Alternative Poly(A) Sites database
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Alternative Poly(A) Sites database
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
APASdb
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Alternative Poly(A) Sites database
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
APASdb
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Alternative Poly(A) Sites database
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
APASdb
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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APASdb can visualize the precise map and usage quantification of different 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. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads. 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). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
Description
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APASdb can visualize the precise map and usage quantification of different 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. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads. 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). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3'-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different 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). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://mosas.sysu.edu.cn/utrWebpage
More detailed information about this field from each metasource.
http://mosas.sysu.edu.cn/utr
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals
PMID: 25378337
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gku1076
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals
PMID: 25378337
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gku1076
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals
PubMed citations: 41.
41 articles citing: APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals
Implications of Poly(A) Tail Processing in Repeat Expansion Diseases. PMID:35203324
Characterization of the 3'UTR of the BTD gene and identification of regulatory elements and microRNAs. PMID:35167647
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution. PMID:34508354
The Detection and Bioinformatic Analysis of Alternative 3' UTR Isoforms as Potential Cancer Biomarkers. PMID:34070203
Alternative polyadenylation: methods, mechanism, function, and role in cancer. PMID:33526057
Fine gene expression regulation by minor sequence variations downstream of the polyadenylation signal. PMID:33517473
Alternative Polyadenylation: a new frontier in post transcriptional regulation. PMID:33292571
Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes. PMID:33291215
Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data. PMID:33193635
Animal-APAdb: a comprehensive animal alternative polyadenylation database. PMID:32986825
Systematics for types and effects of RNA variations. PMID:32951567
CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation. PMID:31964914
PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants. PMID:31767692
APAatlas: decoding alternative polyadenylation across human tissues. PMID:31586392
RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery. PMID:31509743
The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. PMID:31475030
Alternative cleavage and polyadenylation in health and disease. PMID:31267064
PTBP1 mRNA isoforms and regulation of their translation. PMID:31263002
Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences. PMID:31239292
LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. PMID:31106360
Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination. PMID:30819644
Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis. PMID:30669970
Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation. PMID:30416385
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. PMID:30202060
TC3A: The Cancer 3' UTR Atlas. PMID:30053266
Lost in translation: The 3'-UTR of IGF1R as an ancient long noncoding RNA. PMID:29644076
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. PMID:29561359
The effects of alternative splicing on miRNA binding sites in bladder cancer. PMID:29300757
The GAIT translational control system. PMID:29152905
Long 3'UTR of Nurr1 mRNAs is targeted by miRNAs in mesencephalic dopamine neurons. PMID:29145474
PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. PMID:29069441
Major splice variants and multiple polyadenylation site utilization in mRNAs encoding human translation initiation factors eIF4E1 and eIF4E3 regulate the translational regulators? PMID:28942592
Cleavage and polyadenylation: Ending the message expands gene regulation. PMID:28453393
Insertions and Deletions Target Lineage-Defining Genes in Human Cancers. PMID:28089356
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. PMID:27756200
Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. PMID:27489207
PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants. PMID:27446120
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. PMID:27382025
Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data. PMID:27324920
Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. PMID:26546131
Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching. PMID:25875641 - http://dx.doi.org/10.1093/nar/gku1076
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dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna polyadenylation
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
untranslated region
metasource: Fairsharing.org
version: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna polyadenylation
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
untranslated region
metasource: Fairsharing.orgversion: FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna sequences rna polyadenylation regulation of gene expression untranslated region rna sequence
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