CoChat
Sign Up
Cited by 132RNA Research and SplicingGenomics and Phylogenetic StudiesRNA regulation and disease

PolyA_DB: a database for mammalian mRNA polyadenylation

Open access
Zhang, H.·2004·Nucleic Acids Research
DOI 10.1093/nar/gki055PMC PMC540009
Open this paper in CoChat — free accountOpen PDF

Abstract

Messenger RNA polyadenylation is one of the key post-transcriptional events in eukaryotic cells. A large number of genes in mammalian species can undergo alternative polyadenylation, which leads to mRNAs with variable 3' ends. As the 3' end of mRNAs often contains cis elements important for mRNA stability, mRNA localization and translation, the implications of the regulation of polyadenylation can be multifold. Alternative polyadenylation is controlled by cis elements and trans factors, and is believed to occur in a tissue- or disease-specific manner. Given the availability of many databases devoted to other aspects of mRNA metabolism, such as transcriptional initiation and splicing, systematic information on polyadenylation, including alternative polyadenylation and its regulation, is noticeably lacking. Here, we present a database named polyA_DB, through which we strive to provide several types of information regarding polyadenylation in mammalian species: (i) polyadenylation sites and their locations with respect to the genomic structure of genes; (ii) cis elements surrounding polyadenylation sites; (iii) comparison of polyadenylation configuration between orthologous genes; and (iv) tissue/organ information for alternative polyadenylation sites. Currently, polyA_DB contains 45,565 polyadenylation sites for 25,097 human and mouse genes, representing the most comprehensive polyadenylation database till date. The database is accessible via the website (http://polya.umdnj.edu/polyadb).

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gki055

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • 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 [43]

    The Results (Data access and visualization; page unavailable) identify polyA_DB as a database of polyadenylation sites, supporting the citation’s identification of the resource. Our copy does not identify the database as PolyADB v.3 or establish that this version supplied the cited measurements. The correlation is presented as a result of the citing study, not a finding attributed to this source. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 20

  1. [1]Colgan D.F. and Manley,J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev., 11, 2755– 2766. 9353246
  2. [2]Lewis J.D., Gunderson,S.I. and Mattaj,I.W. (1995) The influence of 5′ and 3′ end structures on pre-mRNA metabolism. J. Cell Sci. Suppl., 19, 13– 19. 8655642
  3. [3]Gehring N.H., Frede,U., Neu-Yilik,G., Hundsdoerfer,P., Vetter,B., Hentze,M.W. and Kulozik,A.E. (2001) Increased efficiency of mRNA 3′ end formation: a new genetic mechanism contributing to hereditary thrombophilia. Nature Genet., 28, 389– 392. 11443298
  4. [4]Beaudoing E., Freier,S., Wyatt,J.R., Claverie,J.M. and Gautheret,D. (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res., 10, 1001– 1010. 10899149 PMC310884
  5. [5]Zarudnaya M.I., Kolomiets,I.M., Potyahaylo,A.L. and Hovorun,D.M. (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res., 31, 1375– 1386. 12595544 PMC149834
  6. [6]Legendre M. and Gautheret,D. (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics, 4, 7. 12600277 PMC151664
  7. [7]Takagaki Y. and Manley,J.L. (1997) RNA recognition by the human polyadenylation factor CstF. Mol. Cell Biol., 17, 3907– 3914. 9199325 PMC232243
  8. [8]MacDonald C.C., Wilusz,J. and Shenk,T. (1994) The 64-kilodalton subunit of the CstF polyadenylation factor binds to pre-mRNAs downstream of the cleavage site and influences cleavage site location. Mol. Cell Biol., 14, 6647– 6654. 7935383 PMC359194
  9. [9]Tabaska J.E. and Zhang,M.Q. (1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231, 77– 86. 10231571
  10. [10]Hajarnavis A., Korf,I. and Durbin,R. (2004) A probabilistic model of 3′ end formation in Caenorhabditis elegans. Nucleic Acids Res., 32, 3392– 3399. 15247332 PMC443532
  11. [11]Graber J.H., Cantor,C.R., Mohr,S.C. and Smith,T.F. (1999) In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl Acad. Sci. USA, 96, 14055– 14060. 10570197 PMC24189
  12. [12]Zhao J., Hyman,L. and Moore,C. (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev., 63, 405– 445. 10357856 PMC98971
  13. [13]Proudfoot N. (1996) Ending the message is not so simple. Cell, 87, 779– 781. 8945502
  14. [14]Calvo O. and Manley,J.L. (2003) Strange bedfellows: polyadenylation factors at the promoter. Genes Dev., 17, 1321– 1327. 12782649
  15. [15]Beaudoing E. and Gautheret,D. (2001) Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res., 11, 1520– 1526. 11544195 PMC311108
  16. [16]Edwalds-Gilbert G., Veraldi,K.L. and Milcarek,C. (1997) Alternative poly(A) site selection in complex transcription units: means to an end? Nucleic Acids Res., 25, 2547– 2561. 9185563 PMC146782
  17. [17]Pruitt K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137– 140. 11125071 PMC29787
  18. [18]Wheeler D.L., Church,D.M., Federhen,S., Lash,A.E., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E., Tatusova,T.A. et al. (2003) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 31, 28– 33. 12519941 PMC165480
  19. [19]Pauws E., van Kampen,A.H., van de Graaf,S.A., de Vijlder,J.J. and Ris-Stalpers,C. (2001) Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res., 29, 1690– 1694. 11292841 PMC31324
  20. [20]Stajich J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611– 1618. 12368254 PMC187536

Cited by

Sorted by citations

Authors
Zhang, H.
Affiliations
New Jersey Institute of Technology (US)
Corresponding author
Zhang, H.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2004-12-17
Volume
33
Issue
Database issue
Pages
D116-D120
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gki055
PMC
PMC540009
OpenAlex
W1976007281
Cited by
132
References
0
Citations by year
2026: 5 · 2025: 8 · 2024: 8 · 2023: 9 · 2022: 5 · 2021: 4 · 2020: 2 · 2019: 3 · 2018: 3 · 2017: 7 · 2016: 6 · 2015: 5 · 2014: 12 · 2013: 8 · 2012: 8
FWCI
2.85
Type
journal article
Language
en
Open access
Licence
other-oa
Locations
  • Nucleic Acids Research (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
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
mRNA polyadenylation, alternative polyadenylation, polyadenylation sites, cis-regulatory elements, trans-acting factors, orthologs, human genes, mouse genes
MeSH terms
Animals, Humans, Poly A, RNA, Messenger, User-Computer Interface, Genome, Polyadenylation, Databases, Nucleic Acid, Mice

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review