The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.
The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.
Skaletsky, H; Kuroda-Kawaguchi, T; Minx, PJ; Cordum, HS; Hillier, L; Brown, LG; Repping, S; Pyntikova, T; Ali, J; Bieri, T; Chinwalla, A; Delehaunty, A; Delehaunty, K; Du, H; Fewell, G; Fulton, L; Fulton, R; Graves, T; Hou, S-F; Latrielle, P; Leonard, S; Mardis, E; Maupin, R; McPherson, J; Miner, T; Nash, W; Nguyen, C; Ozersky, P; Pepin, K; Rock, S; Rohlfing, T; Scott, K; Schultz, B; Strong, C; Tin-Wollam, A; Yang, S-P; Waterston, RH; Wilson, RK; Rozen, S; Page, DC
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