What are Integrons ?

Integrons are versatile gene acquisition systems commonly found in bacterial genomes. These elements are hotspot of genomic complexity that generate phenotypic diversity and shape adaptive responses.

Integrons are composed of three essential core features:

  • intI: Gene encoding an integron integrase. This protein catalyzes recombination between incoming gene cassettes and an integron-associated recombination site.

  • attI: Attachment integrase site. It’s a proximal recombination site which is recognized by the integrase and where gene cassettes may be inserted.

  • Pc: Promoter directing transcription of a cassette-encoded gene.

Integrons acquire new genes as part of gene cassettes. These are simple structures, usually consisting of a single open reading frame (ORF) bounded by a cassette-associated recombination site known as attC. Circular gene cassettes are integrated by site-specific recombination between attI and attC, a process mediated by the intI. This process is reversible, and cassettes can be excised as free circular DNA elements. Insertion at the attI site allows expression of an incoming cassette, driven by the adjacent Pc promoter.



Gillings MR. 2014. Integrons: past, present, and future. Microbiol Mol Biol Rev 78:257–277.

What is IntegronFinder ?

IntegronFinder is a tool that detects integrons in DNA sequences with high accuracy. It combines the use of HMM profiles for the detection of integron integrases, and Covariance Models for the detection of attC sites.

IntegronFinder distinguishes 3 types of elements:

  • Complete integron: Integron including an integrase and at least one attC site,

  • In0 element: Integron including only an integrase,

  • CALIN (Clusters of AttC sites Lacking integron-INtegrases) element: Integron composed of at least two attC sites.


Know more about IntegronFinder.


Néron B. et al. 2022. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms vol. 10,4 700.

How to access to Integrons data ?

IntegronFinder predictions are available through the Comparative Genomics section and the Integrons subsection, in the main navigation menu.

What is the ‘Integron clusters’ table ?

The table Integron clusters enumerates all integron clusters predicted for the selected organism and its replicons.

  • Integron id: Identifier of the integron. Click on it open the detailled IntegronFinder cluster visualization window page, which allows to access to a description of the integron structure.

  • Replicon name and Replicon type give characteristics of the replicon where the integron is found.

  • Begin, End and Length give informations about the location and the length of the integron on the sequence.

  • Integron type: Type of integron (complete, In0, CALIN).

  • Nb of attC: Number of attC sites found in the integron.