Supplementary Information

Supplementary Information for

Hughes, J.F., Skaletsky, H., Pyntikova, T., Minx, P.J., Graves, T., Rozen, S.,
Wilson, R.K., Page, D.C.
Conservation of Y-linked genes during human evolution revealed
by comparative sequencing in chimpanzee. Nature 437, 100-103 (2005)

Figures

Dot-plot analysis of human and chimpanzee sequence
5-Mb inversion mediated by ERV-ERV recombination in chimpanzee lineage
1.5-Mb inversion mediated by recombination between 6 bp inverted repeats in human lineage
Insights into inversions on Y chromosomes gleaned from comparison to the X chromosome
Sequence-based map of chimpanzee X-degenerate sequence
RT-PCR analysis of chimpanzee X-degenerate genes
Comparison of USP9Y gene structures in human and chimpanzee
TMSB4Y: conservation of peptide in human and splice site mutation in chimpanzee
Estimation of gap sizes by fiber-FISH analysis

Tables

Repetitive elements in X-degenerate sequences
Lineage-specific repetitive element integrations
Human-chimpanzee nucleotide substitution rates in coding sequences and introns of X-degenerate genes and pseudogenes
RT-PCR primers and expected product sizes
GenBank accession numbers for chimpanzee cDNA sequences
GenBank accession numbers for chimpanzee BAC and fosmid clones
dot_plot.pl
self_dot_plot.pl

Sequence Files

Supplementary File 1: Chimpanzee X-degenerate sequence contig (10 Mb file)

Supplementary Information for

Figures

Tables

Sequence Files

Alignments