Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: hg19 Primary Table: rmsk Row Count: 5,298,130
Format description: RepeatMasker .out record

field	example	SQL type	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`swScore`	1504	`int(10) unsigned`	Smith Waterman alignment score
`milliDiv`	13	`int(10) unsigned`	Base mismatches in parts per thousand
`milliDel`	4	`int(10) unsigned`	Bases deleted in parts per thousand
`milliIns`	13	`int(10) unsigned`	Bases inserted in parts per thousand
`genoName`	chr1	`varchar(255)`	Genomic sequence name
`genoStart`	10000	`int(10) unsigned`	Start in genomic sequence
`genoEnd`	10468	`int(10) unsigned`	End in genomic sequence
`genoLeft`	-249240153	`int(11)`	-#bases after match in genomic sequence
`strand`	+	`char(1)`	Relative orientation + or -
`repName`	(CCCTAA)n	`varchar(255)`	Name of repeat
`repClass`	Simple_repeat	`varchar(255)`	Class of repeat
`repFamily`	Simple_repeat	`varchar(255)`	Family of repeat
`repStart`	1	`int(11)`	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	463	`int(11)`	End in repeat sequence
`repLeft`	0	`int(11)`	-#bases after match (if strand is +) or start (if strand is -) in repeat sequence
`id`	1	`char(1)`	First digit of id field in RepeatMasker .out file. Best ignored.

bin	swScore	milliDiv	milliDel	milliIns	genoName	genoStart	genoEnd	genoLeft	strand	repName	repClass	repFamily	repStart	repEnd	repLeft	id
585	1504	13	4	13	chr1	10000	10468	-249240153	+	(CCCTAA)n	Simple_repeat	Simple_repeat	1	463	0	1
585	3612	114	270	13	chr1	10468	11447	-249239174	-	TAR1	Satellite	telo	-399	1712	483	2
585	437	235	186	35	chr1	11503	11675	-249238946	-	L1MC	LINE	L1	-2236	5646	5449	3
585	239	294	19	10	chr1	11677	11780	-249238841	-	MER5B	DNA	hAT-Charlie	-74	104	1	4
585	318	230	38	0	chr1	15264	15355	-249235266	-	MIR3	SINE	MIR	-119	143	49	5
585	203	162	0	0	chr1	16712	16749	-249233872	+	(TGG)n	Simple_repeat	Simple_repeat	1	37	0	6
585	239	338	148	0	chr1	18906	19048	-249231573	+	L2a	LINE	L2	2942	3104	-322	7
585	652	346	85	42	chr1	19947	20405	-249230216	+	L3	LINE	CR1	3042	3519	-970	8
585	270	331	7	27	chr1	20530	20679	-249229942	+	Plat_L3	LINE	CR1	2802	2947	-639	9
585	254	279	47	39	chr1	21948	22075	-249228546	+	MLT1K	LTR	ERVL-MaLR	15	142	-453	1

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

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 library of repeats from the Genetic Information Research Institute (GIRI). RepBase 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, 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.

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

Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2007.

RepBase is described in Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420.

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.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8.