Research article
RPS4Y gene family evolution in primates
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* Corresponding author: Montserrat Bosch montse.bosch@irta.es
1 Genètica de la Conservació Animal, Institut de Recerca i Tecnologia Agroalimentàries, Crta. de Cabrils km2, 08348 Cabrils, Spain
2 Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain
3 Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
4 Departament de Genètica, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
BMC Evolutionary Biology 2008, 8:142 doi:10.1186/1471-2148-8-142
Published: 13 May 2008Additional files
Additional file 1:
Additional figure 1: Primate RPS4 protein alignment. Four different Pfam domains are marked in different colors. Nucleotide positions under positive selection in the human RPS4Y2 lineage are highlighted in red squares.
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Additional file 2:
Supplementary table 1. Samples information: INPRIMAT code, species name, sex and DNA source are given.
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Additional file 3:
Supplementary table 2. Primers designed to specifically amplify RPS4Y2 and RPS4Y1 in different primate species. Nomenclature: e.g. C1E3F1 = C1 (specific for RPS4Y copy 1), E3 (located in exon3), F (forward), and 1 (first primer designed in this location). CY means primer that amplifies both Y-linked copies. mRNAYF and mRNAYR were used to amplify the pseudogene.
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Additional file 4:
Supplementary table 3. Resulting fragments using different primer combinations. E.g. Reg1C1a = Reg1 for region 1 (intron3), C1 for copy 1, a for first fragment amplified. Nomenclature analogue for region 2 (intron6). CY means there is no Y-linked copy specificity. MgCl2 [mM] column shows the concentrations used in the experiments and TExp is the experimental annealing temperature (TD) means that PCR program included touch down cycles. Three letter code indicate the species amplified with each primer pair.
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Additional file 5:
Supplementary table 4. Accession numbers of intronic and pseudogenic sequences generated in this study. Code: Y1 for RPS4Y1, Y2 for RPS4Y2, Y for unique RPS4Y gene, and ψ for pseudogene.
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Additional file 6:
Supplementary table 5. Accession numbers of nucleotide and protein sequences used from GenBank for cDNA and protein analyses. Y1 is used for RPS4Y1, Y2 is used for RPS4Y2, and X is used for RPS4X genes.
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