| URL: | http://www.polya-db.org/v3 |
| Full name: | POLYA |
| Description: | PolyA_DB version 3.1 catalogs polyA sites (PASs) in genomes using deep sequencing data.Gene annotations are mainly based on NCBI Gene and RefSeq databases, and supplemented by the Ensembl database. Strand-specific RNA-seq data are used to extend the 3' end of genes. PASs are identified using data from the 3' end region extraction and sequencing (3'READS) method. Syntenic regions across human, mouse and rat are used to annotate conserved PASs in mammals. |
| Year founded: | 2018 |
| Last update: | |
| Version: | 3 |
| Accessibility: |
Unaccessible
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| Country/Region: | United States |
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| University/Institution: | Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey |
| Address: | Bin Tian Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ 07103, USA |
| City: | NEWYORK |
| Province/State: | |
| Country/Region: | United States |
| Contact name (PI/Team): | Bin Tian |
| Contact email (PI/Helpdesk): | btian@rutgers.edu |
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PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. [PMID: 29069441]
PolyA_DB is a database cataloging cleavage and polyadenylation sites (PASs) in several genomes. Previous versions were based mainly on expressed sequence tags (ESTs), which had a limited amount and could lead to inaccurate PAS identification due to the presence of internal A-rich sequences in transcripts. Here, we present an updated version of the database based solely on deep sequencing data. First, PASs are mapped by the 3' region extraction and deep sequencing (3'READS) method, ensuring unequivocal PAS identification. Second, a large volume of data based on diverse biological samples increases PAS coverage by 3.5-fold over the EST-based version and provides PAS usage information. Third, strand-specific RNA-seq data are used to extend annotated 3' ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. Fourth, conservation information of PAS across mammals sheds light on significance of APA sites. The database (URL: http://www.polya-db.org/v3 ) currently holds PASs in human, mouse, rat and chicken, and has links to the UCSC genome browser for further visualization and for integration with other genomic data. |