Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: dm6    Primary Table: nestedRepeats    Row Count: 8,390
fieldexampleSQL type info
bin 585smallint(6) range
chrom chr2Lvarchar(255) values
chromStart 312int(10) unsigned range
chromEnd 612int(10) unsigned range
name HETRP_DMvarchar(255) values
score 347int(10) unsigned range
strand +char(1) values
thickStart 312int(10) unsigned range
thickEnd 612int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(11) range
blockSizes 96,156,longblob  
chromStarts 0,144,longblob  
blockStrands +,+,longblob  
id 2int(10) unsigned range
repClass Satellitevarchar(255) values
repFamily Satellitevarchar(255) values

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsblockStrandsidrepClassrepFamily
585chr2L312612HETRP_DM347+3126120296,156,0,144,+,+,2SatelliteSatellite
585chr2L7701070HETRP_DM347+77010700296,156,0,144,+,+,3SatelliteSatellite
585chr2L12281528HETRP_DM347+122815280296,156,0,144,+,+,4SatelliteSatellite
585chr2L16861986HETRP_DM347+168619860296,156,0,144,+,+,5SatelliteSatellite
585chr2L21442444HETRP_DM347+214424440296,156,0,144,+,+,6SatelliteSatellite
585chr2L26022902HETRP_DM347+260229020296,156,0,144,+,+,7SatelliteSatellite
585chr2L30603360HETRP_DM347+306033600296,156,0,144,+,+,8SatelliteSatellite
585chr2L35183818HETRP_DM347+351838180296,156,0,144,+,+,9SatelliteSatellite
585chr2L39764276HETRP_DM347+397642760296,156,0,144,+,+,10SatelliteSatellite
585chr2L44344734HETRP_DM347+443447340296,156,0,144,+,+,11SatelliteSatellite

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