PolyASite
General Information
Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, differentiation and disease development. PolyASite is a portal to the curated set of poly(A) sites inferred from publicly available 3’ end sequencing datasets. It allows efficient finding, exploration and export of poly(A) sites in several organisms. In constructing our poly(A) site atlas, we applied uniform quality measures, including the flagging of putative internal priming sites, to input datasets originating from different 3’ end sequencing techniques, cell types or tissues. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. While other existing alternative polyadenylation databases rely on a single experimental method, or on poly(A) site estimation from RNA-seq data, PolyASite is built on data from several 3’ end sequencing techniques. This allows a broader coverage of cell types and poly(A) sites to support further genomics studies.
How to cite this record
FAIRsharing.org: PolyASite; PolyASite; DOI: https://doi.org/10.25504/FAIRsharing.V52Eqe;
Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Sep 30 2020 10:34 p.m.
Publication for citation
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing.
Herrmann CJ,Schmidt R,Kanitz A,Artimo P,Gruber AJ,Zavolan M; Nucleic Acids Res ;
2019;
10.1093/nar/gkz918;
Record added: Nov. 6, 2019, 3:04 p.m.
Record updated:
Dec. 2, 2019, 1:58 p.m. by mzavolan.
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Edits to 'https://fairsharing.org/FAIRsharing.V52Eqe' by 'mzavolan' at 13:58, 02 Dec 2019 (approved):
'supportLinks' has been modified:
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email|christina.herrmann@unibas.ch
online documentation|https://polyasite.unibas.ch/protocols
online documentation|https://polyasite.unibas.ch/about
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email|polyasite-biozentrum@unibas.ch
online documentation|https://polyasite.unibas.ch/protocols
online documentation|https://polyasite.unibas.ch/about
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email|polyasite-biozentrum@unibas.ch
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email|christina.herrmann@unibas.ch
Edits to 'https://fairsharing.org/FAIRsharing.V52Eqe' by 'The FAIRsharing Team' at 20:42, 06 Nov 2019 (approved):
'supportLinks' has been modified:
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email|christina.herrmann@unibas.ch
online documentation|https://polyasite.unibas.ch/protocols
online documentation|https://polyasite.unibas.ch/about
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email|christina.herrmann@unibas.ch
online documentation|https://polyasite.unibas.ch/protocols
online documentation|https://polyasite.unibas.ch/about
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Bioinformatics
Genetics
Transcriptomics
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Bioinformatics
Genetics
Transcriptomics
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PAQR / KAPAC||https://github.com/zavolanlab/PAQR_KAPAC
TECtool||https://github.com/zavolanlab/TECtool
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PAQR / KAPAC||https://github.com/zavolanlab/PAQR_KAPAC
TECtool||https://github.com/zavolanlab/TECtool
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Gene expression data
RNA polyadenylation
RNA-seq assay
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RNA polyadenylation
RNA-seq assay
ribonucleic acid
transcript
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PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing.
Herrmann CJ,Schmidt R,Kanitz A,Artimo P,Gruber AJ,Zavolan M
Nucleic Acids Res 2019
View Paper (PubMed)
View Publication
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