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: DvirCAF1 Primary Table: rmsk Row Count: 178,922 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	4923	`int(10) unsigned`	range
`milliDiv`	90	`int(10) unsigned`	range
`milliDel`	5	`int(10) unsigned`	range
`milliIns`	75	`int(10) unsigned`	range
`genoName`	scaffold_0	`varchar(255)`	values
`genoStart`	5	`int(10) unsigned`	range
`genoEnd`	1616	`int(10) unsigned`	range
`genoLeft`	-2760	`int(11)`	range
`strand`	+	`char(1)`	values
`repName`	RepeatScout_361	`varchar(255)`	values
`repClass`	Unknown	`varchar(255)`	values
`repFamily`	Unknown	`varchar(255)`	values
`repStart`	1	`int(11)`	range
`repEnd`	751	`int(11)`	range
`repLeft`	-1831	`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	4923	90	5	75	scaffold_0	5	1616	-2760	+	RepeatScout_361	Unknown	Unknown	1	751	-1831	1
585	4776	91	4	107	scaffold_0	524	2452	-1924	-	Helitron-2_DVir	RC	Helitron	-8188	953	1	2
585	5502	83	2	42	scaffold_0	1870	2872	-1504	+	RepeatScout_361	Unknown	Unknown	1	549	-2033	3
585	3824	102	5	87	scaffold_0	2872	3602	-774	-	Helitron-2_DVir	RC	Helitron	-8188	953	163	4
585	4132	99	4	75	scaffold_0	3598	4375	-1	-	Helitron-2_DVir	RC	Helitron	-8188	953	4	5
585	5502	83	2	42	scaffold_0	3602	3969	-407	+	RepeatScout_361	Unknown	Unknown	550	751	-1831	3
585	595	104	51	20	scaffold_1	0	98	-4893	+	RepeatScout_1782	Unknown	Unknown	3	103	-104	6
585	283	100	0	0	scaffold_1	87	127	-4864	-	RepeatScout_4847	RC	Helitron	-34	45	6	7
585	5226	88	10	7	scaffold_1	98	1161	-3830	-	Helitron-2N1_DVir	RC	Helitron	-8188	953	162	8
585	5281	96	3	7	scaffold_1	203	2266	-2725	+	RepeatScout_361	Unknown	Unknown	1	806	-1776	9

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