|
The first version of the Maize Repeat Database contained 485
characterized maize repeat sequences from the
TIGR Cereal
Repeat Database. To these
we added
repetitive sequences downloaded from GenBank and a file of
retrotransposon sequences
compiled by Phillip SanMiguel (Purdue University). In addition we searched our maize
genomic assemblies (AZMs) to
identify new repeats. Any sequence within an AZM that showed at least
80%
identity over a minimum stretch of 100 bp with an entry in the TIGR
Cereal
Repeat Database was coded accordingly and added to the Maize Repeat
Database.
The current version (Version 4.0) of the Maize Repeat Database is available for download. The
database exists as three separate files: “characterized repeats” (623 sequences),
uncharacterized repeats” (21,133 sequences),
and “RECON-predicted repeats” (5035 sequences).
Click below to download:
Characterized maize repeat sequences
Uncharacterized maize repeat sequences
RECON-predicted maize repeat sequences
The table below provides a breakdown of the number of sequences in each repeat
category for different versions of the Maize Repeat Database.
|
Repeat Category
|
V1.0
|
V2.0
|
V3.0
|
V4.0
|
|
Transposable
Elements
|
|
|
|
|
|
Retrotransposons
|
244
|
6,432
|
11,794
|
18,510
|
|
Transposons
|
94
|
494
|
284
|
617
|
|
MITES
|
46
|
293
|
265
|
816
|
|
Centromeric and Telomeric sequences
|
|
|
|
|
|
Centromere-related
|
34
|
166
|
158
|
353
|
|
Telomere-related
|
2
|
15
|
2
|
26
|
|
Ribosomal genes
|
21
|
253
|
139
|
273
|
|
Other repetitive
sequences
|
|
|
|
|
|
Known repetitive sequences
|
29
|
1,373
|
38
|
1,041
|
|
Unknown repetitive sequences
|
15
|
95
|
92
|
102
|
|
RECON-predicted repeats
|
0
|
0
|
0
|
5,053
|
|
Total # repeat sequences
|
485
|
9,121
|
12,772
|
26,791
|
|
