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Protocols

polyadq specifications

Information


Unique identifier OMICS_06162
Name polyadq
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for polyadq

polyadq citations

 (8)
library_books

Detection of subclonal L1 transductions in colorectal cancer by long distance inverse PCR and Nanopore sequencing

2017
Sci Rep
PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] nylation signal of the L1 and the next strongest polyadenylation signal on its 3′ flanking region (Fig. , Supplementary Table ). Strength of polyadenylation signals at this region was estimated using polyadq scores (http://rulai.cshl.edu/tools/polyadq/polyadq_form.html). Primers were designed using Primer3 (http://primer3.ut.ee) and their specificity was checked using NCBI Primer-BLAST (available […]

library_books

Multiple Novel Nesprin 1 and Nesprin 2 Variants Act as Versatile Tissue Specific Intracellular Scaffolds

2012
PLoS One
PMCID: 3388047
PMID: 22768332
DOI: 10.1371/journal.pone.0040098

[…] tart codon. Only those 3′UTR sequences which already included a poly(A) tail or contained at least one poly(A) site downstream of the initial ORF termination codon, as determined by scanning with the polyAdq program or manually for non-canonical poly(A) signals, were considered for further study.The majority of UTRs identified by RACE or through the EST screen were verified by PCR and DNA sequenci […]

library_books

Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron 5 of the Sheep SCF Gene: A Novel Splice Variant

2012
PLoS One
PMCID: 3376141
PMID: 22719917
DOI: 10.1371/journal.pone.0038657

[…] graphical representation of SCF amino acid and nucleic acid multiple sequence alignment was drawn by a sequence logo generator, WebLogo (v. 2.8.2) . SCF polyadenylation sites were predicted using the polyADQ web server . Alternative splicing pattern of the ovine SCF transcripts with human, mouse reference assembly were predicted using ACEVIEW and Alternative Splicing and Transcript Diversity (AST […]

call_split

Intronic L1 Retrotransposons and Nested Genes Cause Transcriptional Interference by Inducing Intron Retention, Exonization and Cryptic Polyadenylation

2011
PLoS One
PMCID: 3192792
PMID: 22022525
DOI: 10.1371/journal.pone.0026099
call_split See protocol

[…] and cryptic polyadenylation. Exon-intron structure of the host and nested genes or intronic L1s was analyzed by Spidey . Splice sites were predicted with NNSPLICE 0.9 version and polyA signals with POLYADQ . DNA repeats were determined by Repeatmasker (A.F.A. Smit, R. Hubley & P. Green, unpublished data). Tissue-specific expression of the host and nested genes was determined by using NCBI UniGen […]

library_books

A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina

2010
PLoS One
PMCID: 2927423
PMID: 20808762
DOI: 10.1371/journal.pone.0012315

[…] alignments, G+C and antigenicity profiles, and PCR primer optimization were performed using MacVector (Accelrys) software and NCBI BLAST servers. Math5 polyadenylation sites were predicted using the polyADQ web server (rulai.cshl.org/tools/polyadq/). Scores were calculated for a 6.0 kb sequence extending from the transcription start site (), using default threshold values. RNA secondary structur […]

call_split

Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae

2009
Genet Mol Biol
PMCID: 3032949
PMID: 21637656
DOI: 10.1590/S1415-47572009005000003
call_split See protocol

[…] predicted transcription start sites (TSS). The core promoters found in this search were examined for the presence of TATA box sequences using the TRANSFACFind search engine (http://motif.genome.jp/).POLYADQ, a eukaryotic polyadenylation (poly A) signal search engine (Cold Spring Harbor Laboratory, http://rulai.cshl.org/tools/polyadq/polyadq_form.html) was used to predict transcription termination […]


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polyadq institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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