2/1/09: major
data update;
available for hg18

1/1/09: dbRIP
relocates to Brock

8/1/06: dbRIP
available at UCSC hg17

6/22/06: dbRIP
Release 2

7/25/05: dbRIP
Release 1

5/12/05: Test Release

Other Human Variation DB

HGMD
HGVS
dbSNP
HGVbase
ALFRED

Mutation Journals

Human Mutat Mutat Res

Related Websites

Definition

Deininger: Alu insertion movie

Retrotransposons constitute over 40% of the human genome and consist of several millions of family members. They play important roles in shaping the structure and evolution of the genome and in participating in gene functioning and regulation. Since L1, Alu, and SVA retrotransposons are currently active in the human genome, their recent and ongoing retrotranspositional insertions generate a unique and important class of genetic polymorphisms (for the presence or absence of an insertion) among and within human populations. As such, they are useful genetic markers in population genetics studies due to their identical-by-descent and essentially homoplasy-free nature. Additionally, some polymorphic insertions are known to be responsible for a variety of human genetic diseases. dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs), in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. dbRIP contains all currently known Alu, L1, and SVA polymorphic insertion loci in the human genome.

Uses of dbRIP (a few examples):

• Querying Retrotransposon Insertion Polymorphisms (RIPs): Using SearchdbRIP, you may query RIPs by RIP IDs, RIP subfamily, gene context, ethnic group name, allele frequency, disease association, etc. Using Genome Gateway, you may query RIPs by genetic IDs (gene IDs, accessions, STS, etc), and chromosome locations; Using BLAT you may search RIP by DNA or protein sequences.
• Identifying RIPs associated with particular genes: to do this, you identify the gene of your interest as you normally do with the UCSC browser and then check the polymorphic RIP tracks for the presence of polymorphic insertions. By clicking on the individual RIP, you can obtain detailed information for each polymorphic locus with regard to sequences (flanking, TSDs, elements), classification, primers, disease association, location in gene context, and publications describing the polymorphism (click when RIP subfamily ID is displayed by mouse over the RIP tick) (example).
• Genome-wide browsing of RIPs: you can pick a chromosome or a particular genomic region and browse all available RIPs in this region along with other genome information provided in the UCSC genome browser.
• Verifying newly identified retrontransposon insertions: check to see whether a putatively new insertion represents a previously known polymorphic locus or is a novel polymorphic locus.
• Genome-wide view of all RIPs from one selected class or all classes (Genome plots).
• Downloading the entire set of RIP data. The downloadable files include the sequences of the elements and/or flanking regions for large scale analyses, such as studying the trend of new insertions and identifying insertions specific to a particular ethnic group, etc.

• Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20, 2006.
• Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, Aburatani H, Jones K, Redon R, Hurles M, Armengol L, Estivill X, Mural RJ, Lee C, Scherer SW, Feuk L. Genome assembly comparison identifies structural variants in the human genome. Nat Gen 38:1413-1418, 2006.
• Lindsay SJ, Khajavi M, Lupski JR, Hurles ME. A Chromosomal Rearrangement Hotspot Can Be IdentifiedA Chromosomal Rearrangement Hotspot Can Be Identified from Population Genetic Variation and Is Coincident with a Hotspot for Allelic Recombination. Am J Hum Gen 79:890-902, 2006.
• Konkel M*, Wang J*, Liang P, Batzer MA. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene 390:18-27, 2007.
• Lee, J, Cordaux R, Han K, Wang J, Hedges DJ, Batzer MA*, Liang P*. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene 390:28-38, 2007.
• Chen J, Ferec C, Cooper DN. Mechanism of Alu Integration into the human genome. Genomic Med (advanced online publication on March 28, 2007).
• Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet 23:183-191, 2007.
• Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, Anders BA,Fowlkes JD, Boissinot S, Furano AV, Ray DA, Rogers AR, Batzer MA, Jorde LB. Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions. Hum Hered 2006;62(1):30-46. Epub 2006 Sep 21.
• Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. The Diploid Genome Sequence of an Individual Human. PLoS Biol 5: e254, 2007. doi:10.1371/journal.pbio.0050254.