Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID

Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID

Database: bosTau4 Primary Table: nestedRepeats Row Count: 499,257
Format description: BED12+ describing joined (by ID) fragments of repeats from RepeatMasker.

field	example	SQL type	info	description
`bin`	585	`smallint`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Chromosome (or contig, scaffold, etc.)
`chromStart`	9235	`int unsigned`	range	Start position in chromosome
`chromEnd`	10107	`int unsigned`	range	End position in chromosome
`name`	L1MD2	`varchar(255)`	values	Name of item
`score`	406	`int unsigned`	range	Average of fragment identity scores, transformed into 0..1000 range for shading.
`strand`	+	`char(1)`	values	+, -, or . for mixed (some fragments +, some -)
`thickStart`	9235	`int unsigned`	range	for BED compatibility -- same as chromStart
`thickEnd`	10107	`int unsigned`	range	for BED compatibility -- same as chromEnd
`reserved`	0	`int unsigned`	range	for BED compatibility
`blockCount`	2	`int`	range	Number of blocks
`blockSizes`	390,215,	`longblob`		Comma separated list of block (fragment) sizes
`chromStarts`	0,657,	`longblob`		Start positions relative to chromStart
`blockStrands`	+,+,	`longblob`		Strand of each fragment.
`id`	141621	`int unsigned`	range	RepeatMasker-assigned ID used to join fragments.
`repClass`	LINE	`varchar(255)`	values	Class of repeat
`repFamily`	L1	`varchar(255)`	values	Family of repeat

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	blockStrands	id	repClass	repFamily
585	chr1	9235	10107	L1MD2	406	+	9235	10107	2	390,215,	0,657,	+,+,	141621	LINE	L1
585	chr1	14297	14606	(TTATA)n	623	+	14297	14606	2	96,180,	0,129,	+,+,	141632	Simple_repeat	Simple_repeat
585	chr1	16579	16934	(TA)n	658	+	16579	16934	2	154,176,	0,179,	+,+,	141638	Simple_repeat	Simple_repeat
585	chr1	19367	22298	BovB	682	-	19367	22298	3	831,1579,386,	0,902,2545,	-,-,-,	141647	LINE	RTE
585	chr1	58252	59199	L1_BT	666	-	58252	59199	2	370,306,	0,641,	-,-,	141715	LINE	L1
585	chr1	69329	71301	BovB	782	-	69329	71301	2	852,1049,	0,923,	-,-,	141743	LINE	RTE
585	chr1	71429	71874	(TA)n	598	+	71429	71874	3	168,84,142,	0,199,303,	+,+,+,	141746	Simple_repeat	Simple_repeat
585	chr1	72836	73022	(TA)n	720	+	72836	73022	2	123,43,	0,143,	+,+,	141749	Simple_repeat	Simple_repeat
585	chr1	76582	77728	BovB	599	+	76582	77728	2	117,386,	0,760,	+,+,	141760	LINE	RTE
585	chr1	80734	81209	L2c	85	+	80734	81209	2	142,213,	0,262,	+,+,	141766	LINE	L2

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Interrupted Rpts (nestedRepeats) Track Description

Description

This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000) in the References section below.

The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output.

Display Conventions and Configuration

In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, then arrows are added to the horizontal line to indicate strand. In dense or squish mode, labels and arrows are omitted, and in dense mode, all items are collapsed to fit on a single row.

Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments, unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100%, and then mapped to the range 0 - 1000 for shading in the browser.

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. See the FAQ for more information.

Credits

Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track.

References

Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2007.

RepBase is described in Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420.

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6): 657-63.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8.