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Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes
2006
PLoS Computational Biology
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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
2005
PLoS Computational Biology
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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
2003
Genome Research
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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
2009
Genome Biology
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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
2003
Nature
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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
2006
BMC Genomics
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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
2009
BMC Genomics
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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
2004
Nature
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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"
2005
Genomics
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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
2012
Comparative and Functional Genomics
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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
2009
BMC Genomics
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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
2004
Genome Research
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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
2009
Bioinformatics
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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
2011
Human Genomics
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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
2004
Nature
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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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