S1 Appendix - Did Androgen-Binding Protein Paralogs Undergo Neo- and/or Subfunctionalization as the Abp Gene Region Expanded in the Mouse Genome?

Contains the following files: S1 File. Primer sets used in this study. S2 File. Additional details of Methods. S3 File. Guide trees used in the CODEML analyses (see also Table 2). S4 File. List of all 64 Abp paralogs with GenBank accession numbers and coordinates. S5 File. Two-dimensional (2D) gel separations of mouse tear proteins. The first dimension was isoelectric focusing (IEF) and the second dimension was SDS gel electrophoresis (SDS). A separation of male tear proteins is shown at the top and a separation of female tear proteins is shown at the bottom. The four red rectangles in each gel cover the likely IEF and SDS ranges and the top and bottom flanking pieces marked M5 (or F5) and M6 (or F6) covered the remaining protein staining regions. All six pieces of each gel were excised and analyzed in LC-MS/MS. S6 File. Coverage of transcripts and peptides used to identify ABPA subunits in mouse tears. Also shown are a24 and a27 transcripts lacking protein sequences. Transcript sequences identified from cDNA are translated into protein sequence shown in green lowercase typeface. Residues shaded green are individually diagnostic for the paralog in question; those shaded in red are diagnostic as a haplotype. S7 File. Coverage of transcripts and peptides used to identify ABPBG subunits in mouse tears. Also shown are bg26 and bg27 transcripts lacking protein sequences. Transcript sequences identified in PCR from cDNA libraries are translated into protein sequence shown in green lowercase typeface. Residues shaded green are individually diagnostic for the paralog in question; those shaded in red are diagnostic as a haplotype. S8 File. Putative pseudogenes listed by clade and categorized by their changes. Four paralogs (bg3, bg10, bg15 and bg17) are highlighted in green because we identify transcript and protein sequences. S9 File. Data from qPCR analyses. S10 File. Ka/Ks analysis of Abpa and Abpbg transcript coding regions. (PDF)