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Use splice junctions to your advantage in qPCR

Tips for simplifying your assay design process

Get recommendations for avoiding PCR amplification of genomic DNA, as well as for identifying and quantifying splice variants, in this article on designing qPCR assays that span splice junctions.

Quantitative, real-time PCR (qPCR; Figure 1) has become the gold standard for gene expression analysis. This method is fast, accurate, and sensitive, and requires less sample input than for northern blots, ribonuclease protection assays, semi-quantitative RT-PCR, and competitive RT-PCR.

Figure 1. A typical qPCR workflow. For accurate gene expression results, researchers typically design across exon-exon junctions to avoid genomic DNA (gDNA) amplification and detection. Using RNA isolation protocols that minimize DNA contamination or including a DNase treatment step can also help avoid gDNA amplification.

How qPCR assays span splice junctions

qPCR assays designed to span exon-exon junctions can be used to distinguish and quantify splice variants, detect all splice variants, or even detect species-specific gene expression. Depending on the structure of your gene of interest, there is more than one way to design primers that span exon-exon boundaries. For example, one of the primers can be designed with one end complementary to the 3′ end of one exon and the other end complementary to the 5′ end of the next downstream exon (Figure 2A), so that amplification will only occur if this primer binds to cDNA from a spliced mRNA transcript. Alternatively, the forward and reverse primers can be designed to hybridize to different exons that are separated by a large intron or large intron-exon region (Figure 2B and 2C). Under typical PCR cycling conditions, amplification of the smaller cDNA-based amplicon will be favored over the larger gDNA-based amplicon.

intron exon boundary splice 

There are a few situations where you might need to design a qPCR assay with a probe that spans the exon-exon junction (e.g., for expression analysis of some alternatively spliced genes). However, if the primers amplify gDNA, PCR efficiency of the desired amplicon could be affected, since gDNA amplification will not be detected by a probe using this design strategy.

Tip #1: For human, mouse, and rat genes, select from PrimeTime Predesigned qPCR Assays

Up-to-date, reliable predesigned assays

Combining expertise in programming, bioinformatics, molecular biology, and nucleic acid thermodynamics, IDT scientists have developed a robust design algorithm to produce a collection of PrimeTime Predesigned qPCR Assays for most human, rat, and mouse genes. This design process uses the cleanest possible target sequence information (including up-to-date SNP and intron-exon junction locations), and stresses accurate Tm prediction and protection against off-target amplification. The algorithm includes additional secondary design considerations and scoring criteria, such as analysis of polynucleotide runs, short sequence repeats, and hetero- and homo-dimer folding energies.

Note: if you want to design probes that span exon-exon junctions, see Tip #2 to learn how to customize your PrimeTime assay.

Using PrimeTime Predesigned Assays

If you are studying human, mouse, or rat genes, the predesigned qPCR assays, which are available with or without probes, allow you to choose from multiple assays that target different locations within a single gene. From the Predesigned qPCR Assays ordering page, you can view the assays in 4 short steps:

  1. Enter the Gene Symbol or RefSeq accession number.
  2. Note: If you are reordering an assay, you only need to enter the IDT Assay ID as the search criterion. Assay IDs can be found on your tube labels, order history, and specification sheets. (Representative Assay ID: Hs.PT.58.19228441)

  3. Select the species (Human, Mouse, or Rat).
  4. Select the desired Assay Configuration (5′ nuclease assay with primers and probe, or intercalating dye assay with only primers).
  5. Click Search (see Figure 3 for representative results).
PrimeTime qPCR Assays results of splice variants 

Choosing assays that span exon-exon junctions

The results section of the PrimeTime Predesigned qPCR Assay ordering tool provides a wealth of information, some of which will not be covered here, but all details are available online by placing your cursor over, or clicking on, the info buttons. In Figure 3, boxes highlight the results columns that are useful for choosing assay(s) that avoid genomic DNA amplification or that can distinguish cDNAs reverse transcribed from alternatively spliced mRNAs. Here are our recommendations:

Header Description Recommendation

Assay ID


  • .g: The assay may detect genomic DNA.

  • .gs: Assays configured as primers only (intercalating dye-base assays) may detect genomic DNA, while assays configured as primers and probe (5′ nuclease assay) will not.

  • To avoid potential amplification of genomic DNA, do not use an assay with a .g suffix.

  • Additionally, if you are using intercalating dye-based assays, do not use an assay with a .gs suffix.

Detects All Variants

  • Yes: All known splice variants are detected by the assay.

  • No: Only some splice variants are detected by the assay. The number in parentheses in the RefSeq # column shows the number of variants detected.

Selection is based on your research goals.

  • If you do not need to discriminate splicing isoforms, choose assays with a “yes”.

  • If you want to examine specific splice variants, choose assays with a “no”. Then review the Exon Location column to determine which variants are detected.

Exon Location

  • Single exon number: The primers (and probe) hybridize within a single exon, and will likely amplify genomic DNA (e.g., Figure 3, Assay ID Hs.PT.58.24349547.g).

  • Multiple exon numbers: The assay spans multiple exons, such that the PCR amplicon spans the junction between the exons. If the intervening introns and exons are <500 bp, it is possible that some assays will detect genomic DNA (e.g., Figure 3, Assay ID Hs.PT.58.40761082.g).

Use your knowledge about the structure of your gene combined with information about Assay ID suffixes, Variants, and Exon Location to make your assay selection.

Tip #2: When your samples are not from human, mouse, or rat, use the PrimerQuest® Tool to create custom PrimeTime qPCR Assays

Selecting custom assays

The PrimerQuest Tool is the program of choice for designing qPCR primers/probes, sequencing oligonucleotides, and custom primers. Because of its utility, it is one of the most highly accessed pages on the IDT website. Briefly, the four main steps for using the PrimerQuest Tool include the following:

  1. Enter sequence
  2. Choose design
  3. Customize your design parameters
  4. Select and order assays

The PrimerQuest Tool provides live designs that, by default, do not take exon junction locations into consideration, so that assay results can be returned faster. The following tip focuses on Step 3 above—how to adjust the custom design parameters to create primers that span exon-exon junctions.

Finding the appropriate intron-exon boundaries for your gene

Find your sequence in the NCBI nucleotide database using the gene name or GenBank accession number. If you start with the gene name, narrow your search results to your species of interest and choose your sequence. Scroll down to the "Features" section of your sequence results to obtain the exon boundary numbers (for some genes, it may be important to understand transcript variants, exon organization, and SNP locations).

Customizing your qPCR assays

  1. Use your GenBank accession number to download your sequence into the PrimerQuest Tool, and click on Show Custom Design Parameters in the Choose Your Design section.
  2. Select qPCR (2 Primers + Probe) or qPCR Intercalating Dyes (Primers only) in the box on the right, and scroll down to the Custom Target Region
  3. To design one of your primers (or probe) to span an exon-exon junction (Figure 2A), simply enter the nucleotide number(s) of the 3′ end of the exon(s) into the Overlap Junction List (Figure 4). The results page includes the numbers of the starting and ending nucleotides for each primer and probe, so you will be able to tell which oligo overlaps the exon-exon junction.
  4. exon-exon-boundary 
  5. To have your primers hybridize to different exons (Figures 2B and 2C), enter the range(s) of nucleotide numbers ±10 from your exon boundaries in the Target Region List under Primer Focus Region.
  6. capture-different-exons 
  7. If no assays are found, use the notes at the bottom of the results page to adjust parameters in a new assay search (click on adjust parameters on the results page).

    For example, the results shown in Figure 6 indicate that >375 possible designs for each primer and probe were evaluated (top: Possible designs), and at least 20 met all design requirements for each primer and probe (bottom: Number met design parameters). However, all 1020 possible assay designs produce amplicon sizes outside the specified range (last column: Pair). In this scenario, consider adjusting the boundaries of the excluded region. As further refinements, you might consider adjusting the range of %GC content, the overlap on the 3′ and 5′ end of the primer, and/or the maximum or minimum acceptable Tm.

Figure 6. Representative results from a customized search that failed to produce acceptable qPCR assay. The notes at the bottom (blue box) can be used to adjust design parameters in a follow up assay search.


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  1. Vandenbroucke II, Vandesompele J, et al. (2001) Quantification of splice variants using real-time PCR. Nucleic Acids Res 29(13):e68.

Published Jun 28, 2016