Exercise 1: Submission of a protein coding gene

1c. Filling out the "Submit to GenBank" form

Our sequence is now ready to submit to GenBank. Select the sequence and go Tools → Submit to GenBank. Type in a Submission name (e.g. Tutorial 1), and check Save a local file (.tar). This will save your submission to your hard drive rather than submitting it to GenBank. 

Now click Edit Publisher Details and add your name and address details. You also need to add the title of the journal article that this sequence will appear in under Reference title. If your paper is not yet published, check the "Unpublished" button. It doesn't matter if you don't yet know the name of your journal article - an approximate name is OK, as this will be updated when the accession numbers for the sequence are published in an article. For the purposes of this tutorial, type "TEST" next to Reference Title and click OK.

We now need to map the fields that we set up on our document in Exercise 1a onto the GenBank fields. Firstly, enter a project name, such as "tuatara MHC" - this is for your reference purposes. Next, click on the arrows next to Specimen Voucher to bring up a drop-down menu. You will see that the GenBank Submission fields that we added in Exercise 1a appear as options here. Select Specimen Voucher (GenBank Submission).




Select the following to populate the other fields: Organism = Organism, Genetic code = Standard; Sequence ID = Sequence ID (GenBank Submission). For Molecule Type select "Genomic DNA", and for Genomic Location select "Genomic". The other fields (Identified by, Collected by, Country, Collection Date etc) can be left displaying None. We also need to add the Tissue type field that we added to our document in Exercise 1a. Check Include extra fields and click Choose..., then enter Field Name Tissue_type and Field Value Tissue type (GenBank Submission). Click OK.




To add the gene, CDS and exon annotations into our submission, check the Include Features/Annotations box. Finally, make sure the Include Primers box is unchecked, as we are not submitting primers with this sequence. Your Submit to GenBank dialog box should now look like this:




You can now click OK to test the submission, but before you do this double-check that you have chosen to Save as a local file, not Upload submission, as we do not want to submit the tutorial sequence to GenBank! After you click OK, you will get a discrepancy report. This is given for every submission and does not necessarily mean your submission contains errors. If there are errors that are likely to interfere with the submission you will see a Validation Errors/Warnings window instead, detailing errors that should be attended to before the submission proceeds.

If you wish to see a preview of what your submission will look like in Genbank format, click the Genbank Preview tab above the Discrepancy report.

Click Save Tar File to save the .tar file to your desktop. You have now completed a test submission of a protein coding gene. If you wish to submit real data to GenBank, simply check the Upload submission box rather than Save a local file.


Exercise 2: Submission of an alignment of non-coding mtDNA sequences