The Chromodomain Type 1 Integrase-like (CIN-1) is the name we give to the pool of transposases typically encoded by the the self-synthesizing Maverick/Polinton transposons of eukaryotes (Feschotte & Pritham 2005; Pritham et al. 2007; Kapitonov & Jurka 2006). CIN1 TRs present an integrase-like core with no N-terminal HHCC module and a C-terminal chromodomain (Koonin et al. 1995; Wright et al. 2005; Singleton & Levin 2002), similar to that found in the integrases (INTs) coded by Ty3/Gypsy chromoviruses and a particular clade of Ty1/Copia elements called CoDi-I (Maumus et al. 2009; Llorens et al. 2009). The chromodomain (the chromatin organization modifier) is a small protein module involved in chromatin re-modeling, regulation of gene expression (Koonin et al. 1995), and differential host genome integration of LTR retroelements Wright et al. 2005; Singleton & Levin 2002).
CIN-1 TRs where originally described (together with SCAN/KRAB INTs), as members of a large pool of INTs related to FOB1 and LTR retroelement INTs (Gao & Voytas 2005). Because of the assumption of a cellular role for these enzymes, they were called cellular integrases (C-INTs). The accepted notion in the origin of these enzymes was that they evolve from LTR retroelement INTs but such hypothesis underwent an exciting turn with the discovery that CIN-1 TRs are not host genes but TR components of Maverick/Polinton transposons. Evaluation of insect genomes such as that of the Pea Aphid Acyrthosiphon pisum (The International Aphid Genomics Consortium 2010) however suggests that CIN-1 TRs can also be found as Solo-TR encoding transposons organized as both intron-exon structured genes and as single ORFs without introns of 0.8-2.4 kb (Llorens et al. manuscript in preparation). For simplicity´s sake the figure below shows the genomic structure without introns.
There are three complementary classifications for CIN-1 TRs. Based on sequence these enzymes can be classified as DDE TRs and INTs. Based on INT-like structural potential similarities, CIN-1 TRs 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. Based on their usual mobile genetic element carrier these enzymes can be classified as Maverick/Polinton transposons (Feschotte & Pritham 2005; Pritham et al. 2007; Kapitonov & Jurka 2006).