Schema for RepeatMasker - Repeating Elements by RepeatMasker

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Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: DperCAF1 Primary Table: rmsk Row Count: 129,639 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	286	`int(10) unsigned`	range
`milliDiv`	373	`int(10) unsigned`	range
`milliDel`	17	`int(10) unsigned`	range
`milliIns`	56	`int(10) unsigned`	range
`genoName`	super_0	`varchar(255)`	values
`genoStart`	523	`int(10) unsigned`	range
`genoEnd`	792	`int(10) unsigned`	range
`genoLeft`	-11822196	`int(11)`	range
`strand`	+	`char(1)`	values
`repName`	TransibN3_DP	`varchar(255)`	values
`repClass`	DNA	`varchar(255)`	values
`repFamily`	CMC-Transib	`varchar(255)`	values
`repStart`	841	`int(11)`	range
`repEnd`	1187	`int(11)`	range
`repLeft`	-360	`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	286	373	17	56	super_0	523	792	-11822196	+	TransibN3_DP	DNA	CMC-Transib	841	1187	-360	1
585	246	175	12	26	super_0	1615	1697	-11821291	-	RepeatScout_328	Unknown	Unknown	-186	69	5	2
585	229	151	37	18	super_0	6404	6458	-11816530	+	RepeatScout_4431	Unknown	Unknown	3	57	0	3
585	403	104	184	10	super_0	6496	6583	-11816405	+	RepeatScout_3764	Unknown	Unknown	14	115	-10	4
585	359	261	24	43	super_0	8197	8361	-11814627	-	RepeatScout_2374	Unknown	Unknown	-19	250	90	5
585	242	114	0	0	super_0	19505	19540	-11803448	+	BEL-1_DPer-I	LTR	Pao	407	441	-7347	6
585	235	200	0	0	super_0	26369	26429	-11796559	+	RepeatScout_394	Unknown	Unknown	1	60	-39	7
585	374	207	31	45	super_0	29621	29789	-11793199	+	RepeatScout_5208	LTR	Gypsy	124	397	-782	8
585	286	293	74	83	super_0	30937	31179	-11791809	+	RepeatScout_3577	DNA	MULE-NOF	29	268	-13	9
585	366	261	91	50	super_0	31207	31494	-11791494	+	RepeatScout_3573	Unknown	Unknown	45	342	-130	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