Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: mm39    Primary Table: rmsk    Row Count: 5,320,771   Data last updated: 2020-07-30
Format description: RepeatMasker .out record
fieldexampleSQL type description
bin 608smallint(5) unsigned Indexing field to speed chromosome range queries.
swScore 3667int(10) unsigned Smith Waterman alignment score
milliDiv 67int(10) unsigned Base mismatches in parts per thousand
milliDel 0int(10) unsigned Bases deleted in parts per thousand
milliIns 10int(10) unsigned Bases inserted in parts per thousand
genoName chr1varchar(255) Genomic sequence name
genoStart 3050293int(10) unsigned Start in genomic sequence
genoEnd 3050775int(10) unsigned End in genomic sequence
genoLeft -192103504int(11) -#bases after match in genomic sequence
strand +char(1) Relative orientation + or -
repName L1MdA_VIvarchar(255) Name of repeat
repClass LINEvarchar(255) Class of repeat
repFamily L1varchar(255) Family of repeat
repStart 6094int(11) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd 6570int(11) End in repeat sequence
repLeft -6int(11) -#bases after match (if strand is +) or start (if strand is -) in repeat sequence
id 1char(1) First digit of id field in RepeatMasker .out file. Best ignored.

Sample Rows
 
binswScoremilliDivmilliDelmilliInsgenoNamegenoStartgenoEndgenoLeftstrandrepNamerepClassrepFamilyrepStartrepEndrepLeftid
608366767010chr130502933050775-192103504+L1MdA_VILINEL160946570-61
6082422652239chr130510443051146-192103133-ID2SINEID-4810452
60813116067chr130511593051191-192103088+(TGCT)nSimple_repeatSimple_repeat13003
60830328911236chr130512313051371-192102908+Tigger9aDNATcMar-Tigger88239-4934
60857929311722chr130518073051992-192102287+Tigger5b_GlireDNATcMar-Tigger39243-1105
6083852573442chr130521013052219-192102060+PB1D10SINEAlu111706
60816107032chr130528613052893-192101386+(TATCAA)nSimple_repeatSimple_repeat13107
60824731200chr130539353054012-192100267-L1MC4LINEL1-797724571698
60816242786535chr130540383054829-192099450-L1MB4LINEL1-30615053359
60866000chr130548303054886-192099393+(AC)nSimple_repeatSimple_repeat15601

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 (2000) in the References section below. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our "makeDb/doc/" directory.

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)
  • 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.

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

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