Supplementary Information for

Hughes, J.F., Skaletsky, H., Pyntikova, T., Graves, T., Minx, P.J., Fulton, R.S.,
McGrath, S.D., Warren, W.C., Locke, D.P., Mardis, E.R., van Daalen, S.K.M.,
Repping, S., Friedman, C., Trask, B.J., Rozen, S., Wilson, R.K., Page, D.C.

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.

Notes

Supplementary notes

Figures

  • Figure 1     Annotated sequence of the chimpanzee MSY
  • Figure 2     Positions of informative sequence family variants (SFVs) along chimpanzee ampliconic sequnce
  • Figure 3-1  Extended metaphase FISH analysis to place and orient contigs 1-5     Figure legend
  • Figure 3-2     Figure legend
  • Figure 3-3     Figure legend
  • Figure 3-4     Figure legend
  • Figure 4      Two-color interphase FISH results
  • Figure 5-1      Confirmation of copy number of amplicons by interphase FISH analysis
  • Figure 5-2      Confirmation of copy number of amplicons by interphase FISH analysis
  • Figure 6      Positions of chimpanzee MSY genes
  • Figure 7      RT-PCR analysis of chimpanzee ampliconic genes
  • Figure 8      Dot-plot comparison of chimpanzee and human MSY sequences
  • Figure 10     Intervals alignable to human sequence on the chimpanzee MSY
  • Figure 11     Triangular dot plot of ampliconic portion of the chimpanzee MSY
  • Figure 12     Electronic fractination of chimpanzee and human MSY sequences
  • Figure 13     Dot plot and percent divergence analysis of tandem palindrome array
  • Figure 14     Positions of chimpanzee endogenous retroviruses (CERVs) on chimpanzee MSY

    Tables

  • Table 1.     BAC (CHORI-251) and fosmid (CHORI-1251) clones
  • Table 2.     Sequence characteristics and repeat content of chimpanzee and human MSY sequences
  • Table 3.     Comparative analysis of chimpanzee and human ampliconic genes
  • Table 4.     Pseudogenes on the chimpanzee MSY
  • Table 5.     Primers for RT-PCR analysis of chimpanzee ampliconic genes

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