Description

Repeat Masker track from the *.rm.out.gz files delivered with the GRCh38 release. As loaded in hg38, featureBits indicates a coverage of:

1581568556 bases of 3209286105 (49.281%) in intersection

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

  1849444 SINE
  1586141 LINE
   759248 LTR
   502186 DNA
   433789 Simple_repeat
   396378 Low_complexity
    10198 Satellite
     5884 LTR?
     4595 snRNA
     4163 Retroposon
     2802 Unknown
     2157 DNA?
     2154 tRNA
     1915 rRNA
     1860 RC
     1784 srpRNA
     1397 scRNA
      822 RNA
      488 SINE?
      445 RC?

  5567850 total
The RepeatMasker.run file indicates:

The repeat files provided for this assembly were generated using RepeatMasker. 
  Smit, AFA, Hubley, R & Green, P., 
  RepeatMasker Open-3.0.
  1996-2004 .

VERSION:
RepeatMasker version open-3.3.0 , sensitive mode
run with blastp version 2.0MP-WashU [01-Jan-2006] [linux24-i786-ILP32F64 2006-01-02T05:13:21]
RepBase Update 20120418, RM database version 20120418

PARAMETERS:
RepeatMasker -engine wublast -species 'homo sapiens' -s -no_is -cutoff 255 -frag 20000

REPEATS:
RepeatMasker Database: RepeatMaskerLib.embl
Version: 20120418
Species: homo sapiens ( homo sapiens )

1327 ancestral and ubiquitous sequence(s) with a total length of 1470616 bp
9 lineage specific sequence(s) with a total length of 7404 bp
--------------------------------------------------------------------------------
1336 sequence(s) with a total length of 1478020 bp

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