Description

Repeat Masker track constructed with the usual UCSC standard cross-match alignment engine.

As loaded in hg38, featureBits indicates a coverage of:
1586326530 bases of 3209286105 (49.429%) in intersection

With the following profile of item counts in these classes of repeats:

  1852545 SINE
  1570523 LINE
   748597 LTR
   703682 Simple_repeat
   499108 DNA
   102856 Low_complexity
     7962 Satellite
     5750 Retroposon
     5667 LTR?
     5622 Unknown
     4516 snRNA
     3294 DNA?
     2026 tRNA
     1840 rRNA
     1784 RC
     1672 srpRNA
     1420 scRNA
      704 RNA
      411 RC?
       38 SINE?

  5520017 total

Display Conventions and Configuration

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

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. PMID: 10973072

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. PMID: 10607616

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846