Abstract:
:O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hansen JE,Lund O,Nilsson J,Rapacki K,Brunak Sdoi
10.1093/nar/26.1.387subject
Has Abstractpub_date
1998-01-01 00:00:00pages
387-9issue
1eissn
0305-1048issn
1362-4962pii
gkb063journal_volume
26pub_type
杂志文章abstract::Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp569
更新日期:2009-09-01 00:00:00
abstract::The nucleolus is a unique structural component of interphase nuclei where the ribosomal genes, trans-cribed by RNA polymerase I (RNA pol I), are organized. In the present study, the repair of UV-induced photolesions was investigated in the ribosomal DNA (rDNA) in relation to RNA pol I transcription. We used hamster ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.12.2511
更新日期:1999-06-15 00:00:00
abstract::The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1009
更新日期:2010-01-01 00:00:00
abstract::Methods for increasing the transient level of expression of transfected DNA in cultured Drosophila cells have been examined. Here we show that cells exposed to the steroid hormone 20-hydroxyecdysone for 48h prior to transfection show an 4 to 5 fold increase in the levels of expression of transfected DNA. By analysis, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9255
更新日期:1987-11-25 00:00:00
abstract::Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.5.1150
更新日期:1998-03-01 00:00:00
abstract::Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1089
更新日期:2015-12-02 00:00:00
abstract::The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1070
更新日期:2018-01-04 00:00:00
abstract::A cDNA that encodes a transcription factor able to recognize the thyroglobulin gene promoter in vitro was isolated from a dog thyroid cDNA expression library in lambda gt11. The library was screened with a multimerized 20 bp-oligonucleotide probe corresponding to the -126 to -107 bp region of the bovine thyroglobulin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.5.1121
更新日期:1991-03-11 00:00:00
abstract::The tumor suppressor gene, p53, is rarely mutated in neuroblastomas (NB) at the time of diagnosis, but its dysfunction could result from a nonfunctional conformation or cytoplasmic sequestration of the wild-type p53 protein. However, p53 mutation, when it occurs, is found in NB tumors with drug resistance acquired ove...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl619
更新日期:2006-01-01 00:00:00
abstract::Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa515
更新日期:2020-09-04 00:00:00
abstract::We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.e64
更新日期:2001-07-01 00:00:00
abstract::In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky670
更新日期:2018-09-28 00:00:00
abstract::Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.12.2725
更新日期:1980-06-25 00:00:00
abstract::The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4331
更新日期:1988-05-25 00:00:00
abstract::Details of polynucleotide flexibility may be probed through a combination of semiempirical potential energy calculations and statistical mechanical analyses. The pseudorotational motions of the furanose and the long-range correlated rotations of the chain backbone are described briefly here. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.3.777
更新日期:1982-02-11 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::Transcription is the first step in gene expression, and it is the step at which most of the regulation of expression occurs. Although sequenced prokaryotic genomes provide a wealth of information, transcriptional regulatory networks are still poorly understood using the available genomic information, largely because a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr795
更新日期:2012-02-01 00:00:00
abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq834
更新日期:2011-01-01 00:00:00
abstract::Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa545
更新日期:2020-08-20 00:00:00
abstract::Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.22.5203
更新日期:1998-11-15 00:00:00
abstract::A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1055
更新日期:2016-01-08 00:00:00
abstract::Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx389
更新日期:2017-07-03 00:00:00
abstract::To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.5.975
更新日期:1992-03-11 00:00:00
abstract::Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx999
更新日期:2017-12-01 00:00:00
abstract::Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.3057
更新日期:1978-08-01 00:00:00
abstract::Transcriptional regulation of the delta-aminolevulinic acid synthetase gene of Rhizobium meliloti was investigated under conditions of normal vegetative growth and during symbiosis with the legume host alfalfa. S1 nuclease mapping and DNA sequence analysis indicated that transcription originates from two sites separat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.16.5965
更新日期:1985-08-26 00:00:00
abstract::WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg092
更新日期:2003-01-01 00:00:00
abstract::Human cytomegalovirus (HCMV) terminase is composed of subunits pUL56 (130 kDa) and pUL89 ( approximately 75 kDa), encoded by the UL56 and UL89 genes. In a recent investigation, we demonstrated that the main ATPase activity is associated with the large terminase subunit pUL56. The protein has two putative ATP-binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg229
更新日期:2003-03-01 00:00:00
abstract::Inhibition of an RNA processing reaction after treatment with the Ca2(+)-dependent micrococcal nuclease (MN) is often used as a criterion for the presence of a required RNA or ribonucleoprotein component in the system. Following MN digestion, the nuclease is inactivated with EGTA and radiolabeled substrate is added to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.22.6625
更新日期:1990-11-25 00:00:00
abstract::Saccharomyces cerevisiae chl1 mutants have a significant increase in the rate of chromosome missegregation. CHL1 encodes a 99 kDa predicted protein with an ATP binding site consensus, a putative helix-turn-helix DNA binding motif, and homology to helicases. Using site-directed mutagenesis, I show that mutations that a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.16.3056
更新日期:2000-08-15 00:00:00