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
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)
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.
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.
Thanks to Arian Smit and GIRI
for providing the tools and repeat libraries used to generate this track.
Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
Repbase Update is described in
Repbase update: a database and an electronic journal of
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):
Smit AF. The origin of interspersed repeats in the human genome.
Curr Opin Genet Dev. 1996 Dec;6(6):743-8.