An accessible database for mouse and human whole transcriptome qPCR primers

Bioinformatics. 2013 May 15;29(10):1355-6. doi: 10.1093/bioinformatics/btt145. Epub 2013 Mar 28.


Motivation: Real time quantitative polymerase chain reaction (qPCR) is an important tool in quantitative studies of DNA and RNA molecules; especially in transcriptome studies, where different primer combinations allow identification of specific transcripts such as splice variants or precursor messenger RNA. Several softwares that implement various rules for optimal primer design are available. Nevertheless, as designing qPCR primers needs to be done manually, the repeated task is tedious, time consuming and prone to errors.

Results: We used a set of rules to automatically design all possible exon-exon and intron-exon junctions in the human and mouse transcriptomes. The resulting database is included as a track in the UCSC genome browser, making it widely accessible and easy to use.

Availability: The database is available from the UCSC genome browser (, track name 'Whole Transcriptome qPCR Primers' for the hg19 (Human) and mm10 (Mouse) genome versions. Batch query is available in the following:

Contact: or

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA Primers / genetics*
  • Databases, Genetic
  • Exons
  • Humans
  • Introns
  • Mice
  • Real-Time Polymerase Chain Reaction*
  • Software
  • Transcriptome*


  • DNA Primers