Schema for RepeatMasker - Repeating Elements by RepeatMasker

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Schema for RepeatMasker - Repeating Elements by RepeatMasker

Database: DbiaGB2 Primary Table: rmsk Row Count: 137,501 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`swScore`	2481	`int(10) unsigned`	range
`milliDiv`	127	`int(10) unsigned`	range
`milliDel`	0	`int(10) unsigned`	range
`milliIns`	0	`int(10) unsigned`	range
`genoName`	AFFD02000001	`varchar(255)`	values
`genoStart`	0	`int(10) unsigned`	range
`genoEnd`	379	`int(10) unsigned`	range
`genoLeft`	-1175	`int(11)`	range
`strand`	-	`char(1)`	values
`repName`	Gypsy-26_DPse-I	`varchar(255)`	values
`repClass`	LTR	`varchar(255)`	values
`repFamily`	Gypsy	`varchar(255)`	values
`repStart`	-4496	`int(11)`	range
`repEnd`	1609	`int(11)`	range
`repLeft`	1231	`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	2481	127	0	0	AFFD02000001	0	379	-1175	-	Gypsy-26_DPse-I	LTR	Gypsy	-4496	1609	1231	1
585	669	162	239	0	AFFD02000001	372	539	-1015	-	RepeatScout_4183	LTR	Gypsy	-93	653	447	2
585	1123	142	41	6	AFFD02000001	507	751	-803	-	Gypsy-28_DBp-I	LTR	Gypsy	-1168	5301	5095	3
585	2522	168	117	1	AFFD02000001	737	1554	0	-	Gypsy-28_DBp-I	LTR	Gypsy	-1576	4538	3620	3
585	2445	57	86	26	AFFD02000006	0	362	-760	-	RepeatScout_361	LTR	Gypsy	-429	383	1	4
585	2260	54	127	0	AFFD02000006	362	433	-689	-	RepeatScout_4806	Unknown	Unknown	-245	111	1	5
585	2992	69	73	2	AFFD02000006	433	849	-273	+	RepeatScout_152	Unknown	Unknown	1	412	0	6
585	1385	109	10	5	AFFD02000006	693	895	-227	-	RepeatScout_2681	LTR	Gypsy	-16	341	139	7
585	2595	56	98	3	AFFD02000006	764	1122	0	-	RepeatScout_349	Unknown	Unknown	0	561	170	8
585	559	176	32	8	AFFD02000007	0	126	-2261	-	RepeatScout_279	RC	Helitron	-84	151	23	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