reading frame of the CDS feature?
  Select 1, 2 or 3, appropriately.

References:
Offset of the frame at translation initiation by codon_start
[Nucleotide Sequence Submission System] How to fix error message: “First codon [***] is not a start codon.” / “Final codon [***] is not a stop codon.”?
[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."?

2. Have you specify correct genetic code for /transl_table qualifier?
See followings and specify genetic code, appropriately.

References
The Genetic Codes
About /transl_table qualifier
[Nucleotide Sequence Submission System] How to fix error message: "Invalid value [***] for [transl_table] qualifier."?

3. Are there really some stop codons in the range of CDS feature because of frame shift, nonsense mutation, or some other reason?

3-1. In case of pseudogene
Click [Select Qualifier] button beside CDS and add /pseudogene qualifier. Then, you can specify /pseudogene qualifier with its controlled vocabularies.
See also b) considered pseudogene in detail.

3-2. In cases of unsure whether it is pseudogene or not, the reason of stop codon is uncertain, or on the process of diversity increasing related to acquired immunity, describe misc_feature, not CDS feature.
See a) Putative nonsense mutation, frameshift caused by uncertain reason, or on the process of diversity increasing related to acquired immunity for IgG etc. in detail.

In other cases. There are some possibilities to output this error because of ribosomal slippage, RNA editing, exceptional amino acid usage, transpon insertion and so on.

Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to confirm translated amino acid sequences (i.e. /translation qualifier) for CDS features? NSSS submission

You can confirm amino acid sequences for CDS features as follows.

1. Download UME_win.zip (for Windows) or UME_mac.zip (for MacOSX) from Mass Submission System.
2. Download both annotation and sequence files at 8. Finish on DDBJ Nucleotide Sequence Submission System.
3. Run UME and load both annotation and sequence files. Then click [Execute] of transChecker.

The function to confirm amino acid sequences will be applied on DDBJ Nucleotide Sequence Submission System.

References
How can I input amino acid sequnce (/translation qualifier) for CDS feature?
The amino acid sequence in the value of /translation qualifier seems to be incorrect.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "MGA:No entry name is found other than [ COMMON ], without feature [ DATATYPE/type=MGA ]."? NSSS submission

Though you have not yet enter either /organism or /mol_type on annotation table, you click [Confirm] button.
You must fill mandatory items of annotation (feature, location, qualifier) before clicking [Confirm] button.

On 7.Annotation, click [Select Qualifier] button beside 'source', and select qualifiers as needed. Then, click [Edit] button beside entry name and input /organism and others. Note that it is required to input at least one feature other than source.
See also 7.Annotation – How to input an organism name.

Last Updated:July 7, 2014
What is secondary accession number? format search submission update

INSD; International Nucleotide Sequence Database are composed of DDBJ, ENA and NCBI, and collect experimentally determined nucleotide sequence data.
A unique accession number issued by INSD for each submitted sequence data is defined as the INSD accession number.
On DDBJ flat file, the accession number is described in ACCESSION line.

If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s).

In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows.

example
ACCESSION   AB999999 AB888888 AB777777
AB999999 -- primary accession number
AB888888 AB777777 -- secondary accession number

You can find the same updated entry with both the primary and the secondary accession numbers, in general.
However, if the old entry with secondary accession number has previously been open to the public, the old one is not removed. So, you can find the old record by getentry.

References
getentry HELP
INSDC Status Document: Replaced
Why is the retracted data still available?
Last Updated:July 7, 2014
What are the browser that the DDBJ service supports? ARSA BLAST NSSS PR search
DDBJ recommend using the following OS and browsers to use our servises.
DDBJ HP
OS:Windows7 or later , Mac OSX10.9 or later
Browser:Firefox latest versions , Chrome latest versions
DDBJ Nucleotide Sequence Submission System
Browser:Firefox , Chrome
D-way Submission System
Browser:Firefox latest version, Chrome latest version
BLAST / ARSA
OS:Windows7 or later , Mac OSX10.6 or later
Browser:IE10.X , IE9.X , Firefox , Chrome , Safari5.X or later
However, the OS, browser environment recommended above is subject to change without prior notice.
Last Updated:November 24, 2016
Is there any restriction of sequence length to submit to DDBJ? MSS NSSS submission
Upper limit
If the sequence is really observed, there is no upper limitation of the sequence length to submit to DDBJ.
However, we can not accept any operationally joined sequence, for example, joining chromosomes. We accept each chromosome sequence, respectively.
For sequences greater than 500 kbases in its length, please submit by using Mass Submission System (MSS) instead of Nucleotide Sequence Submission System (NSSS).
Lower limit
For minimum length, DDBJ has no systematic restriction, however, when the sequence is less than 20 bp in its length, our system outputs "warning" to your data.
When the sequence has biological significance, even if it is a short sequence, DDBJ accepts the submission of it. However, we consider that more than fifteen bases would be required to describe something in general, such as full length of small RNA transcript, some of specific tag sequence and so on.
References
Is there any case to reject submission to DDBJ?
Acceptable data for DDBJ
Last Updated:February 26, 2016
Where to submit variation data, such as single nucleotide variations, structural variations, copy number variations (CNVs) and so on? category submission

At DDBJ, we do not provide any official services to accept SNV, CGH analysis, microarray, variation and so on.
We assume that you can submit your data at NCBI or EBI.
Please submit to some of followings. If you have any questions, please ask each database, directly.

NCBI: Gene Expression Omnibus (GEO), dbSNP, dbVar, ClinVar
EBI: ArrayExpress, European Variation Archive (EVA), Database of Genomic Variants archive (DGVa)

If your data are derived from human subjects, it may be required to submit your data to either of following controlled access databases.
The database of Genotypes and Phenotypes (dbGaP)
European Genome-phenome Archive (EGA)
Japanese Genotype-phenotype Archive (JGA)

References
After submission of SNP data to DDBJ, will it automatically reflect to dbSNP?
How to submit sequence data related to DNA polymorphism?
Last Updated:March 3, 2016
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