Polyadenylation site databases | RNA modification data analysis
Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation.
A web-accessible database which can visualize the precise map and usage quantification of different alternative polyadenylation (APA) isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs).
Provides a largest database of alternative polyadenylation (APA) in plants, including rice, Arabidopsis, Medicago truncatula, and Chlamydomonas reinhardtii. PlantAPA is a database for query, visualization, and analysis of poly(A) sites in plants, which can profile heterogeneous cleavage sites and quantify expression pattern of poly(A) sites across different conditions. It provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions.
A database of vertebrate polyadenylation (PA) sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser.
Provides information regarding polyadenylation in several vertebrate species. PolyA_DB is a web resource which contains comprehensive information regarding polyadenylation, including poly(A) sites in the context of gene structure, cDNA/EST evidence for poly(A) sites, polyadenylation signals (PASs), conservation of polyadenylation configuration between orthologs and tissue/organ information for poly(A) site usage.
Compiles information about Alternative polyadenylation (APA) usage in human cancers. TC3A contains a collection of APA events for more than 10 000 tumors across 32 cancer types. Users can download, query, visualize and run analytic functions to discover APA usage’s effects. The repository aims to promote APA usage as an additional dimension to existing cancer genomic analysis.
Supplies high-confidence poly(A) sites. PolyAsite was constructed using an analysis of a large number of 3′ end sequencing data sets. It contains a set of putative cleavage sites that resulted from the mapping of all of the reads obtained in these 3′ end sequencing studies. This platform enables users to filter sites of interest based on the number of supporting protocols, the identified poly(A) signals, and/or the genomic context of the clusters.
A web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events.