Schema for RepeatMasker - Repeating Elements by RepeatMasker

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: DgriCAF1 Primary Table: rmsk Row Count: 204,216 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	17951	`int(10) unsigned`	range
`milliDiv`	10	`int(10) unsigned`	range
`milliDel`	1	`int(10) unsigned`	range
`milliIns`	0	`int(10) unsigned`	range
`genoName`	scaffold_0	`varchar(255)`	values
`genoStart`	4	`int(10) unsigned`	range
`genoEnd`	1966	`int(10) unsigned`	range
`genoLeft`	-2204	`int(11)`	range
`strand`	-	`char(1)`	values
`repName`	Copia-1_DGri-I	`varchar(255)`	values
`repClass`	LTR	`varchar(255)`	values
`repFamily`	Copia	`varchar(255)`	values
`repStart`	0	`int(11)`	range
`repEnd`	4126	`int(11)`	range
`repLeft`	2164	`int(11)`	range
`id`	1	`char(1)`	values

Sample Rows

bin	swScore	milliDiv	milliDel	milliIns	genoName	genoStart	genoEnd	genoLeft	strand	repName	repClass	repFamily	repStart	repEnd	repLeft	id
585	17951	10	1	0	scaffold_0	4	1966	-2204	-	Copia-1_DGri-I	LTR	Copia	0	4126	2164	1
585	3500	13	0	3	scaffold_0	1957	2345	-1825	-	RepeatScout_1283	LTR	Copia	-781	1108	722	2
585	10063	65	31	4	scaffold_0	2340	4170	0	+	RepeatScout_1351	LTR	Gypsy	1261	3188	-2530	3
585	14223	21	14	38	scaffold_1	0	2759	0	+	RepeatScout_5	RC	Helitron	1	2204	0	4
585	15688	25	19	30	scaffold_10	0	2250	0	+	RepeatScout_5	RC	Helitron	1	2188	-16	5
585	10405	149	52	38	scaffold_1000	8	2355	-100	+	Gypsy-5_DGri-I	LTR	Gypsy	79	2937	-4724	6
585	685	41	0	31	scaffold_1000	2355	2455	0	+	RepeatScout_37	LINE	LOA	1	97	-4398	7
585	9663	43	26	13	scaffold_10000	0	1211	-5103	+	RepeatScout_33	LINE	Jockey	249	1474	-683	8
585	9074	44	36	5	scaffold_10000	1093	2805	-3509	+	RepeatScout_44	LINE	I-Jockey	1	1423	0	9
585	18221	37	6	3	scaffold_10000	1954	5425	-889	+	RepeatScout_60	LINE	Jockey	1	2126	0	1

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