Schema for RepeatMasker - Repeating Elements by RepeatMasker

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Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: DbipGB2 Primary Table: rmsk Row Count: 131,213 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	6437	`int(10) unsigned`	range
`milliDiv`	13	`int(10) unsigned`	range
`milliDel`	47	`int(10) unsigned`	range
`milliIns`	6	`int(10) unsigned`	range
`genoName`	AFFE02000007	`varchar(255)`	values
`genoStart`	0	`int(10) unsigned`	range
`genoEnd`	1067	`int(10) unsigned`	range
`genoLeft`	0	`int(11)`	range
`strand`	+	`char(1)`	values
`repName`	RepeatScout_4446	`varchar(255)`	values
`repClass`	Unknown	`varchar(255)`	values
`repFamily`	Unknown	`varchar(255)`	values
`repStart`	1	`int(11)`	range
`repEnd`	825	`int(11)`	range
`repLeft`	-467	`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	6437	13	47	6	AFFE02000007	0	1067	0	+	RepeatScout_4446	Unknown	Unknown	1	825	-467	1
585	1461	34	6	6	AFFE02000023	0	179	-14024	+	RepeatScout_4005	LINE	CR1	2054	2232	0	2
585	1271	152	4	117	AFFE02000023	142	449	-13754	-	Mariner-6_DK	DNA	TcMar-Tc1	-238	1399	1054	3
585	10061	40	41	8	AFFE02000023	488	1756	-12447	+	Jockey-14_DBp	LINE	I-Jockey	8	1316	-3326	4
585	4163	35	17	8	AFFE02000023	1763	2143	-12060	+	Jockey-14_DBp	LINE	I-Jockey	1570	2062	-2580	4
585	424	277	0	0	AFFE02000023	2143	2255	-11948	+	RepeatScout_4129	Unknown	Unknown	1	112	-1624	5
585	4163	35	17	8	AFFE02000023	2255	2558	-11645	+	Jockey-14_DBp	LINE	I-Jockey	2063	2458	-2184	4
585	5990	52	64	7	AFFE02000023	2569	3338	-10865	+	RepeatScout_4016	LINE	Jockey	2487	3298	-314	6
585	8313	45	25	0	AFFE02000023	3337	4344	-9859	+	Jockey-14_DBp	LINE	I-Jockey	3547	4578	-64	4
585	3681	130	32	44	AFFE02000023	4345	5029	-9174	-	Mariner-6_DK	DNA	TcMar-Tc1	-880	689	14	3

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