Abstract:
:The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dinkel H,Chica C,Via A,Gould CM,Jensen LJ,Gibson TJ,Diella Fdoi
10.1093/nar/gkq1104subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D261-7issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1104journal_volume
39pub_type
杂志文章abstract::A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.20.4092
更新日期:1995-10-25 00:00:00
abstract::High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw984
更新日期:2017-02-28 00:00:00
abstract::Light-inducible systems allow spatiotemporal control of a variety of biological activities. Here, we report newly optimized optogenetic tools to induce transcription with light in mammalian cells, using the Arabidopsis photoreceptor Flavin Kelch-repeat F-box 1 (FKF1) and its binding partner GIGANTEA (GI) as well as CR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx804
更新日期:2017-11-16 00:00:00
abstract::Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of target site recognition. Cleavage specificity is typically evaluated by low throughput assays (T7 endonucleas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv137
更新日期:2015-03-31 00:00:00
abstract::DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv251
更新日期:2015-04-30 00:00:00
abstract::The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this inform...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1036
更新日期:2019-01-08 00:00:00
abstract::Computer programs, implemented on an Univac II00/80 computer system, for the identification and characterization of protein coding genes and for the analysis of nucleic acid sequences, are described. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part1.281
更新日期:1984-01-11 00:00:00
abstract::Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz431
更新日期:2019-07-26 00:00:00
abstract::The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg070
更新日期:2003-01-01 00:00:00
abstract::Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj058
更新日期:2006-01-01 00:00:00
abstract::Peptide nucleic acids (PNAs) can bind to homopurine/homopyrimidine sequences of double-stranded DNA targets in a sequence-specific manner and form [PNA]2/DNA triplexes with single-stranded DNA D-loop structures at the PNA binding sites. These D-loop structures have been found to have a capacity to initiate transcripti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.13.2806
更新日期:1999-07-01 00:00:00
abstract::A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1316
更新日期:2017-03-17 00:00:00
abstract::Earlier we have shown that exogenous expression of HIPPI, a molecular partner of Huntingtin interacting protein HIP-1, induces apoptosis and increases expression of caspases-1, -8 and -10 in HeLa and Neuro2A cells. The C-terminal pseudo death effector domain of HIPPI (pDED-HIPPI) specifically interacts with the putati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1011
更新日期:2010-01-01 00:00:00
abstract::Liquid-liquid phase separation plays an important role in a variety of cellular processes, including the formation of membrane-less organelles, the cytoskeleton, signalling complexes, and many other biological supramolecular assemblies. Studies on the molecular basis of phase separation in cells have focused on protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz978
更新日期:2019-12-16 00:00:00
abstract::The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn232
更新日期:2008-06-01 00:00:00
abstract::A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw786
更新日期:2017-01-25 00:00:00
abstract::Plastid mRNA stability is tightly regulated by external signals such as light. We have investigated the biochemical mechanism responsible for the dark-induced decrease of relative half-lives for mRNAs encoding photosynthetic proteins. Protein fractions isolated from plastids of light-grown and dark-adapted plants corr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf561
更新日期:2002-10-15 00:00:00
abstract::Sae2 cooperates with the Mre11-Rad50-Xrs2 (MRX) complex to initiate resection of DNA double-strand breaks (DSBs) and to maintain the DSB ends in close proximity to allow their repair. How these diverse MRX-Sae2 functions contribute to DNA damage resistance is not known. Here, we describe mre11 alleles that suppress th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky086
更新日期:2018-04-06 00:00:00
abstract::Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj517
更新日期:2006-02-21 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1036
更新日期:2014-11-10 00:00:00
abstract::Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.24.10213
更新日期:1989-12-25 00:00:00
abstract::Molecular mechanisms that regulate gene expression can occur either before or after transcription. The information for post-transcriptional regulation can lie within the sequence or structure of the RNA transcript and it has been proposed that G-quadruplex nucleic acid sequence motifs may regulate translation as well ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn511
更新日期:2008-11-01 00:00:00
abstract::The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2801
更新日期:1978-08-01 00:00:00
abstract::The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2443
更新日期:1986-03-25 00:00:00
abstract::An immunofluorescence assay was developed to identify proteins specifically binding to oligonucleoside phosphorodithioate (ODN) aptamers from a bead-bound ODN library. Accordingly, NF-kappaB p50 protein was incubated with either bead-bound NF-kappaB consensus sequence or a bead-bound ODN combinatorial library and adso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng054
更新日期:2003-05-15 00:00:00
abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1062
更新日期:2008-03-01 00:00:00
abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2483
更新日期:1979-06-11 00:00:00
abstract::Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recomb...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.2.256
更新日期:1995-01-25 00:00:00
abstract::Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks231
更新日期:2012-07-01 00:00:00
abstract::Human transcription factor Sp1 contains three contiguous repeats of the C2H2-type zinc finger motif and binds to the decanucleotide sequence 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3' (GC box). In order to determine whether the three-zinc finger peptide Sp1(530-623) has selectivity for sequence outside the GC box, we used a sel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.24.4920
更新日期:2001-12-15 00:00:00