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Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes

Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents
2006 PLoS Computational Biology  
Citation: Suyama M, Harrington E, Bork P, Torrents D (2006) Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PLoS Comput Biol 2(6): e76.  ...  The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures.  ...  Acknowledgments The authors are grateful to all members of the Bork group for the helpful discussions. Author contributions. MS, PB, and DT conceived and designed the experiments.  ... 
doi:10.1371/journal.pcbi.0020076 pmid:16846249 pmcid:PMC1484586 fatcat:hvccxke4bjcidnmlvkx55h6bqa

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes

Mikita Suyama, Eoghan Harrington, Peer - Bork, David Torrents
2005 PLoS Computational Biology  
Citation: Suyama M, Harrington E, Bork P, Torrents D (2006) Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PLoS Comput Biol 2(6): e76.  ...  The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures.  ...  Acknowledgments The authors are grateful to all members of the Bork group for the helpful discussions. Author contributions. MS, PB, and DT conceived and designed the experiments.  ... 
doi:10.1371/journal.pcbi.0020076.eor fatcat:nb46knhulbdcjexstoks75ap4m

A Genome-Wide Survey of Human Pseudogenes

D. Torrents
2003 Genome Research  
A comparative analysis with the mouse genome showed that 70% of these pseudogenes have a retrotranspositional origin (processed), and the rest arose by segmental duplication (nonprocessed).  ...  We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide substitutions  ...  ACKNOWLEDGMENTS We thank Caroline Hadley and Patrick Aloy for manuscript revision. The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.1455503 pmid:14656963 pmcid:PMC403797 fatcat:i7r7gurxxbcnjfj3fbykxr5p4q

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

Suganthi Balasubramanian, Deyou Zheng, Yuen-Jong Liu, Gang Fang, Adam Frankish, Nicholas Carriero, Rebecca Robilotto, Philip Cayting, Mark Gerstein
2009 Genome Biology  
We report the first large-scale comparative analysis of ribosomal protein pseudogenes in four mammalian genomes (human, chimpanzee, mouse and rat).  ...  The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions.  ...  Acknowledgements SB thanks the anonymous reviewer for helpful comments and Ekta Khurana for valuable discussions. This work was funded by a grant from NIH, grant number 5U54HG004555-02.  ... 
doi:10.1186/gb-2009-10-1-r2 pmid:19123937 pmcid:PMC2687790 fatcat:mxunbpu4vrfzbnfq6yhdwnhnri

The DNA sequence of human chromosome 7

LaDeana W. Hillier, Robert S. Fulton, Lucinda A. Fulton, Tina A. Graves, Kymberlie H. Pepin, Caryn Wagner-McPherson, Dan Layman, Jason Maas, Sara Jaeger, Rebecca Walker, Kristine Wylie, Mandeep Sekhon (+95 others)
2003 Nature  
We also acknowledge the efforts of the respective staff of the Washington University Genome Sequencing Center and the University of Washington Genome Center. We thank E.  ...  Center; Joint Genome Institute; Human Genome Studies Group, Los Alamos.  ...  Virtually all pseudogenes (94%) could be aligned to another region in the human genome with higher sequence identity than to any region in the mouse genome, suggesting that they originated after the human-mouse  ... 
doi:10.1038/nature01782 pmid:12853948 fatcat:fv2z3hsqnndx5fwjf4e2um5ija

Duplication and relocation of the functional DPY19L2 gene within low copy repeats

Andrew R Carson, Joseph Cheung, Stephen W Scherer
2006 BMC Genomics  
We characterize the genomic structure and gene content of eight related LCRs on human Chromosomes 7 and 12.  ...  One of these genes, DPY19L2, is found on Chromosome 12 and is not syntenic with its mouse orthologue. Instead, the human locus syntenic to mouse Dpy19l2 contains a pseudogene, DPY19L2P1.  ...  S.W.S. is an Investigator of the Canadian Institute of Health Research and International Scholar of the Howard Hughes Medical Institute.  ... 
doi:10.1186/1471-2164-7-45 pmid:16526957 pmcid:PMC1475853 fatcat:w3aor5n23zahflybuexmlcr4pi

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity

Yuen-Jong Liu, Deyou Zheng, Suganthi Balasubramanian, Nicholas Carriero, Ekta Khurana, Rebecca Robilotto, Mark B Gerstein
2009 BMC Genomics  
We assembled the first comprehensive catalog of the processed and duplicated pseudogenes of glycolytic enzymes in many vertebrate model-organism genomes, including human, chimpanzee, mouse, rat, chicken  ...  Furthermore, the number of GAPDH pseudogenes varies significantly among the genomes we studied: none in zebrafish, pufferfish, fruitfly, and worm, 1 in chicken, 50 in chimpanzee, 62 in human, 331 in mouse  ...  Acknowledgements We would like to acknowledge financial support from grants from the NIH and from the Yale University School of Medicine Summer Research Grant.  ... 
doi:10.1186/1471-2164-10-480 pmid:19835609 pmcid:PMC2770531 fatcat:oitbgvqhtneuff2homp3i23nbm

The sequence and analysis of duplication-rich human chromosome 16

Joel Martin, Cliff Han, Laurie A. Gordon, Astrid Terry, Shyam Prabhakar, Xinwei She, Gary Xie, Uffe Hellsten, Yee Man Chan, Michael Altherr, Olivier Couronne, Andrea Aerts (+110 others)
2004 Nature  
Gordon of the University of Washington for his assistance in developing and customizing finishing tools, and T. Furey and G.  ...  for pre-publication access to the dog genome assembly; and the Washington University Genome Sequencing Center for pre-publication access to the chicken genomic assembly.  ...  Duplication analysis of chromosome 16 We performed a detailed analysis of duplicated genomic sequence ($90% sequence identity and $1 kb in length) comparing chromosome 16 against the July 2003 assembly  ... 
doi:10.1038/nature03187 pmid:15616553 fatcat:vyvlvbpo6fg4fjvaquzsfubwmy

Evolutionarily plastic regions at human 3p21.3 coincide with tumor breakpoints identified by the "elimination test"

E. Darai, M. Kost-Alimova, H. Kiss, H. Kansoul, G. Klein, S. Imreh
2005 Genomics  
Finally, all genes from these regions underwent horizontal evolution in mammals, with formation of new genes and expansion of gene families, which were displayed in the human genome as tandem gene duplications  ...  breakpoint cluster region, comparing human, mouse, and chicken genomes, suggesting a nonrandom involvement of tumor breakpoint regions in chromosome evolution.  ...  Dumanski for critically reviewing the manuscript and Gyö rgy Stuber for his contribution.  ... 
doi:10.1016/j.ygeno.2005.04.003 pmid:15913951 fatcat:vvyxllv2vzghfpibgxqjhvic5y

Pseudogenes

Yusuf Tutar
2012 Comparative and Functional Genomics  
Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA.  ...  Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called "genomic fossils" and treated as "junk DNA" several years.  ...  Tutar acknowledges the Turkish Academy of Sciences (TUBA-GEBIP).  ... 
doi:10.1155/2012/424526 pmid:22611337 pmcid:PMC3352212 fatcat:ks4u7wocvzdetfs3wkl3pctrje

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome

Clara Amid, Linda M Rehaume, Kelly L Brown, James GR Gilbert, Gordon Dougan, Robert EW Hancock, Jennifer L Harrow
2009 BMC Genomics  
Here we present the first full manual genomic annotation of the mouse defensin region on Chromosome 8 of the reference strain C57BL/6J, and the analysis of the orthologous regions of the human and rat  ...  Defensins have been studied for over two decades and their naming has become a critical issue due to incorrect identification of defensin genes derived from different mouse strains and the duplicated nature  ...  Trust, Genome BC and Genome Prairie through the "Pathogenomics of Innate Immunity" research program, and the Foundation for National Institutes of Health through the Grand Challenges in Global Health  ... 
doi:10.1186/1471-2164-10-606 pmid:20003482 pmcid:PMC2807441 fatcat:szlp5tihbbevxpwe4xcrftzaxq

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

A.-M. Mallon
2004 Genome Research  
This analysis will facilitate functional genomic analysis of Del36H and provides insights into mouse genome evolution. 4  ...  The human region is lost in some deletion syndromes and is the site of several disease loci. Heterozygous Del36H mice show numerous phenotypes and may model aspects of human genetic disease.  ...  of BACs, Stephen Keenan and Eduardo Eyras for their help with the analysis, and the Sanger Institute mouse mapping and sequencing groups.  ... 
doi:10.1101/gr.2478604 pmid:15364904 pmcid:PMC524412 fatcat:264st5chrvcznchnz2gwaholtm

CNVVdb: a database of copy number variations across vertebrate genomes

F.-C. Chen, Y.-Z. Chen, T.-J. Chuang
2009 Bioinformatics  
CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions.  ...  Additional information is also given for the genes that are included in the returned regions, including gene description, alternatively spliced transcripts, gene ontology descriptions and other biologically  ...  ACKNOWLEDGEMENTS We thank the system manager of the UCSC Genome Browser for providing Chimpanzee, Macaque, Mouse, Rat, Chicken and Stickleback self-alignments.  ... 
doi:10.1093/bioinformatics/btp166 pmid:19321736 pmcid:PMC2682513 fatcat:c4ktg7uzhjclhnf3hscn57ofzy

Update on the aldehyde dehydrogenase gene (ALDH) superfamily

Brian Jackson, Chad Brocker, David C Thompson, William Black, Konstandinos Vasiliou, Daniel W Nebert, Vasilis Vasiliou
2011 Human Genomics  
Recent improvements in DNA and protein sequencing have led to the identification of many new ALDH family members. To date, the human genome contains 19 known ALDH genes, as well as many pseudogenes.  ...  Members of the aldehyde dehydrogenase gene (ALDH) superfamily play an important role in the enzymic detoxification of endogenous and exogenous aldehydes and in the formation of molecules that are important  ...  This work was supported, in part, by the following NIH grants:  ... 
doi:10.1186/1479-7364-5-4-283 pmid:21712190 pmcid:PMC3392178 fatcat:2jo4tt57y5ejvbktho65kubxsi

The DNA sequence and comparative analysis of human chromosome 5

Jeremy Schmutz, Joel Martin, Astrid Terry, Olivier Couronne, Jane Grimwood, Steve Lowry, Laurie A. Gordon, Duncan Scott, Gary Xie, Wayne Huang, Uffe Hellsten, Mary Tran-Gyamfi (+64 others)
2004 Nature  
Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities.  ...  These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including  ...  Butler and E. Fields for technical support, D. Gordon of the University of Washington for his assistance in developing and customizing finishing tools, T. Furey and G.  ... 
doi:10.1038/nature02919 pmid:15372022 fatcat:sz2lpkgewfdofgszqb7injtsbu
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