Description

This track was created by using a more recent version (3.2.7, Jan. 2009) of Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence, as well as a modified version of the query sequence in which all the annotated repeats have been masked. RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka, J. (2000) in the References section below.

Results from the original RepeatMasker run have been kept in the RepeatMasker track in order to avoid disrupting any analyses performed on the original run's results.

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:

• Short interspersed nuclear elements (SINE), which include ALUs
• Long interspersed nuclear elements (LINE)
• Long terminal repeat elements (LTR), which include retroposons
• DNA repeat elements (DNA)
• Simple repeats (micro-satellites)
• Low complexity repeats
• Satellite repeats
• RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
• Other repeats, which includes class RC (Rolling Circle)
• Unknown

The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading.

Methods

UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet.

Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information.

Credits

Thanks to Arian Smit and GIRI for providing the tools and repeat libraries used to generate this track.

References

Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2007.

Repbase Update is described in Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420.

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6): 657-63.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8.