Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: DyakCAF1    Primary Table: nestedRepeats    Row Count: 8,885   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(6) range
chrom chr2Lvarchar(255) values
chromStart 658int(10) unsigned range
chromEnd 2063int(10) unsigned range
name RepeatScout_4418varchar(255) values
score 517int(10) unsigned range
strand -char(1) values
thickStart 658int(10) unsigned range
thickEnd 2063int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(11) range
blockSizes 989,404,longblob  
chromStarts 0,1001,longblob  
blockStrands -,-,longblob  
id 1int(10) unsigned range
repClass LTRvarchar(255) values
repFamily Gypsyvarchar(255) values

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsblockStrandsidrepClassrepFamily
585chr2L6582063RepeatScout_4418517-658206302989,404,0,1001,-,-,1LTRGypsy
585chr2L55445888RepeatScout_783334+5544588802121,176,0,168,+,+,5SatelliteSatellite
585chr2L1331322325DNAREP1_DSim329-133132232502196,356,0,8656,-,-,12RCHelitron
586chr2L163743163924RepeatScout_4429418-1637431639240244,43,0,138,-,-,39RCHelitron
586chr2L232483234840TART_DV273-2324832348400316,112,159,0,159,2198,-,-,-,57LINEI-Jockey
587chr2L316512316707RepeatScout_544380-31651231670702123,31,0,164,-,-,68DNACMC-EnSpm
588chr2L442369442529R1A_DAn316-4423694425290225,48,0,112,-,-,85LINER1
589chr2L527908528144RepeatScout_4284335+5279085281440273,125,0,111,+,+,95SatelliteSatellite
589chr2L624384624565P_DG242-6243846245650246,35,0,146,-,-,107DNAP
592chr2L10077401008003Gypsy8-I_Dpse577+100774010080030255,59,0,204,+,+,152LTRGypsy

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