PolyA_DB statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PolyA_DB specifications

Information


Unique identifier OMICS_06154
Name PolyA_DB
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Publications for PolyA_DB

PolyA_DB citations

 (10)
library_books

Cis acting elements in its 3′ UTR mediate post transcriptional regulation of KRAS

2016
Oncotarget
PMCID: 4914247
PMID: 26930719
DOI: 10.18632/oncotarget.7599

[…] ifferent lengths of the KRAS 3′ UTR (Figure ). The pAPA1, 2, 3, and 4 reporter constructs correspond to each of the four predicted polyadenylation sites for the KRAS 3′ UTR, as currently annotated in polyA_DB in UCSC Genome Browser []. The pAPA2Δ reporter corresponds to an additional polyadenylation site, which was previously listed in the human 2007 annotation in AceView []. Following separate tr […]

library_books

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

2015
PLoS One
PMCID: 4699828
PMID: 26713853
DOI: 10.1371/journal.pone.0145417

[…] were defined as known poly(A) sites, EST poly(A) sites and novel poly(A) sites according to their overlap (or absence of overlap) with annotated poly(A) sites (within 30 bp of the 3’UTR end) or Mouse PolyA_DB sites (poly(A) sites detected by EST data in previously published literature []). […]

library_books

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non Coding and Coding RNAs

2014
PLoS One
PMCID: 4010412
PMID: 24796678
DOI: 10.1371/journal.pone.0093846

[…] NA-Seq reads were aligned to reference genome (UCSC, hg19) using Tophat 1.3.1 by default parameters for Applied Biosystems' Colorspace format. Uniquely mapped reads were kept for downstream analysis. PolyA_DB together with the 3′ ends of transcripts from UCSC, RefSeq, Aceview annotations were collected as a comprehensive APA database . For each annotated cleavage site, the number of reads in the u […]

library_books

Microarray Meta Analysis of RNA Binding Protein Functions in Alternative Polyadenylation

2014
PLoS One
PMCID: 3951239
PMID: 24622240
DOI: 10.1371/journal.pone.0090774

[…] nome browser. The information of 3′ ends of mRNA transcripts was integrated into poly(A) site database. We extracted 3′ UTRs from KG annotations and merged them into clusters if any overlaps occurred.Polya_DB2 is a comprehensive poly(A) database across different animals constructed by Lee et al. . We downloaded all poly(A) sites in Polya_DB2 for mouse Mm5 genome. The genomic coordinates in Mm5 wer […]

library_books

Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron Sequence Retaining Transcripts in Mouse and Rat Neurons

2013
PLoS One
PMCID: 3789819
PMID: 24098440
DOI: 10.1371/journal.pone.0076194

[…] CAN [] and TWINSCAN [] to minimize any other possible cryptic translated sequences. Second, we also screened the introns with retained sequence for the presence of intronic poly(A)-sites by using the PolyA_DB2 database which reports poly(A) sites obtained using alignments between cDNA/ESTs and genome sequences [], and removed those that contained a poly(A) site. Third, we examined the remaining re […]

library_books

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non coding Transcripts

2013
PLoS Genet
PMCID: 3688553
PMID: 23818875
DOI: 10.1371/journal.pgen.1003594

[…] wser tool in UCSC genome browser and the overlap intervals tool in Galaxy (version 1.0.0).Intersection of SNPs with validated and predicted polyadenylation sites was performed using annotation in the PolyA-DB database (PolyA_DB 1 and PolyA_SVM) on UCSC (table browser tool). Detection of SNPs within polyadenylation signals was performed by extracting the strand specific sequence five nucleotide ups […]

Citations

Looking to check out a full list of citations?

PolyA_DB institution(s)
Department of Biochemistry and Molecular Biology, New Jersey Medical School University of Medicine and Dentistry of New Jersey, Newark, NJ, USA

PolyA_DB reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PolyA_DB