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About Repbase Update

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 P41LM006252.

Comments and suggestions

If you have any comments or suggestions about improving Repbase or access to it, feel free to email us.

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
dcotrep.ref Other Dicot Plants
mcotrep.ref Other Monocot Plants
grasrep.ref Other Grass Plants
plnrep.ref Other Plants
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.


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