Cin4, an insert altering the structure of the A1 gene in Zea mays , exhibits properties of nonviral retrotransposons

A wild‐type allele of the A1 gene of Zea mays contains a 1.1‐kb‐long insert termed Cin4‐1, which alters the structure of the transcription unit compared to other A1 alleles. The Cin4‐1 element is a member of a family of elements occurring in 50–100 copies in the maize genome. Genomic cloning and sequence analysis of several family members and their flanking regions allowed classification of Cin4 as a nonviral retrotransposon. Individual Cin4 elements terminate in an oligo(A) track of variable size (6–11 residues) at their 3′‐end. The 5′‐ends of family members are heterogeneously truncated with respect to the longest Cin4 element. Cin4 elements are flanked by small direct duplications, the size of which varies between 3 and 16 bp. On the basis of a comparison of the target sequence and the sequence of Cin4 we suggest and discuss a model of the mechanism of Cin4 integration via in situ cDNA synthesis on an RNA template. The longest Cin4 element analysed so far has two non‐overlapping open reading frames (ORFs) comprising 2793 nucleotides (ORF1) and 3489 nucleotides (ORF2). The putative 1163 amino acid long Cin4 protein derived from the sequence of ORF2 has the capacity to encode a reverse transcriptase‐like protein and a DNA‐binding domain. The conservation pattern of these two domains and the overall organisation of Cin4 is similar to that detected in nonviral retrotransposons in animals. The origin and function of Cin4 are discussed.