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SoyBase and the Soybean Breeder's Toolbox
Integrating Genetics and Molecular Biology for Soybean Researchers

Williams 82 Transposable Element Database

Repetitive Element Categories


Browse Repetitive Elements

     Click on a green value to retrieve the records for TEs in that category.

Transposable Element Map Position Data


Visualize TEs in the context of the soybean genetic map

Clicking on a chromosome or linkage group below will show the genetic map with each class of transposable element in a separate column. The Feature Options at the bottom of the page determines which TE classes are shown. Similarly the Display Options can be used to alter the map's size and other display attributes.
Linkage Group

Chromosome Number 		A1


05		A2


08		B1


11		B2


14		C1


04		C2


06		D1a


01		D1b


02		D2


17		E


15		F


13		G


18		H


12		I


20		J


16		K


09		L


19		M


07		N


03		O


10


Visualize TEs in the context of the soybean sequence map

Click on a chromosome or linkage group below to show the genomic sequence along with all classes of transposable elements. Specific classes of TEs can be also be shown separately using the check boxes at the bottom of the page.
Linkage Group

Chromosome Number 		A1


5		A2


8		B1


11		B2


14		C1


4		C2


6		D1a


1		D1b


2		D2


17		E


15		F


13		G


18		H


12		I


20		J


16		K


9		L


19		M


7		N


3		O


10



Transposable Element BLAST Search


BLAST your sequences against the TE database

Clicking on the green link below will open the SoyBase BLAST page with the G. max transposable elements already selected as the target database.
   BLAST TE Database



Search and Retrieve TE sequences


Search for TE sequences based on region


Search for a transposable element by name

   
Choose a chromosome to retrieve all TEs

Chromosomal Region Search

1. Choose a chromosome from the soybean genomic sequence  

2. Enter a chromosomal position in base pairs to search around    bp

3. Select a search window size around your position in which to search for transposable elements. For example a choice of 100 kb will result in a 200 kb window centered on the indicated chromosomal position.  

    
  OR  
1. Enter a soybean gene model name from the genomic sequence (eg. Glyma01g34110)  

2. Select a search window size around your gene-call in which to search for transposable elements. For example a choice of 100 kb will result in a window extending 100 kb from each end of the gene model.  

    



TE Bulk Download


To download All Transposable Elements as a FASTA file click the button below


    Click here for an example


To download a Summary of all Transposable Elements as a tab delimited file click the button below


    Click here for an example

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