Cousin-of-GIN integrase type 1 (CGIN1) is a host intron-exon integrase gene of 6-7 kb restricted to the eutherian genomes (Marco & Marin 2009) which was called as such because of their apparent relationship with the integrases (INTs) coded by Retroviridae retroviruses (Marco & Marin 2009). The protein product of CGIN1 shows a typical INT core with GPY/F module thought to mediate multimerization (Ebina et al. 2008), preceded by a RNase H domain and two modules, respectively called CGIN (undescribed) and NYN domain (Marco & Marin 2009).
Phylogenetic screenings suggest that CGIN1 proteins are much more similar to the INTs coded by certain Ty3/Gypsy clades than to Retroviridae INTs. At this point the most parsimonious explanation in the origin of CGIN1 genes is that they evolve from the recombination and subsequent domestication of the RNaseH-INT component of a Ty3/Gypsy transposon with other genetic elements (CGIN and NYN domains) during eutherian evolution. And while, there is not yet sufficient information to determine the true Ty3/Gypsy origin of CGIN1 genes the biological distribution of these genes is restricted to the eutherian genomes and to our knowledge no CGIN1 gene has been yet described in sauropsids organisms.
There are two complementary classifications for CGIN1 INTs. Based on sequence these enzymes can be classified as DDE transposases (TRs) and INTs. Based on INT-like structural potential similarities, they are members of the Retroviral Integrase Superfamily (Nowotny 2009) of nucleic acid-processing enzymes involved in; a) selfish evolution; b) replication and repair of DNA; c) recombination and gene fusion; d) RNA-mediated gene silencing; and e) oncogenesis.