Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: DbiaGB2    Primary Table: nestedRepeats    Row Count: 11,474   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(6) range
chrom AFFD02000001varchar(255) values
chromStart 507int(10) unsigned range
chromEnd 1554int(10) unsigned range
name Gypsy-28_DBp-Ivarchar(255) values
score 525int(10) unsigned range
strand -char(1) values
thickStart 507int(10) unsigned range
thickEnd 1554int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(11) range
blockSizes 244,803,longblob  
chromStarts 0,244,longblob  
blockStrands -,-,longblob  
id 3int(10) unsigned range
repClass LTRvarchar(255) values
repFamily Gypsyvarchar(255) values

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsblockStrandsidrepClassrepFamily
585AFFD020000015071554Gypsy-28_DBp-I525-507155402244,803,0,244,-,-,3LTRGypsy
585AFFD020000071412387RepeatScout_1548417-141238702202,515,0,1731,-,-,11RCHelitron
585AFFD020000236721150CR1-12_DTa398-672115002112,350,0,128,-,-,35LINECR1
585AFFD020000396751067RepeatScout_4388298-675106702137,86,0,306,-,-,53UnknownUnknown
585AFFD02000046230548RepeatScout_4943684-23054802129,73,0,245,-,-,62UnknownUnknown
585AFFD020000537081053RepeatScout_4240262+708105302151,166,0,179,+,+,77UnknownUnknown
585AFFD02000064428631RepeatScout_1657516-42863103118,45,40,0,118,163,-,-,-,87UnknownUnknown
585AFFD0200006820092599Gypsy-4_DKi-I244-2009259903213,219,88,0,240,502,-,-,-,98LTRGypsy
585AFFD0200007328623274RepeatScout_30517-2862327402332,80,0,332,-,-,106LTRGypsy
585AFFD0200007337493886RepeatScout_297540+374938860220,56,0,81,+,+,107LTRPao

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