Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID |
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Database: bosTau4 Primary Table: nestedRepeats Row Count: 499,257
Format description: BED12+ describing joined (by ID) fragments of repeats from RepeatMasker.
field | example | SQL type | info | description |
bin | 585 | smallint | range | Indexing field to speed chromosome range queries. |
chrom | chr1 | varchar(255) | values | Chromosome (or contig, scaffold, etc.) |
chromStart | 9235 | int unsigned | range | Start position in chromosome |
chromEnd | 10107 | int unsigned | range | End position in chromosome |
name | L1MD2 | varchar(255) | values | Name of item |
score | 406 | int 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 | 9235 | int unsigned | range | for BED compatibility -- same as chromStart |
thickEnd | 10107 | int unsigned | range | for BED compatibility -- same as chromEnd |
reserved | 0 | int unsigned | range | for BED compatibility |
blockCount | 2 | int | range | Number of blocks |
blockSizes | 390,215, | longblob | | Comma separated list of block (fragment) sizes |
chromStarts | 0,657, | longblob | | Start positions relative to chromStart |
blockStrands | +,+, | longblob | | Strand of each fragment. |
id | 141621 | int unsigned | range | RepeatMasker-assigned ID used to join fragments. |
repClass | LINE | varchar(255) | values | Class of repeat |
repFamily | L1 | varchar(255) | values | Family of repeat |
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bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | blockStrands | id | repClass | repFamily |
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585 | chr1 | 9235 | 10107 | L1MD2 | 406 | + | 9235 | 10107 | 0 | 2 | 390,215, | 0,657, | +,+, | 141621 | LINE | L1 |
585 | chr1 | 14297 | 14606 | (TTATA)n | 623 | + | 14297 | 14606 | 0 | 2 | 96,180, | 0,129, | +,+, | 141632 | Simple_repeat | Simple_repeat |
585 | chr1 | 16579 | 16934 | (TA)n | 658 | + | 16579 | 16934 | 0 | 2 | 154,176, | 0,179, | +,+, | 141638 | Simple_repeat | Simple_repeat |
585 | chr1 | 19367 | 22298 | BovB | 682 | - | 19367 | 22298 | 0 | 3 | 831,1579,386, | 0,902,2545, | -,-,-, | 141647 | LINE | RTE |
585 | chr1 | 58252 | 59199 | L1_BT | 666 | - | 58252 | 59199 | 0 | 2 | 370,306, | 0,641, | -,-, | 141715 | LINE | L1 |
585 | chr1 | 69329 | 71301 | BovB | 782 | - | 69329 | 71301 | 0 | 2 | 852,1049, | 0,923, | -,-, | 141743 | LINE | RTE |
585 | chr1 | 71429 | 71874 | (TA)n | 598 | + | 71429 | 71874 | 0 | 3 | 168,84,142, | 0,199,303, | +,+,+, | 141746 | Simple_repeat | Simple_repeat |
585 | chr1 | 72836 | 73022 | (TA)n | 720 | + | 72836 | 73022 | 0 | 2 | 123,43, | 0,143, | +,+, | 141749 | Simple_repeat | Simple_repeat |
585 | chr1 | 76582 | 77728 | BovB | 599 | + | 76582 | 77728 | 0 | 2 | 117,386, | 0,760, | +,+, | 141760 | LINE | RTE |
585 | chr1 | 80734 | 81209 | L2c | 85 | + | 80734 | 81209 | 0 | 2 | 142,213, | 0,262, | +,+, | 141766 | LINE | L2 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Interrupted Rpts (nestedRepeats) Track Description |
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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 library of repeats from the
Genetic
Information Research Institute (GIRI).
RepBase is described in Jurka, J. (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, then arrows are added to the
horizontal line to indicate 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 and Green, P. RepeatMasker Open-3.0.
http://www.repeatmasker.org. 1996-2007.
RepBase is described in
Jurka J.
Repbase update: a database and an electronic journal of
repetitive elements.
Trends Genet. 2000 Sep;16(9):418-420.
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.
Smit AF. The origin of interspersed repeats in the human genome.
Curr Opin Genet Dev. 1996 Dec;6(6):743-8.
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