Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: cerSim1    Primary Table: nestedRepeats    Row Count: 376,386   Data last updated: 2012-08-28
Format description: BED12+ describing joined (by ID) fragments of repeats from RepeatMasker
fieldexampleSQL type info description
bin 585smallint(6) range Indexing field to speed chromosome range queries.
chrom AKZM01053786varchar(255) values Chromosome (or contig, scaffold, etc.)
chromStart 19535int(10) unsigned range Start position in chromosome
chromEnd 21450int(10) unsigned range End position in chromosome
name L1M3varchar(255) values Name of item
score 644int(10) 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 19535int(10) unsigned range for BED compatibility -- same as chromStart
thickEnd 21450int(10) unsigned range for BED compatibility -- same as chromEnd
reserved 0int(10) unsigned range for BED compatibility
blockCount 2int(11) range Number of blocks
blockSizes 909,753,longblob   Comma separated list of block (fragment) sizes
chromStarts 0,1162,longblob   Start positions relative to chromStart
blockStrands +,+,longblob   Strand of each fragment
id 3097145int(10) unsigned range RepeatMasker-assigned ID used to join fragments
repClass LINEvarchar(255) values Class of repeat
repFamily L1varchar(255) values Family of repeat

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsblockStrandsidrepClassrepFamily
585AKZM010537861953521450L1M3644+195352145002909,753,0,1162,+,+,3097145LINEL1
585AKZM010537863847639756L2a100-38476397560472,187,155,148,0,206,582,1132,-,-,-,-,3097159LINEL2
585AKZM010537866074361438L1MA9485-607436143802125,144,0,551,-,-,3097177LINEL1
585AKZM010537866483266505MLT1G3376+648326650503148,875,565,0,221,1108,+,+,+,3097181LTRERVL-MaLR
585AKZM010537867018471164L2b105+701847116402687,277,0,703,+,+,3097190LINEL2
585AKZM0105412860766654MARNA146-607666540262,210,0,368,-,-,3098883DNATcMar-Mariner
585AKZM010541281436914937L1ME4b177-143691493702438,130,0,438,-,-,3098891LINEL1
585AKZM010541281587617751L1M5234-158761775102854,71,0,1804,-,-,3098893LINEL1
585AKZM0105413761327035L1ME3G263-6132703502141,215,0,688,-,-,3099315LINEL1
585AKZM010541372076321691L2b253+20763216910271,78,0,850,+,+,3099335LINEL2

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 Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (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, arrows are added to the horizontal line to indicate the 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, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Repbase Update is described in:

Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072

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. PMID: 10607616

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846