dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans

Human Mutation
Jianxin WangPing Liang

Abstract

Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. Since certain types of retrotransposons, particularly members of the Alu, L1, and SVA families, are still active, their recent and ongoing propagation generates a unique and important class of human genomic diversity/polymorphism (for the presence and absence of an insertion) with some elements known to cause genetic diseases. So far, over 2,300, 500, and 80 Alu, L1, and SVA insertions, respectively, have been reported to be polymorphic and many more are yet to be discovered. We present here the Database of Retrotransposon Insertion Polymorphisms (dbRIP; http://falcon.roswellpark.org:9090), a highly integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). dbRIP currently contains a nonredundant list of 1,625, 407, and 63 polymorphic Alu, L1, and SVA elements, respectively, or a total of 2,095 RIPs. In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along with all other genome annotation information. Users can query the database by a vari...Continue Reading

References

Jul 11, 1991·Nucleic Acids Research·M A BatzerP L Deininger
Jun 1, 1991·Current Opinion in Cell Biology·J D Boeke, K B Chapman
Oct 31, 1991·Nature·M R WallaceF S Collins
Mar 1, 1991·Genomics·M A Batzer, P L Deininger
Jul 25, 1995·Biochimica Et Biophysica Acta·S S ArcotM A Batzer
Jan 1, 1996·Journal of Molecular Evolution·M A BatzerE Zuckerkandl
Jun 1, 1996·Nature Genetics·Y MikiY Nakamura
May 1, 1997·Nature Genetics·J D Boeke
May 1, 1997·Nature Genetics·D M SassamanH H Kazazian
Aug 11, 1998·Nature Genetics·U SchwahnW Berger
Jun 25, 1999·Molecular Genetics and Metabolism·P L Deininger, M A Batzer
Feb 24, 2000·Nucleic Acids Research·E M OstertagH H Kazazian
Jun 1, 2000·Molecular Biology and Evolution·S BoissinotA V Furano
Feb 17, 2001·American Journal of Human Genetics·W S WatkinsL B Jorde
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Nov 9, 2001·Annual Review of Genetics·E M Ostertag, H H Kazazian
Apr 5, 2002·Genome Research·W James Kent
May 4, 2002·Nature Reviews. Genetics·Mark A Batzer, Prescott L Deininger
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Oct 9, 2002·Genome Research·Prescott L Deininger, Mark A Batzer
Nov 5, 2002·Nature Genetics·Eric M OstertagHaig H Kazazian
Jan 31, 2003·American Journal of Human Genetics·Michael J BamshadLynn B Jorde
Feb 19, 2003·Journal of Molecular Biology·Abdel Halim SalemMark A Batzer
Feb 26, 2003·Human Genetics·Anton BuzdinEugene Sverdlov
Mar 13, 2003·American Journal of Human Genetics·Richard M BadgeJohn V Moran
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brook BrouhaHaig H Kazazian
Jun 5, 2003·Molecular Biology and Evolution·Bethaney J VincentMark A Batzer
Aug 5, 2003·Nature Genetics·Marie DewannieuxThierry Heidmann
Nov 25, 2003·American Journal of Human Genetics·Eric M OstertagHaig H Kazazian
Mar 11, 2004·Journal of Molecular Evolution·Jinchuan XingMark A Batzer
Jun 16, 2004·Genome Research·Stéphane BoissinotAnthony V Furano
Aug 18, 2004·Journal of Molecular Biology·Anthony C OtienoMark A Batzer
Oct 30, 2004·Genetics·E Andrew BennettScott E Devine
Nov 17, 2004·Cytogenetic and Genome Research·A-H SalemM A Batzer
Dec 14, 2004·Human Genomics·Anthony B CarterMark A Batzer
Dec 21, 2004·Nucleic Acids Research·Fan HsuW James Kent
Feb 24, 2005·BMC Evolutionary Biology·Abdel-Halim SalemMark A Batzer
Aug 12, 2005·Cytogenetic and Genome Research·A BuzdinE Sverdlov

❮ Previous
Next ❯

Citations

Aug 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mateusz JanickiGuojun Yang
Feb 25, 2010·European Journal of Human Genetics : EJHG·Ilgar Z MamedovYury B Lebedev
Nov 1, 2011·Nature·J Kenneth BaillieGeoffrey J Faulkner
Oct 30, 2012·Nature·George R YoungGeorge Kassiotis
May 26, 2011·Nucleic Acids Research·Kamal Rawal, Ram Ramaswamy
Oct 7, 2008·Genome Research·E Andrew BennettScott E Devine
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
May 15, 2009·Genome Research·Jinchuan XingLynn B Jorde
Oct 29, 2010·Genome Research·Adam D Ewing, Haig H Kazazian
Dec 7, 2010·Genome Research·Fereydoun HormozdiariEvan E Eichler
Nov 4, 2011·Genome Research·Fereydoun HormozdiariS Cenk Sahinalp
Jun 30, 2012·Science·Eunjung LeeUNKNOWN Cancer Genome Atlas Research Network
May 2, 2012·BMC Bioinformatics·Jón Ingi Sveinbjörnsson, Bjarni V Halldórsson
Mar 29, 2008·BMC Evolutionary Biology·Uberto PozzoliManuela Sironi
Nov 18, 2009·BMC Genomics·David J WitherspoonLynn B Jorde
Jul 2, 2010·BMC Genomics·David J WitherspoonLynn B Jorde
Dec 22, 2011·BMC Genomics·Alexandre de AndradeMarcelo B Soares
Sep 24, 2009·Genome Biology·Sanjida H RangwalaHaig H Kazazian
May 17, 2011·PLoS Computational Biology·Ying ZhangDixie L Mager
Aug 31, 2011·PLoS Genetics·Chip StewartUNKNOWN 1000 Genomes Project
Aug 8, 2013·Nucleic Acids Research·Matei DavidMichael Brudno
Sep 18, 2014·BMC Genomics·Jiantao WuGabor T Marth
May 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Alexandre KuhnWilliam F Burkholder
Aug 2, 2011·Annual Review of Genomics and Human Genetics·Christine R BeckJohn V Moran
Apr 12, 2011·FEBS Letters·Geoffrey J Faulkner
Oct 17, 2008·Genomic Medicine·Jian-Min ChenDavid N Cooper
Dec 1, 2009·Trends in Genetics : TIG·John S MattickGeoffrey J Faulkner
Feb 24, 2016·ELife·Gilad D EvronyChristopher A Walsh
Mar 3, 2007·Trends in Genetics : TIG·Ryan E MillsScott E Devine
Mar 19, 2016·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Guia GuffantiFabio Macciardi
Mar 4, 2014·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Guia GuffantiFabio Macciardi

❮ Previous
Next ❯

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