Repbase Update (RU) is a database of prototypic sequences representing repetitive DNA from different eukaryotic species. RU has been developed since 1990 under the direction of Jerzy Jurka (Principal Investigator), currently at Genetic Information Research Institute. RU is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).

Most prototypic sequences from RU are consensus sequences of large families and subfamilies of repeats. Smaller families are represented by sequence examples. RU describes many families of repeats unreported anywhere else. Therefore, it was referred to as an "electronic journal." Individual contributions are documented in RU version released in EMBL format. Unfortunately, RU is often used in a FASTA format which removes references to the original authors and can lead to misrepresentation. To remedy the situation, effective September 1 2001 we created a separate electronic journal, Repbase Reports, which will publish all new data to be compiled in RU. 

Acknowledgments

This project is currently supported by the NIH grant 5-P41-LM006252-10.

For more information on Repbase Update see:

• Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110:462-467
• Kapitonov, V.V., Pavlicek, A., Jurka, J. Anthology of human repetitive DNA. Encyclopedia of Molecular Cell Biology and Molecular Medicine (Vol. 1, pp. 251-305). Meyers, R.A., ed., Wiley-VCH Verlag GmbH & Co. KGaA Weinheim (2004).
• Jurka, J., Kapitonov, V.V., Smit, A.F.A. Repetitive elements: detection. Nature Encyclopedia of the Human Genome (Cooper, N.D., ed.), vol. 5, pp. 9-14, Nature Publishing Group, London, New York and Tokyo (2003)
• Jurka, J. Repetitive DNA: detection, annotation, and analysis. In Introduction to Bioinformatics: A Theoretical and Practical Approach. (Krawetz, S.A. and Womble D.D., eds), chapter 8, pp. 151-167, Humana Press, Totowa NJ (2003).
• Jurka, J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 9:418-420 (2000)
• Smit AF. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9:657-663
• Jurka, J. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8:333-337 (1998).

An example of a sequence entry to Repbase Update in EMBL format:

The following table shows the flat-file contents of Repbase Update. Users can also use our online browser interface to extract custom subsets of Repbase Update.

Name	Type of repeat families
simple.ref	Simple (macrosatellites)
humrep.ref	Human (primate)
humsub.ref	Alu (primate)
rodrep.ref	Rodent
mamrep.ref	Other mammalian
pseudo.ref	Retroposed psuedogenes
fngrep.ref	Fungi
fugrep.ref	Pufferfish
zebrep.ref	Zebrafish
zebunc.ref	Zebrafish unclassified
vrtrep.ref	Other vertebrate
celrep.ref	Caenorhabditis elegans
cinrep.ref	Ciona intestinalis
cinunc.ref	Ciona intestinalis unclassified
diarep.ref	Thalassiosira pseudonana
drorep.ref	Drosophila
angrep.ref	Anopheles gambiae
invrep.ref	Other Invertebrate (animals)
athrep.ref	Arabidopsis thaliana
oryrep.ref	Oryza sativa
plnrep.ref	Other Plant
chlrep.ref	Chlamydomonas reinhardtii
cbrrep.ref	Caenorhabditis briggsae
spurep.ref	Strongylocentrotus purpuratus
nemrep.ref	Nematostella vectensis
tmpnemrep.ref	Nematostella vectensis (includes non-annotated TEs)
tmplanrep.ref	Branchiostoma floridae (includes non-annotated TEs)
tmpxenrep.ref	Xenopus tropicalis (includes non-annotated TEs)

Subdirectory ./appendix/ contains older versions of sequences that were updated or deleted at some point.