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- "Unpublished"; In cases of preparing paper, during paper submission, or you do not prepare any publication.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.