NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

The GenBank Submissions Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-.

  • This publication is provided for historical reference only and the information may be out of date.

This publication is provided for historical reference only and the information may be out of date.

Cover of The GenBank Submissions Handbook

The GenBank Submissions Handbook [Internet].

Show details

The “Primers” Page

and .

Estimated reading time: 4 minutes

Purpose

The BankIt submission tool “Primers” page is where you will provide the PCR primers you used to amplify the nucleic acid that you sequenced. The information we ask for in this page includes:

  • The sequence of the forward and reverse PCR primers for each primer reaction set
  • The names of the forward and reverse PCR primers for each primer reaction set

Do NOT submit sequencing primers in this page. This page is for entering the PCR primers used to amplify the nucleic acid that you sequenced.

Note: PCR primers are optional and are not required for a submission.

Single Sequence Submissions

If you submitted a single sequence in the “Nucleotide” page of the form, when you get to the “Primers” page, you will see primer sequence examples followed by text/name boxes for your primers (Figure 18):

Figure 18: . The “Primers” page when a single sequence is submitted.

Figure 18:

The “Primers” page when a single sequence is submitted. Figure text gives instructions for entering primer sequences and names.

Starting with the text box on the far left:

1.

Place the sequence of your forward (fwd) primer in the first box.

2.

Place the name of the forward primer in the second box.

3.

Place the sequence of your reverse (rev) primer in the third box.

4.

Place the name of the reverse primer in the fourth box.

Note: The primers you enter in these text boxes are PCR primers for nucleic acid amplification, and NOT sequencing primers.

Additional Primer Pairs for the Same Reaction Set

If you have additional pair(s) of forward and reverse primers for your PCR reaction mixture, click the “Add” button to get text boxes for another pair of forward and reverse primers (Figure 19). You can click the “Add” button as many times as you have primer pairs for this reaction mixture.

Figure 19: . The “Primers” page when a single sequence is submitted and the “Add” button is clicked twice.

Figure 19:

The “Primers” page when a single sequence is submitted and the “Add” button is clicked twice. Figure text gives instructions for using the “Add” button to enter more primers in a reaction set.

Additional PCR Reaction Sets for Your Sequence

  • If you have another PCR reaction for the sequence you are submitting, click the “Add Another Primer Reaction Set” to get a set of boxes where you can add the forward and reverse primers for the additional reaction set (Figure 20).
  • You can click the “Add” button to get text boxes for another primer set for this new reaction. You can click the “Add” button as many times as you have primer pairs for this reaction mixture.
  • Once you have finished entering the primer pairs for this new reaction, if you have any additional reaction mixtures for this sequence, click the “Add Another Primer Reaction Set” button as many times as you have PCR reaction sets for this sequence that you need to add.
Figure 20: . The “Primers” page when a single sequence is submitted and the “Add Another Primer Reaction Set” button is clicked once.

Figure 20:

The “Primers” page when a single sequence is submitted and the “Add Another Primer Reaction Set” button is clicked once. Figure text gives instructions for using the “Add Another Primer Reaction Set” button (more...)

Check Your Primer Sequences before Continuing

Once you have finished entering the PCR primers for the sequence you are submitting, click the “Continue’ button” to refresh the static table at the bottom of the “Primers” page with the sequences you have entered. Once the table has refreshed, check your primer sequences to be sure they are correct. Once you have verified that your primer sequences are correct, click the “Continue” button again to go to the next page of the form.

Multiple Sequence Submissions

If you submitted multiple sequences in the “Nucleotide” page of the form, when you get to the “Primers” page, you will be given a choice of uploading a Primers Table File or using the BankIt form to enter your primers. (Figure 21)

Figure 21: . The “Primers” page when multiple sequences are submitted.

Figure 21:

The “Primers” page when multiple sequences are submitted. Figure text gives hints for selecting a primer submission method.

If the primer sets are different for each of the sequences:

1.

Select the “Upload Primers Table File” button. When you do, a text box and “Browse” button will appear.

2.

Use the “Browse” button to select the Primers Table File from your local computer.

3.

Click the “Continue” button to load your Primers Table File.

4.

The primers you submitted in your Primers Table File will be displayed in the “Primers” table at the bottom of the page.

5.

Check the Primers table at the bottom of the page to verify that the primer sequences displayed are correct.

6.

Click the “Continue” button to go to the next page of the form.

Instructions for creating a Primers Table File are available from BankIt Help.

If the Primer Sets are the Same for all the Sequences:

Select the “Input PCR Primers” button. When you do, primer sequence examples followed by text/name boxes for your primers will appear (Figure 22):

Figure 22: . The “Primers” page when multiple sequences are submitted and the “Input PCR primers” button is selected.

Figure 22:

The “Primers” page when multiple sequences are submitted and the “Input PCR primers” button is selected. Figure text gives instructions for entering primer sequences and names.

Starting with the text box on the far left:

1.

Place the sequence of your forward (fwd) primer in the first box.

2.

Place the name of the forward primer in the second box.

3.

Place the sequence of your reverse (rev) primer in the third box.

4.

Place the name of the reverse primer in the fourth box.

If you have additional primer pairs for the same reaction set, see the instructions in the single sequence submission section for entering additional primer pairs in the form.

If you have additional PCR reaction sets for your sequences see the instructions in the single sequence submission section for entering additional PCR reaction sets in the form.

Check Your Primer Sequences before Continuing

Once you have finished entering the PCR primers for the sequence you are submitting, click the “Continue” button to refresh the static table at the bottom of the “Primers” page with the sequences you have entered. Once the table has refreshed, check your primer sequences to be sure they are correct. Once you have verified that your primer sequences are correct, click the “Continue” button again to go to the next page of the form.

Common Mistakes Made While Filling Out the “Primers” Page

  • Mistake: Entering the primer sequences and names in the wrong text boxes.

    Fix: Be sure to read the text boxes carefully before entering your data. Starting on the left, you enter the forward primer sequence in the first box and the name for this primer in the second box. Then you enter the reverse primer sequence in the third box and the name for this primer in the fourth box.
  • Mistake: Entering sequencing primers instead of PCR primers.

    Fix:
    This page is for entering PCR primers used to amplify the nucleic acid that you sequenced. Do not enter sequencing primers on this page.

Views

Other titles in this collection

Recent Activity

    Your browsing activity is empty.

    Activity recording is turned off.

    Turn recording back on

    See more...