Abstract:
:The Gene Context Tool (GeConT) allows users to visualize the genomic context of a gene or a group of genes and their orthologous relationships within fully sequenced bacterial genomes. The new version of the server incorporates information from the COG, Pfam and KEGG databases, allowing users to have an integrated graphical representation of the function of genes at multiple levels, their phylogenetic distribution and their genomic context. The sequence of any of the genes can be easily retrieved, as well as the 5' or 3' regulatory regions, greatly facilitating further types of analysis. GeConT 2 is available at: http://bioinfo.ibt.unam.mx/gecont.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Martinez-Guerrero CE,Ciria R,Abreu-Goodger C,Moreno-Hagelsieb G,Merino Edoi
10.1093/nar/gkn330subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W176-80issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn330journal_volume
36pub_type
杂志文章abstract::Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm515
更新日期:2007-01-01 00:00:00
abstract::Sgs1 is a member of the RecQ family of DNA helicases, which have been implicated in genomic stability, cancer and ageing. Srs2 is another DNA helicase that shares several phenotypic features with Sgs1 and double sgs1srs2 mutants have a severe synthetic growth phenotype. This suggests that there may be functional overl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.5.1103
更新日期:2002-03-01 00:00:00
abstract::The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv575
更新日期:2015-10-15 00:00:00
abstract::Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv768
更新日期:2015-09-18 00:00:00
abstract::The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.8.1388
更新日期:1995-04-25 00:00:00
abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Stud...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw992
更新日期:2017-01-04 00:00:00
abstract::The gene encoding DNA polymerase alpha from the human malaria parasite Plasmodium falciparum has been sequenced and characterised. The deduced amino acid sequence possesses the seven sequence motifs which characterise eukaryotic replicative DNA polymerases (I-VII) and four of five motifs (A-E) identified in alpha DNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.16.3643
更新日期:1993-08-11 00:00:00
abstract::The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.1977
更新日期:1985-03-25 00:00:00
abstract::With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl045
更新日期:2006-07-01 00:00:00
abstract::Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch fr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr664
更新日期:2011-12-01 00:00:00
abstract::Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp235
更新日期:2009-06-01 00:00:00
abstract::In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1257
更新日期:2011-04-01 00:00:00
abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.21.4423
更新日期:2001-11-01 00:00:00
abstract::p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky455
更新日期:2018-07-06 00:00:00
abstract::The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz344
更新日期:2019-07-09 00:00:00
abstract::A mutation in a gene dicA of Escherichia coli leads to temperature-sensitive cell division, by allowing expression of a nearby division inhibition gene dicB (1). We have now established the sequence of the DicA region and identified DicA as a 15.5 KD protein. A second gene dicC transcribed divergently from dicA and co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6821
更新日期:1986-09-11 00:00:00
abstract::Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1271
更新日期:2013-02-01 00:00:00
abstract::A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku306
更新日期:2014-07-01 00:00:00
abstract::The two-step process of selection and counter-selection is a standard way to enable genetic modification and engineering of bacterial genomes using homologous recombination methods. The tetA and sacB genes are contained in a DNA cassette and confer a novel dual counter-selection system. Expression of tetA confers bact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1075
更新日期:2013-12-01 00:00:00
abstract::The nucleotide sequence of the celD gene, encoding the previously crystallized endoglucanase D of Clostridium thermocellum, is reported. The enzyme shares a conserved, reiterated domain with the COOH-terminal end of endoglucanases A and B from the same organism. The overexpression in Escherichia coli of celD subcloned...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8605
更新日期:1986-11-11 00:00:00
abstract::The Escherichia coli RuvC protein is an endonuclease that resolves Holliday junctions. In vitro, the protein shows efficient structure-specific binding of Holliday junctions, yet the rate of junction resolution is remarkably low. We have mapped the sites of cleavage on a synthetic junction through which a crossover ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2490
更新日期:1994-07-11 00:00:00
abstract::Polyadenylation is a co-transcriptional process that modifies mRNA 3'-ends in eukaryotes. In yeast, CF IA and CPF constitute the core 3'-end maturation complex. CF IA comprises Rna14p, Rna15p, Pcf11p and Clp1p. CF IA interacts with the C-terminal domain of RNA Pol II largest subunit via Pcf11p which links pre-mRNA 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr800
更新日期:2012-02-01 00:00:00
abstract::DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.21.6597
更新日期:1982-11-11 00:00:00
abstract::Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1107
更新日期:2014-02-01 00:00:00
abstract::Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change cer...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gku773
更新日期:2014-01-01 00:00:00
abstract::The nuclear receptor vitamin D receptor (VDR) is known to associate with two vitamin D response element (VDRE) containing chromatin regions of the insulin-like growth factor binding protein 3 (IGFBP3) gene. In non-malignant MCF-10A human mammary cells, we show that the natural VDR ligand 1α,25-dihydroxyvitamin D(3) (1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq820
更新日期:2011-01-01 00:00:00
abstract::Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3273
更新日期:1985-05-10 00:00:00
abstract::Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by expansion of CTG triplet repeats in 3'-untranslated region of DMPK gene. The pathomechanism of DM1 is driven by accumulation of toxic transcripts containing expanded CUG repeats (CUG(exp)) in nuclear foci which sequester several ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv163
更新日期:2015-03-31 00:00:00
abstract::ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1108
更新日期:2018-01-04 00:00:00
abstract::During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky658
更新日期:2018-09-28 00:00:00