PolyA-DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

Document Type

Article

Publication Date

1-1-2018

Abstract

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.

Identifier

85040923317 (Scopus)

Publication Title

Nucleic Acids Research

External Full Text Location

https://doi.org/10.1093/nar/gkx1000

e-ISSN

13624962

ISSN

03051048

PubMed ID

29069441

First Page

D315

Last Page

D319

Issue

D1

Volume

46

Grant

R01GM084089

Fund Ref

National Institute of General Medical Sciences

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