To determine average conservation of X chromosome genes, we obtained Ensembl orthologs and MAFFT alignments for as many genes as possible. The conservation at every amino acid was determined using Scorecons, and the average protein conservation for each gene computed for each species. The value cited refers to a human-mouse comparison, but similar results were obtained for other species. Sequence lengths and exon information was obtained from Ensembl. Paralog comparison was based on Ensembl compara one-to-one paralogs. Brain expression of X genes was compared using data from the HugeIndex database38 and from previously published work39.
