. Embedded within these repeat elements are also present some encoded genes. Surprisingly, many of these genes in the centromere express themselves in methylated state in the seedlings and remain silent, when these are unmethylated in mature tissue. B-chromosomes in maize have also been shown to carry in these centromeres a specific repeat element having strong homology with the knob repeat of maize. In rice also several centromeric repeat DNA elements have been described.

Sequence analysis revealed that most of these elements are derived from retrotransposons of Ty3/gypsy-class, which is specific to the cetromeric region of grass chromosomes. One of these sequences, which is characterized as 155-bp satellite repeat, and described as CentO (earlier named as RCS2) is unique to rice centromeres. The breakpoints of centromeric misdivision, were also shown to be located in this sequence, so that it should be a key component of functional rice centromere.