E. Balakirev and F. Ayala, Pseudogenes: Are They ???Junk??? or Functional DNA?, Annual Review of Genetics, vol.37, issue.1, pp.123-151, 2003.
DOI : 10.1146/annurev.genet.37.040103.103949

D. Zheng and M. Gerstein, The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?, Trends in Genetics, vol.23, issue.5, pp.219-224, 2007.
DOI : 10.1016/j.tig.2007.03.003

B. Pei, C. Sisu, A. Frankish, C. Howald, L. Habegger et al., The GENCODE pseudogene resource, Genome Biology, vol.13, issue.9, p.51
DOI : 10.1016/j.cell.2007.05.009

L. Poliseno, Pseudogenes: Newly Discovered Players in Human Cancer, Science Signaling, vol.5, issue.242, p.5
DOI : 10.1126/scisignal.2002858

M. Mcenteeg, O. Brienk, . Benlarbin, O. Loscherc, . Fagainc et al., The former annotated human pseudogene dihydrofolate reductase-like 1 (DHFRL1) is expressed and functional, Proceedings of the National Academy of Sciences, vol.108, issue.37, pp.15157-15162, 2011.
DOI : 10.1073/pnas.1103605108

J. Mccarrey and K. Thomas, Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene, Nature, vol.326, issue.6112, pp.501-505, 1987.
DOI : 10.1038/326501a0

H. Pai, R. Kommaddi, S. Chinta, T. Mori, M. Boyd et al., Aframeshift mutation and alternate splicing in human brain generate a functional form of the pseudogene cytochrome P4502D7 that demethylates codeine to morphine, pp.27927383-27389

J. Zhang, X. Wang, M. Li, J. Han, C. B. Wang et al., NANOGP8 is a retrogene expressed in cancers, FEBS Journal, vol.22, issue.8, pp.2731723-1730, 2006.
DOI : 10.1006/abio.1976.9999

C. Sun, O. Orozco, D. Olson, E. Choi, E. Garber et al., CRIPTO3, a presumed pseudogene, is expressed in cancer, Biochemical and Biophysical Research Communications, vol.377, issue.1, pp.215-220, 2008.
DOI : 10.1016/j.bbrc.2008.09.113

K. Takahashi, K. Mitsui, and S. Yamanaka, Role of ERas in promoting tumour-like properties in mouse embryonic stem cells, Nature, vol.423, issue.6939, pp.423541-545, 2003.
DOI : 10.1038/nature01646

J. Rohozinski, C. Edwards, and M. Anderson, Does expression of the retrogene UTP14c in the ovary pre-dispose women to ovarian cancer? Med Hypotheses, pp.446-449, 2012.

M. Zou, E. Baitei, A. Alzahrani, F. Mohanna, N. Farid et al., Oncogenic Activation of MAP Kinase by BRAF Pseudogene in Thyroid Tumors, Neoplasia, vol.11, issue.1, pp.57-65, 2009.
DOI : 10.1593/neo.81044

H. Kaessmann, N. Vinckenbosch, and M. Long, RNA-based gene duplication: mechanistic and evolutionary insights, Nature Reviews Genetics, vol.24, issue.1, pp.19-31, 2009.
DOI : 10.1038/nrg2487
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690669

E. Chiefari, S. Iiritano, F. Paonessa, L. Pera, I. Arcidiacono et al., Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes, Nature Communications, vol.8, issue.4, p.40, 2010.
DOI : 10.1038/ncomms1040

V. Costa, R. Esposito, M. Aprile, and A. Ciccodicola, Non-coding RNA and pseudogenes in neurodegenerative diseases: ???The (un)Usual Suspects???, Frontiers in Genetics, vol.3, p.231
DOI : 10.3389/fgene.2012.00231

A. Depaoli-roach, Synergistic phosphorylation and activation of ATP-Mg-dependent phosphoprotein phosphatase by F A/GSK-3 and casein kinase II (PC0.7), J Biol Chem, issue.19, pp.25912144-12152, 1984.

A. Aitken, C. Holmes, D. Campbell, T. Resink, P. Cohen et al., Amino acid sequence at the site on protein phosphatase inhibitor-2

C. Holmes, J. Kuret, A. Chisholm, and P. Cohen, Identification of the sites on rabbit skeletal muscle protein phosphatase inhibitor-2 phosphorylated by casein kinase-II, Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, vol.870, issue.3, pp.408-416, 1986.
DOI : 10.1016/0167-4838(86)90248-7

Q. Wang, K. Guan, P. Roach, and A. Depaoli-roach, Phosphorylation and Activation of the ATP-Mg-dependent Protein Phosphatase by the Mitogen-activated Protein Kinase, Journal of Biological Chemistry, vol.270, issue.31, pp.18352-18358, 1995.
DOI : 10.1074/jbc.270.31.18352

F. Puntoni and E. Villamoruzzi, Phosphorylation of the Inhibitor-2 of Protein Phosphatase-1 by cdc2-Cyclin B and GSK3, Biochemical and Biophysical Research Communications, vol.207, issue.2, pp.732-739, 1995.
DOI : 10.1006/bbrc.1995.1248

A. Agarwal-mawal and H. Paudel, Neuronal Cdc2-like Protein Kinase (Cdk5/p25) Is Associated with Protein Phosphatase 1 and Phosphorylates Inhibitor-2, Journal of Biological Chemistry, vol.276, issue.26
DOI : 10.1074/jbc.M010002200

U. Kirchhefer, H. Baba, P. Bokník, K. Breeden, N. Mavila et al., Enhanced cardiac function in mice overexpressing protein phosphatase Inhibitor-2, Cardiovascular Research, vol.68, issue.1, pp.98-108, 2005.
DOI : 10.1016/j.cardiores.2005.05.019

M. Yamada, Y. Ikeda, M. Yano, K. Yoshimura, S. Nishino et al., Inhibition of protein phosphatase 1 by inhibitor-2 gene delivery ameliorates heart failure progression in genetic cardiomyopathy, The FASEB Journal, vol.20, issue.8, pp.201197-1199, 2006.
DOI : 10.1096/fj.05-5299fje

N. Brüchert, N. Mavila, P. Boknik, H. Baba, L. Fabritz et al., Inhibitor-2 prevents protein phosphatase 1-induced cardiac hypertrophy and mortality, AJP: Heart and Circulatory Physiology, vol.295, issue.4, pp.1539-1546, 2008.
DOI : 10.1152/ajpheart.00515.2008

M. Eto, R. Bock, D. Brautigan, and D. Linden, Cerebellar Long-Term Synaptic Depression Requires PKC-Mediated Activation of CPI-17, a Myosin/Moesin Phosphatase Inhibitor, Neuron, vol.36, issue.6, pp.1145-1158, 2002.
DOI : 10.1016/S0896-6273(02)01107-8

C. Leach, S. Shenolikar, and D. Brautigan, Phosphorylation of Phosphatase Inhibitor-2 at Centrosomes during Mitosis, Journal of Biological Chemistry, vol.278, issue.28, pp.26015-26020, 2003.
DOI : 10.1074/jbc.M300782200

D. Satinover, C. Leach, P. Stukenberg, and D. Brautigan, Activation of Aurora-A kinase by protein phosphatase inhibitor-2, a bifunctional signaling protein, Proceedings of the National Academy of Sciences, vol.101, issue.23, pp.8625-8630, 2004.
DOI : 10.1073/pnas.0402966101

W. Wang, P. Stukenberg, and D. Brautigan, Phosphatase Inhibitor-2 Balances Protein Phosphatase 1 and Aurora B Kinase for Chromosome Segregation and Cytokinesis in Human Retinal Epithelial Cells, Molecular Biology of the Cell, vol.19, issue.11, pp.4852-4862, 2008.
DOI : 10.1091/mbc.E08-05-0460

A. Khandani, M. Mohtashami, and A. Camirand, Abstract, Cellular and Molecular Biology Letters, vol.16, issue.4, pp.669-688, 2011.
DOI : 10.2478/s11658-011-0030-z

C. Zambrano, J. Egaña, M. Núñez, R. Maccioni, and C. González-billault, Oxidative stress promotes ?? dephosphorylation in neuronal cells: the roles of cdk5 and PP1, Free Radical Biology and Medicine, vol.36, issue.11, pp.361393-1402, 2004.
DOI : 10.1016/j.freeradbiomed.2004.03.007

S. Vijayaraghavan, D. Stephens, K. Trautman, G. Smith, B. Khatra et al., Sperm Motility Development in the Epididymis is Associated with Decreased Glycogen Synthase Kinase-3 and Protein Phosphatase 1 Activity1, Biology of Reproduction, vol.54, issue.3, pp.709-718, 1996.
DOI : 10.1095/biolreprod54.3.709

G. Smith, D. Wolf, K. Trautman, C. Da, E. Silva et al., Primate Sperm Contain Protein Phosphatase 1, a Biochemical Mediator of Motility1, Biology of Reproduction, vol.54, issue.3, pp.719-727, 1996.
DOI : 10.1095/biolreprod54.3.719

H. Ceulemans, W. Stalmans, and M. Bollen, Regulator-driven functional diversification of protein phosphatase-1 in eukaryotic evolution, BioEssays, vol.387, issue.4, pp.371-381, 2002.
DOI : 10.1002/bies.10069

M. Li, D. Satinover, and D. Brautigan, Phosphorylation and Functions of Inhibitor-2 Family of Proteins, Biochemistry, vol.46, issue.9, pp.2380-2389, 2007.
DOI : 10.1021/bi602369m

J. Maestre, T. Tchenio, O. Dhellin, and T. Heidmann, mRNA retroposition in human cells: processed pseudogene formation, EMBO J, vol.14, issue.24, pp.6333-6338, 1995.

A. Weiner, P. Deininger, and A. Efstratiadis, Nonviral Retroposons: Genes, Pseudogenes, and Transposable Elements Generated by the Reverse Flow of Genetic Information, Annual Review of Biochemistry, vol.55, issue.1, pp.631-661, 1986.
DOI : 10.1146/annurev.bi.55.070186.003215

I. Wu and M. Moses, Cloning of a cDNA Encoding an Isoform of Human Protein Phosphatase Inhibitor 2 from Vascularized Breast Tumor, DNA Sequence, vol.16, issue.1, pp.515-518, 2001.
DOI : 10.3109/10425170109041335

Y. Yamada, H. Watanabe, F. Miura, H. Soejima, M. Uchiyama et al., A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q, Genome Research, vol.14, issue.2, pp.247-266, 2004.
DOI : 10.1101/gr.1351604

D. Gerhard, L. Wagner, E. Feingold, C. Shenmen, L. Grouse et al., The status, quality, and expansion of the NIH full-length cDNA project: the mammalian gene collection (MGC), Genome Res, issue.10B, pp.142121-2127, 2004.

T. Eilon and I. Barash, Distinct gene-expression profiles characterize mammary tumors developed in transgenic mice expressing constitutively active and C-terminally truncated variants of STAT5, BMC Genomics, vol.10, issue.1, p.231, 2009.
DOI : 10.1186/1471-2164-10-231

M. Fardilha, S. Esteves, L. Korrodi-gregório, A. Vintém, S. Domingues et al., Identification of the human testis protein phosphatase 1 interactome, Biochemical Pharmacology, vol.82, issue.10, pp.821403-1415, 2011.
DOI : 10.1016/j.bcp.2011.02.018

W. Murphy, E. Eizirik, O. Brien, S. Madsen, O. Scally et al., Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics, Science, vol.294, issue.5550, pp.2942348-2351, 2001.
DOI : 10.1126/science.1067179

M. Fardilha, S. Esteves, L. Korrodi-gregório, S. Pelech, C. Da et al., Protein phosphatase 1 complexes modulate sperm motility and present novel targets for male infertility, Molecular Human Reproduction, vol.17, issue.8, pp.17466-477, 2011.
DOI : 10.1093/molehr/gar004

V. Mayya and D. Han, Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations, Expert Review of Proteomics, vol.6, issue.6, pp.605-618, 2009.
DOI : 10.1586/epr.09.84

S. Gauci, A. Helbig, M. Slijper, J. Krijgsveld, A. Heck et al., Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach, Analytical Chemistry, vol.81, issue.11, pp.814493-4501, 2009.
DOI : 10.1021/ac9004309

L. Korrodi-gregorio, M. Ferreira, A. Vintem, W. Wu, T. Muller et al., Identification and characterization of two distinct PPP1R2 isoforms in human spermatozoa, BMC Cell Biology, vol.14, issue.1, p.15, 2013.
DOI : 10.1186/1471-2121-14-15

S. Esteves, S. Domingues, C. Da, O. Silva, M. Fardilha et al., Protein phosphatase 1alpha interacting proteins in the human brain, OMICS, vol.2012, issue.1612, pp.3-17

S. Montgomery, M. Sammeth, M. Gutierrez-arcelus, R. Lach, C. Ingle et al., Transcriptome genetics using second generation sequencing in a Caucasian population, Nature, vol.4, issue.7289, pp.464773-777, 2010.
DOI : 10.1038/nature08903

K. Ohshima, M. Hattori, T. Yada, T. Gojobori, Y. Sakaki et al., Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

K. Kleene, E. Mulligan, D. Steiger, K. Donohue, and M. Mastrangelo, The Mouse Gene Encoding the Testis-Specific Isoform of Poly(A) Binding Protein (Pabp2) Is an Expressed Retroposon: Intimations That Gene Expression in Spermatogenic Cells Facilitates the Creation of New Genes, Journal of Molecular Evolution, vol.47, issue.3, pp.47275-281, 1998.
DOI : 10.1007/PL00006385

A. Marques, I. Dupanloup, N. Vinckenbosch, A. Reymond, and H. Kaessmann, Emergence of Young Human Genes after a Burst of Retroposition in Primates, PLoS Biology, vol.22, issue.11, p.357, 2005.
DOI : 10.1371/journal.pbio.0030357.st001

C. Huang, W. Lin, C. Chang, and K. Choo, Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences, BMC Molecular Biology, vol.10, issue.1, p.74, 2009.
DOI : 10.1186/1471-2199-10-74

T. Hurley, Y. J. Zhang, L. Goodwin, K. Zou, Q. et al., Structural Basis for Regulation of Protein Phosphatase 1 by Inhibitor-2, Journal of Biological Chemistry, vol.282, issue.39, pp.28228874-28883, 2007.
DOI : 10.1074/jbc.M703472200

J. Yang, T. Hurley, and A. Depaoli-roach, Interaction of inhibitor-2 with the catalytic subunit of type 1 protein phosphatase, J Biol Chem, issue.30, pp.27522635-22644, 2000.

S. Varmuza, A. Jurisicova, K. Okano, J. Hudson, K. Boekelheide et al., Spermiogenesis Is Impaired in Mice Bearing a Targeted Mutation in the Protein Phosphatase 1c?? Gene, Developmental Biology, vol.205, issue.1, pp.98-110, 1999.
DOI : 10.1006/dbio.1998.9100

R. Chakrabarti, L. Cheng, P. Puri, D. Soler, and S. Vijayaraghavan, Protein phosphatase PP1?2 in sperm morphogenesis and epididymal initiation of sperm motility, Asian Journal of Andrology, vol.9, issue.4, pp.445-452, 2007.
DOI : 10.1111/j.1745-7262.2007.00307.x

N. Vinckenbosch, I. Dupanloup, and H. Kaessmann, Evolutionary fate of retroposed gene copies in the human genome, Proceedings of the National Academy of Sciences, vol.103, issue.9, pp.3220-3225, 2006.
DOI : 10.1073/pnas.0511307103

A. Khachane and P. Harrison, Assessing the genomic evidence for conserved transcribed pseudogenes under selection, BMC Genomics, vol.10, issue.1, p.435, 2009.
DOI : 10.1186/1471-2164-10-435

D. Torgerson and R. Singh, Enhanced adaptive evolution of sperm-expressed genes on the mammalian X chromosome, Heredity, vol.21, issue.1, pp.39-44, 2006.
DOI : 10.1038/sj.hdy.6800749

S. Dorus, E. Wasbrough, J. Busby, E. Wilkin, and T. Karr, Sperm Proteomics Reveals Intensified Selection on Mouse Sperm Membrane and Acrosome Genes, Molecular Biology and Evolution, vol.27, issue.6, pp.1235-1246, 2010.
DOI : 10.1093/molbev/msq007

A. Pandita, A. Balasubramaniam, R. Perrin, P. Shannon, and A. Guha, Malignant and benign ganglioglioma: A pathological and molecular study, Neuro-Oncology, vol.9, issue.2, pp.124-134, 2007.
DOI : 10.1215/15228517-2006-029

R. Pink, K. Wicks, D. Caley, E. Punch, L. Jacobs et al., Pseudogenes: Pseudo-functional or key regulators in health and disease?, RNA, vol.17, issue.5, pp.792-798, 2011.
DOI : 10.1261/rna.2658311

T. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp Ser, vol.41, pp.95-98, 1999.

D. Zwickl, Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, Dissertation, 2006.

D. Swofford and . Paup-*, phylogenetic analysis using parsimony (*and other methods) version 4, 2003.

S. Hedges, J. Dudley, and S. Kumar, TimeTree: a public knowledge-base of divergence times among organisms, Bioinformatics, vol.22, issue.23, pp.2971-2972, 2006.
DOI : 10.1093/bioinformatics/btl505

A. Poon, S. Frost, and S. Pond, Detecting Signatures of Selection from DNA Sequences Using Datamonkey, Methods Mol Biol, vol.537, pp.163-183, 2009.
DOI : 10.1007/978-1-59745-251-9_8

S. Pond and S. Frost, Datamonkey: rapid detection of selective pressure on individual sites of codon alignments, Bioinformatics, vol.21, issue.10, pp.2531-2533, 2005.
DOI : 10.1093/bioinformatics/bti320

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

Z. Yang, R. Nielsen, N. Goldman, and A. Pedersen, Codon-substitution models for heterogeneous selection pressure at amino acid sites, Genetics, vol.155, issue.1, pp.431-449, 2000.

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.282731-2739, 2011.
DOI : 10.1093/molbev/msr121

D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, A. Reymond et al., Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution, Genome Research, vol.17, issue.6
DOI : 10.1101/gr.5586307

H. Thiele, J. Glandorf, and P. Hufnagel, Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction, J Integr Bioinform, vol.7, issue.1, p.141, 2010.

D. Perkins, D. Pappin, D. Creasy, and J. Cottrell, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, vol.447, issue.18, pp.3551-3567, 1999.
DOI : 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

. Korrodi-gregório, Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes, BMC Evolutionary Biology, vol.13, issue.1, p.242, 2013.
DOI : 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2