Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: DsimGB2    Primary Table: rmsk    Row Count: 50,292   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
swScore 1312int(10) unsigned range
milliDiv 81int(10) unsigned range
milliDel 51int(10) unsigned range
milliIns 0int(10) unsigned range
genoName CM002910varchar(255) values
genoStart 0int(10) unsigned range
genoEnd 197int(10) unsigned range
genoLeft -23539334int(11) range
strand -char(1) values
repName RepeatScout_2varchar(255) values
repClass RCvarchar(255) values
repFamily Helitronvarchar(255) values
repStart -80int(11) range
repEnd 279int(11) range
repLeft 73int(11) range
id 1char(1) values

Sample Rows
 
binswScoremilliDivmilliDelmilliInsgenoNamegenoStartgenoEndgenoLeftstrandrepNamerepClassrepFamilyrepStartrepEndrepLeftid
585131281510CM0029100197-23539334-RepeatScout_2RCHelitron-80279731
585507159297CM002910313452-23539079-HETRP_DMSatelliteSatellite-78210909492
5854971533614CM00291010161155-23538376-HETRP_DMSatelliteSatellite-78210909493
58538515600CM00291015871664-23537867-HETRP_DMSatelliteSatellite-177993173
5854921614120CM00291019402086-23537445-HETRP_DMSatelliteSatellite-25184716994
58511821407CM00291020762221-23537310+RepeatScout_122DNAMULE-NOF1144-355
585112115613358CM00291022212500-23537031+FB4_DMDNATcMar-Tc11697-33926
5851124135730CM00291025312822-23536709-FB4_DMDNATcMar-Tc1-307810116837
5853111412009CM00291031253244-23536287-DNAREP1_DSimRCHelitron-2384543368
58511132431082CM00291032473701-23535830+Gypsy-11_DTa-ILTRGypsy54655966-219

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