Schema for RepeatMasker - Repeating Elements by RepeatMasker

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Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: DyakCAF1 Primary Table: rmsk Row Count: 103,484 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	2401	`int(10) unsigned`	range
`milliDiv`	205	`int(10) unsigned`	range
`milliDel`	77	`int(10) unsigned`	range
`milliIns`	6	`int(10) unsigned`	range
`genoName`	chr2L	`varchar(255)`	values
`genoStart`	658	`int(10) unsigned`	range
`genoEnd`	1647	`int(10) unsigned`	range
`genoLeft`	-22322805	`int(11)`	range
`strand`	-	`char(1)`	values
`repName`	RepeatScout_4418	`varchar(255)`	values
`repClass`	LTR	`varchar(255)`	values
`repFamily`	Gypsy	`varchar(255)`	values
`repStart`	-4	`int(11)`	range
`repEnd`	628	`int(11)`	range
`repLeft`	1	`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	2401	205	77	6	chr2L	658	1647	-22322805	-	RepeatScout_4418	LTR	Gypsy	-4	628	1	1
585	2100	82	35	78	chr2L	1659	2063	-22322389	-	Gypsy-21_DY-I	LTR	Gypsy	-9	9262	8742	1
585	1957	75	111	53	chr2L	2110	2477	-22321975	-	Gypsy-21_DY-I	LTR	Gypsy	-31	9240	8742	2
585	2138	65	32	82	chr2L	2524	2914	-22321538	-	Gypsy-21_DY-I	LTR	Gypsy	-31	9240	8742	3
585	2212	73	26	63	chr2L	2961	3372	-22321080	-	Gypsy-21_DY-I	LTR	Gypsy	-31	9240	8742	4
585	340	211	8	140	chr2L	5544	5665	-22318787	+	RepeatScout_783	Satellite	Satellite	792	898	-121	5
585	584	211	11	85	chr2L	5712	5888	-22318564	+	RepeatScout_783	Satellite	Satellite	792	955	-64	5
585	455	213	39	47	chr2L	6177	6391	-22318061	-	DNAREP1_DM	RC	Helitron	-271	323	112	6
585	243	246	0	0	chr2L	7412	7477	-22316975	-	RepeatScout_4198	RC	Helitron	-191	1315	1251	7
585	254	272	21	21	chr2L	8357	8451	-22316001	-	Helitron-N2_DEl	RC	Helitron	-499	95	2	8

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