Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: canFam3    Primary Table: rmsk    Row Count: 4,769,557   Data last updated: 2012-01-06
Format description: RepeatMasker .out record
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
swScore 6094int(10) unsigned Smith Waterman alignment score
milliDiv 84int(10) unsigned Base mismatches in parts per thousand
milliDel 8int(10) unsigned Bases deleted in parts per thousand
milliIns 3int(10) unsigned Bases inserted in parts per thousand
genoName chr1varchar(255) Genomic sequence name
genoStart 100int(10) unsigned Start in genomic sequence
genoEnd 11597int(10) unsigned End in genomic sequence
genoLeft -122667188int(11) -#bases after match in genomic sequence
strand -char(1) Relative orientation + or -
repName Bsvarchar(255) Name of repeat
repClass Satellitevarchar(255) Class of repeat
repFamily Satellitevarchar(255) Family of repeat
repStart -86int(11) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd 11551int(11) End in repeat sequence
repLeft 1int(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
58560948483chr110011597-122667188-BsSatelliteSatellite-861155111
585148158046chr11159711794-122666991-SINEC_CfSINEtRNA-Lys-118812
5854257162349chr11179412493-122666292-BsSatelliteSatellite-55471613
5853203102080chr11318413683-122665102+CfERV1z_LTRLTRERV1145904
5852162374141chr11468414807-122663978+(CACCC)nSimple_repeatSimple_repeat312505
58540826526chr11619616703-122662082-CfERV1a_LTRLTRERV1-250516
5851725756320chr11670417517-122661268-CfERV1-intLTRERV10591951396
585158227330chr11751717700-122661085-SINEC_CfSINEtRNA-Lys018917
5851725756320chr11770019136-122659649-CfERV1-intLTRERV1-781513837096
58527386280chr11913019484-122659301-CfERV1-intLTRERV1-4131178814326

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