An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution

citation_journal_title=Genes Dev; citation_title=The Drosophila segmentation gene runt encodes a novel nuclear regulatory protein that is also expressed in the developing nervous system; citation_author=MA Kania, AS Bonner, JB Duffy, JP Gergen; citation_volume=4; citation_publication_date=1990; citation_pages=1701-1713; citation_doi=10.1101/gad.4.10.1701; citation_id=CR1 citation_journal_title=Cell Biol Int; citation_title=Runx transcription factors and the developmental balance between cell proliferation and differentiation; citation_author=JA Coffman; citation_volume=27; citation_publication_date=2003; citation_pages=315–324; citation_doi=10.1016/S1065-6995(03)00018-0; citation_id=CR2 citation_journal_title=Genomics; citation_title=AML1, AML2, and AML3, the human members of the runt domain gene-family: cDNA structure, expression, and chromosomal localization; citation_author=D Levanon, V Negreanu, Y Bernstein, I Bar-Am, L Avivi, Y Groner; citation_volume=23; citation_publication_date=1994; citation_pages=425-432; citation_doi=10.1006/geno.1994.1519; citation_id=CR3 citation_journal_title=Proc Natl Acad Sci U S A; citation_title=PEBP2/PEA2 represents a family of transcription factors homologous to the products of the Drosophila runt gene and the human AML1 gene; citation_author=E Ogawa, M Maruyama, H Kagoshima, M Inuzuka, J Lu, M Satake, K Shigesada, Y Ito; citation_volume=90; citation_publication_date=1993; citation_pages=6859-6863; citation_doi=10.1073/pnas.90.14.6859; citation_id=CR4 citation_journal_title=Proc Natl Acad Sci U S A; citation_title=Expression of the human acute myeloid leukemia gene AML1 is regulated by two promoter regions; citation_author=MC Ghozi, Y Bernstein, V Negreanu, D Levanon, Y Groner; citation_volume=93; citation_publication_date=1996; citation_pages=1935-1940; citation_doi=10.1073/pnas.93.5.1935; citation_id=CR5 citation_journal_title=Gene; citation_title=The RUNX3 gene - sequence, structure and regulated expression; citation_author=C Bangsow, N Rubins, G Glusman, Y Bernstein, V Negreanu, D Goldenberg, J Lotem, E Ben-Asher, D Lancet, D Levanon, Y Groner; citation_volume=279; citation_publication_date=2001; citation_pages=221-232; citation_doi=10.1016/S0378-1119(01)00760-0; citation_id=CR6 citation_journal_title=Gene; citation_title=Identification and comparative analysis of a second runx3 promoter; citation_author=D Rini, F Calabi; citation_volume=273; citation_publication_date=2001; citation_pages=13-22; citation_doi=10.1016/S0378-1119(01)00579-0; citation_id=CR7 citation_journal_title=Gene; citation_title=Architecture and anatomy of the genomic locus encoding the human leukemia-associated transcription factor RUNX1/AML1; citation_author=D Levanon, G Glusman, T Bangsow, E Ben-Asher, DA Male, N Avidan, C Bangsow, M Hattori, TD Taylor, S Taudien, K Blechschmidt, N Shimizu, A Rosenthal, Y Sakaki, D Lancet, Y Groner; citation_volume=262; citation_publication_date=2001; citation_pages=23-33; citation_doi=10.1016/S0378-1119(00)00532-1; citation_id=CR8 citation_journal_title=Nucleic Acids Res; citation_title=Alternative splicing and genomic structure of the AML1 gene involved in acute myeloid leukemia; citation_author=H Miyoshi, M Ohira, K Shimizu, K Mitani, H Hirai, T Imai, K Yokoyama, E Soeda, M Ohki; citation_volume=23; citation_publication_date=1995; citation_pages=2762-2769; citation_doi=10.1093/nar/23.14.2762; citation_id=CR9 citation_journal_title=Embo J; citation_title=The Runx3 transcription factor regulates development and survival of TrkC dorsal root ganglia neurons; citation_author=D Levanon, D Bettoun, C Harris-Cerruti, E Woolf, V Negreanu, R Eilam, Y Bernstein, D Goldenberg, C Xiao, M Fliegauf, E Kremer, F Otto, O Brenner, A Lev-Tov, Y Groner; citation_volume=21; citation_publication_date=2002; citation_pages=3454-3463; citation_doi=10.1093/emboj/cdf370; citation_id=CR10 citation_journal_title=Proc Natl Acad Sci U S A; citation_title=Proviral insertions induce the expression of bone-specific isoforms of PEBP2alphaA (CBFA1): evidence for a new myc collaborating oncogene; citation_author=M Stewart, A Terry, M Hu, M O'Hara, K Blyth, E Baxter, ER Cameron, DE Onions, JC Neil; citation_volume=94; citation_publication_date=1997; citation_pages=8646-8651; citation_doi=10.1073/pnas.94.16.8646; citation_id=CR11 citation_journal_title=Development; citation_title=A Xenopus homologue of aml-1 reveals unexpected patterning mechanisms leading to the formation of embryonic blood; citation_author=WDJ Tracey, ME Pepling, ME Horb, GH Thomsen, JP Gergen; citation_volume=125; citation_publication_date=1998; citation_pages=1371-1380; citation_id=CR12 citation_journal_title=Gene; citation_title=Genomic characterization of the RUNX2 gene of Fugu rubripes; citation_author=JH Eggers, M Stock, M Fliegauf, B Vonderstrass, F Otto; citation_volume=291; citation_publication_date=2002; citation_pages=159-167; citation_doi=10.1016/S0378-1119(02)00592-9; citation_id=CR13 citation_journal_title=BMC Evolutionary Biology; citation_title=The evolution of runx genes I. A comparative study of sequences from phylogenetically diverse model organisms; citation_author=J Rennert, JA Coffman, AR Mushegian, AJ Robertson; citation_volume=3; citation_publication_date=2003; citation_pages=4; citation_doi=10.1186/1471-2148-3-4; citation_id=CR14 citation_journal_title=Genes Dev; citation_title=Patterning of cells in the Drosophila eye by Lozenge, which shares homologous domains with AML1; citation_author=A Daga, CA Karlovich, K Dumstrei, U Banerjee; citation_volume=10; citation_publication_date=1996; citation_pages=1194-1205; citation_doi=10.1101/gad.10.10.1194; citation_id=CR15 citation_journal_title=Gene; citation_title=cDNA cloning of run, a Caenorhabditis elegans Runt domain encoding gene; citation_author=SC Bae, J Lee; citation_volume=241; citation_publication_date=2000; citation_pages=255-258; citation_doi=10.1016/S0378-1119(99)00488-6; citation_id=CR16 citation_journal_title=Dev Comp Immunol; citation_title=A single amphioxus and sea urchin runt-gene suggests that runt-gene duplications occurred in early chordate evolution.; citation_author=S Stricker, AJ Poustka, U Wiecha, A Stiege, J Hecht, G Panopoulou, A Vilcinskas, S Mundlos, V Seitz; citation_volume=27; citation_publication_date=2003; citation_pages=673-684; citation_doi=10.1016/S0145-305X(03)00037-5; citation_id=CR17 citation_journal_title=Mammalian Genome; citation_title=Segmental paralogy in the human genome: a large-scale triplication on 1p, 6p, and 21q; citation_author=P Strippoli, P D'Addabbo, L Lenzi, S Giannone, S Canaider, R Casadei, L Vitale, P Carinci, M Zannotti; citation_volume=13; citation_publication_date=2002; citation_pages=456-462; citation_doi=10.1007/s00335-001-2157-0; citation_id=CR18 citation_journal_title=Mol Cell Biol; citation_title=Expression pattern, regulation, and biological role of runt domain transcription factor, run, in Caenorhabditis elegans; citation_author=S Nam, YH Jin, QL Li, KY Lee, GB Jeong, Y Ito, J Lee, SC Bae; citation_volume=22; citation_publication_date=2002; citation_pages=547-554; citation_doi=10.1128/MCB.22.2.547-554.2002; citation_id=CR19 citation_journal_title=Bioinformatics; citation_title=GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses; citation_author=G Glusman, D Lancet; citation_volume=16; citation_publication_date=2000; citation_pages=482-483; citation_doi=10.1093/bioinformatics/16.5.482; citation_id=CR20 citation_journal_title=J Mol Biol; citation_title=The RUNX1 Runt domain at 1.25A resolution: a structural switch and specifically bound chloride ions modulate DNA binding; citation_author=S Backstrom, M Wolf-Watz, C Grundstrom, T Hard, T Grundstrom, UH Sauer; citation_volume=322; citation_publication_date=2002; citation_pages=259-272; citation_doi=10.1016/S0022-2836(02)00702-7; citation_id=CR21 citation_journal_title=Genomics; citation_title=Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H); citation_author=J Yu, JM Madison, S Mundlos, F Winston, BR Olsen; citation_volume=53; citation_publication_date=1998; citation_pages=90-96; citation_doi=10.1006/geno.1998.5500; citation_id=CR22 Tetraodon Genome Browser. [ http://www.genoscope.cns.fr/externe/tetraodon ] Zebrafish assembly 6 download. [ ftp://ftp.ensembl.org/pub/traces/zebrafish/assembly/assembly06 ] citation_journal_title=Gene Expr Patterns; citation_title=Duplicate zebrafish runx2 orthologues are expressed in developing skeletal elements; citation_author=MV Flores, VW Tsang, W Hu, M Kalev-Zylinska, J Postlethwait, P Crosier, K Crosier, S Fisher; citation_volume=4; citation_publication_date=2004; citation_pages=573-581; citation_doi=10.1016/j.modgep.2004.01.016; citation_id=CR25 citation_journal_title=Gene; citation_title=Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes; citation_author=Y Van de Peer, T Frickey, JS Taylor, A Meyer; citation_volume=295; citation_publication_date=2002; citation_pages=205-211; citation_doi=10.1016/S0378-1119(02)00689-3; citation_id=CR26 citation_journal_title=Genome Res; citation_title=Four-hundred million years of conserved synteny of human Xp and Xq genes on three Tetraodon chromosomes; citation_author=F Grutzner, HR Crollius, G Lutjens, O Jaillon, J Weissenbach, HH Ropers, T Haaf; citation_volume=12; citation_publication_date=2002; citation_pages=1316-1322; citation_doi=10.1101/gr.222402; citation_id=CR27 citation_journal_title=Genomics; citation_title=Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse; citation_author=LG Lundin; citation_volume=16; citation_publication_date=1993; citation_pages=1-19; citation_doi=10.1006/geno.1993.1133; citation_id=CR28 citation_journal_title=J Mol Evol; citation_title=Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish; citation_author=B Angers, K Gharbi, A Estoup; citation_volume=54; citation_publication_date=2002; citation_pages=501-510; citation_doi=10.1007/s00239-001-0041-x; citation_id=CR29 citation_journal_title=Oncogene; citation_title=Structure and regulated expression of mammalian RUNX genes; citation_author=D Levanon, Y Groner; citation_volume=23; citation_publication_date=2004; citation_pages=4211-4219; citation_doi=10.1038/sj.onc.1207670; citation_id=CR30 citation_journal_title=Genomics; citation_title=Comparison of DNA sequences with protein sequences; citation_author=WR Pearson, T Wood, Z Zhang, W Miller; citation_volume=46; citation_publication_date=1997; citation_pages=24-36; citation_doi=10.1006/geno.1997.4995; citation_id=CR31 JGI Fugu v3.0 Download. [ http://genome.jgi-psf.org/fugu6/fugu6.download.ftp.html ] citation_journal_title=Science; citation_title=Whole genome shotgun assembly and analysis of the genome of Fugu rubripes; citation_author=S Aparicio, J Chapman, E Stupka, N Putnam, JM Chia, PS Dehal, A Christoffels, S Rash, S Hoon, AFA Smit, MD Gelpke, J Roach, T Oh, IY Ho, M Wong, C Detter, F Verhoef, P Predki, A Tay, S Lucas, S Richardson, S Smith, M Clark, Y Edwards, N Doggett, A Zharkikh, SV Tavtigian, D Pruss, M Barnstead, C Evans, H Baden, J Powell, G Glusman, L Rowen, L Hood, YH Tan, G Elgar, T Hawkins, B Venkatesh, D Rokhsar, S Brenner; citation_volume=297; citation_publication_date=2002; citation_pages=1301-1310; citation_doi=10.1126/science.1072104; citation_id=CR33 citation_journal_title=IEEE Eng Med Biol Mag; citation_title=Visualizing large-scale genomic sequences; citation_author=G Glusman, D Lancet; citation_volume=20; citation_publication_date=2001; citation_pages=49-54; citation_doi=10.1109/51.940046; citation_id=CR34 JGI Xenopus download. [ http://genome.jgi-psf.org/pub/JGI_data/Frog ] JGI Ciona v.1. [ http://genome.jgi-psf.org/ciona4/ciona4.download.ftp.html ] JGI Fugu v3.0 BLAST. [ http://aluminum.jgi-psf.org/prod/bin/blast.fugu6.cgi ] citation_journal_title=Genome Res; citation_title=Base-calling of automated sequencer traces using phred. II. Error probabilities.; citation_author=B Ewing, P Green; citation_volume=8; citation_publication_date=1998; citation_pages=186-194; citation_doi=10.1101/gr.8.3.186; citation_id=CR38 citation_journal_title=Methods Enzymol; citation_title=Using CLUSTAL for multiple sequence alignments; citation_author=DG Higgins, JD Thompson, TJ Gibson; citation_volume=266; citation_publication_date=1996; citation_pages=383-402; citation_doi=10.1016/S0076-6879(96)66024-8; citation_id=CR39 citation_journal_title=Mol Biol Evol; citation_title=The neighbor-joining method: a new method for reconstructing phylogenetic trees; citation_author=N Saitou, M Nei; citation_volume=4; citation_publication_date=1987; citation_pages=406-425; citation_id=CR40 citation_journal_title=Comput Appl Biosci; citation_title=TreeView: an application to display phylogenetic trees on personal computers; citation_author=RD Page; citation_volume=12; citation_publication_date=1996; citation_pages=357-358; citation_id=CR41 citation_journal_title=Proc Natl Acad Sci U S A; citation_title=Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammals; citation_author=S Brenner, B Venkatesh, WH Yap, CF Chou, A Tay, S Ponniah, Y Wang, YH Tan; citation_volume=99; citation_publication_date=2002; citation_pages=2936-2941; citation_doi=10.1073/pnas.032680599; citation_id=CR42