Welcome to PolyA_DB, a web resource for analysis of pre-mRNA cleavage and polyadenylation sites (polyA sites)

 


PolyA site databases

PolyA_DB 1

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PolyA_DB version 1 contains human and mouse polyA sites mapped by cDNA/EST sequences.

Reference: Zhang H, Hu J, Recce M, Tian B. (2005). PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. 33:D116-20.
PolyA_DB 2

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PolyA_DB version 2 contains polyA sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are also available.

Reference: Lee JY, Yeh I, Park JY, Tian B. (2007). PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 35:D165-8.

PolyA_DB 3

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PolyA_DB version 3 contains polyA sites mapped by 3'READS. A large volume of data substantially increases polyA site coverage and provides quantitative information about usage. Strand-specific RNA-seq data are used to extend annotated 3' ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. Conservation information of polyA sites across mammals sheds light on the significance of APA.

Reference: Wang R, Nambia R, Zheng D, Tian B. (2018). PolyA DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. Nucleic Acids Res. In press.


PolyA site prediction and cis element analysis

PolyA_SVM

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PolyA_SVM predicts polyA sites using 15 cis elements identified for human polyA sites.

Reference: Cheng Y, Miura RM, Tian B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5.

 
Please contact Bin Tian for questions/comments/suggestions.