Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: DsimGB2    Primary Table: nestedRepeats    Row Count: 3,761   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(6) range
chrom CM002910varchar(255) values
chromStart 1016int(10) unsigned range
chromEnd 1664int(10) unsigned range
name HETRP_DMvarchar(255) values
score 641int(10) unsigned range
strand -char(1) values
thickStart 1016int(10) unsigned range
thickEnd 1664int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(11) range
blockSizes 139,77,longblob  
chromStarts 0,571,longblob  
blockStrands -,-,longblob  
id 3int(10) unsigned range
repClass Satellitevarchar(255) values
repFamily Satellitevarchar(255) values

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsblockStrandsidrepClassrepFamily
585CM00291010161664HETRP_DM641-1016166402139,77,0,571,-,-,3SatelliteSatellite
585CM0029101547615690RepeatScout_8916-15476156900216,12,0,202,-,-,17LTRCopia
585CM0029104219542252Helitron-N2_DBi602-42195422520220,17,0,40,-,-,31RCHelitron
586CM002910181537182027TART_DV258+1815371820270288,146,0,344,+,+,58LINEI-Jockey
586CM002910226199227808TART_DV330-22619922780802425,177,0,1432,-,-,66LINEI-Jockey
586CM002910249330249449BLASTOPIA_LTR982+2493302494490256,53,0,66,+,+,69LTRGypsy
589CM002910578906584394TART_DV392+5789065843940281,125,0,5363,+,+,90LINEI-Jockey
591CM002910851528851677DM412B_LTR876-8515288516770276,64,0,85,-,-,105LTRGypsy
593CM00291011115421111671DMLTR5883-111154211116710261,68,0,61,-,-,118LTRGypsy
594CM00291012488921249562SAR_DM286-124889212495620313,73,22,0,289,648,-,-,-,123SatelliteSatellite

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