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Integrating Genetics and Genomics to Advance Soybean Research



Williams 82 Transposable Element Database

The SoyTE database provides resources and information related to transposable elements (TEs) in the soybean genome. Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and categorized. These TE sequences have been anchored in and integrated with the soybean physical and genetic maps, and are browsable and visualizable at any scale in the sequences of the 20 soybean chromosomes.

SoyTEdb: a comprehensive database of transposable elements in the soybean genome
Jianchang Du, David Grant, Zhixi Tian, Rex T Nelson, Liucun Zhu, Randy C Shoemaker and Jianxin Ma

BMC Genomics (2010) 11:113 doi:10.1186/1471-2164-11-113

Repetitive Element Categories



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

Transposable Element Map Position Data







Transposable Element BLAST Search



   BLAST TE Database



Search and Retrieve TE sequences





  


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




    Click here for an example




    Click here for an example


















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