Description

This track was created by using 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 (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below.

Note that this track was created using a version of RepeatMasker from Nov. 2005 along with Repbase Update 9.11. In hg18, there is also a RepMask 3.2.7 track which was created in 2009 using a newer version of RepeatMasker and Repbase Update. All of the hg18 tracks are based upon this original track and not upon the newer RepMask 3.2.7 track.

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.

A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.

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, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track.

References

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

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.