Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: DanaCAF1    Primary Table: rmsk    Row Count: 233,139   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
swScore 455int(10) unsigned range
milliDiv 190int(10) unsigned range
milliDel 33int(10) unsigned range
milliIns 42int(10) unsigned range
genoName scaffold_0varchar(255) values
genoStart 353int(10) unsigned range
genoEnd 474int(10) unsigned range
genoLeft -595int(11) range
strand -char(1) values
repName RepeatScout_319varchar(255) values
repClass Unknownvarchar(255) values
repFamily Unknownvarchar(255) values
repStart -10int(11) range
repEnd 120int(11) range
repLeft 1int(11) range
id 1char(1) values

Sample Rows
 
binswScoremilliDivmilliDelmilliInsgenoNamegenoStartgenoEndgenoLeftstrandrepNamerepClassrepFamilyrepStartrepEndrepLeftid
5854551903342scaffold_0353474-595-RepeatScout_319UnknownUnknown-1012011
5851403160842scaffold_0406704-365+RepeatScout_6320UnknownUnknown1227-882
58512806206scaffold_0704867-202-RepeatScout_5066UnknownUnknown-316213
5851403160842scaffold_0867975-94+RepeatScout_6320UnknownUnknown228311-42
585432138548scaffold_09631051-18-RepeatScout_5066UnknownUnknown-1184874
5851510170220scaffold_1014830-RepeatScout_7657UnknownUnknown-431115
5852534771910scaffold_10087-4427+RepeatScout_6320UnknownUnknown136-7916
585150778369scaffold_1087307-4207-RepeatScout_1893UnknownUnknown0243187
5852534771910scaffold_10307643-3871+RepeatScout_6320UnknownUnknown37176-6516
58516288490scaffold_10643869-3645-RepeatScout_1893UnknownUnknown0243168

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RepeatMasker (rmsk) Track Description
 

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, J. (2000) in the References section below.

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)
  • 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

Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-20. PMID: 10973072