Potential Intron Polymorphism (PIP) in TGB

    With the help of complete genomic sequence information of model plants Arabidopsis, it is possible to predict the joints between adjacent exons after splicing (or termed 'intron positions' for short) in homologous ESTs of tobacco. This would allow developing potential intron polymorphism (PIP) markers in tabacco by designing primers in exons flanking the target intron(Yang L. et al., 2007). PIP primers were designed using program ePrimer3 on a 120bp sequence, which were cut from the tobacco EST sequences with 60bp on each side of the alternative splicing joint positions .

Query PIP Database

    The PIPs can be searched by ID, PlantGDB ID, and Gene name.

PIP Summary Statistics
  N. benthamiana N. tabacum N.langsdorffii x N.sanderae N. sylvestris Total Download
No. of PIP 2,676 8,223 790 699 12,388

 

Develop PIP

    This tool finds splicing site and potential intron information, and then develops PIP markers based on the appropriate expressed sequences submitted by users.

PIP Downloads

  All of the data in our PIP database can be available in this website.


     Reference: Long Yang, Gulei Jin, Xiangqian Zhao, Yan Zheng, Zhaohua Xu and Weiren Wu. (2007) PIP: a database of potential intron polymorphism markers. Bioinformatics, 23, 2174-2177.

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