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A significant fraction of the human Y chromosome is composed of DNA sequences which have homologues on the X chromosome or autosomes in humans and non-human primates. However, most human Y-chromosome sequences so far examined do not have homologues on the Y chromosomes of other primates. This observation suggests that a significant proportion of the human Y chromosome is composed of sequences that have acquired their Y-chromosome association since humans diverged from other primates. More than 50% of the human Y chromosome is composed of a variety of repeated DNAs which, with one known exception, can be distinguished from homologues elsewhere in the genome. These include the alphoid repeats, the major human SINE (Alu repeats) and several additional families of repeats which account for the majority of Y-chromosome repeated DNA. The alphoid sequences tandemly clustered near the centromere on the Y chromosome can be distinguished from those on other chromosomes by both sequence and repeat organization, while the majority of Y-chromosome Alu repeats have little homology with genomic consensus Alu sequences. In contrast, the Y-chromosome LINE repeats cannot be distinguished from LINEs found on other chromosomes. It has been proposed that both SINE and LINE repeats have been dispersed throughout the genome by mechanisms that involve RNA intermediates. The difference in the relationship of the Y-chromosome Alu and LINE repeats to their respective family members elsewhere in the genome makes it possible that their dispersal to the Y chromosome has occurred by different mechanisms or at different rates. In addition to the SINE and LINE repeats, the human Y chromosome contains a group of repeated DNA elements originally identified as 3.4 and 2.1 kb fragments in HaeIII digests of male genomic DNA. Although the 3.4 and 2.1 kb Y repeats do not cross-react, both exist as tandem clusters of alternating Y-specific and non-Y-specific sequences. The 3.4 kb Y repeats contain at least three distinct sequences with autosomal homologies interspersed in various ways with a collection of several different Y-specific repeat sequences. Individual recombinant clones derived from isolated 3.4 kb HaeIII Y fragments have been identified which do not cross-react. Thus, the 3.4 kb HaeIII Y fragments are a heterogeneous mixture of sequences which have in common the regular occurrence of HaeIII restriction sites at 3.4 kb intervals and an organization as tandem clusters at various sites along the Y-long arm.(ABSTRACT TRUNCATED AT 400 WORDS)
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