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Cited by 239RNA Research and SplicingGenomics and Phylogenetic StudiesRNA regulation and disease

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

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Wang, Ruijia, Nambiar, Ram, Zheng, Dinghai, Tian, Bin·2018·Nucleic Acids Research
DOI 10.1093/nar/gkx1000PMC PMC5753232
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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.

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  • Predicted tissue-pooled distal-to-proximal polyadenylation coverage ratios of held-out genes were highly correlated with measurements from GTEx (Spearman's R = 0.81) and PolyADB v.3.

    “Predicted tissue-pooled distal-to-proximal polyadenylation coverage ratios of held-out genes were highly correlated with measurements from GTEx (Spearman’s R = 0.81; Supplementary Fig. 3f) and PolyADB v.3 (refs. 43,44) (Supplementary Fig. 3g).”

    From Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation (2025) · cites this paper as [44]

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Cited by

Sorted by citations

Authors
Wang, R., Nambiar, R., Zheng, D., & Tian, B.
Affiliations
  • Rutgers Cancer Institute (US)
  • New Jersey Institute of Technology (US)
Corresponding author
Tian, Bin
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2017-10-23
Volume
46
Issue
D1
Pages
D315-D319
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkx1000
PMC
PMC5753232
OpenAlex
W2766614445
Cited by
239
References
1
Citations by year
2026: 20 · 2025: 28 · 2024: 29 · 2023: 31 · 2022: 25 · 2021: 51 · 2020: 28 · 2019: 19 · 2018: 7 · 2017: 1
FWCI
6.15
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
National Institute of General Medical Sciences (R01GM084089)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
polyadenylation, alternative polyadenylation, deep sequencing, strand-specific RNA-seq, human, mice, rats, chickens
MeSH terms
Animals, Chickens, Humans, User-Computer Interface, Genome, Sequence Analysis, RNA, Polyadenylation, Databases, Genetic, Mice, Rats, High-Throughput Nucleotide Sequencing, RNA Cleavage

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