Abstract:
:The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Childers CP,Reese JT,Sundaram JP,Vile DC,Dickens CM,Childs KL,Salih H,Bennett AK,Hagen DE,Adelson DL,Elsik CGdoi
10.1093/nar/gkq1235subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D830-4issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1235journal_volume
39pub_type
杂志文章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::To determine whether methylation changes in specific DNA sequences of the albumin and AFP genes are implicated in the modulation of transcriptional activity during rat liver development and neoplasia we have analysed the methylation pattern of C-C-G-G sequences within these genes in DNA isolated from fetal and adult h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.13.4335
更新日期:1983-07-11 00:00:00
abstract::RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks289
更新日期:2012-08-01 00:00:00
abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv081
更新日期:2015-02-27 00:00:00
abstract::Poly(pyrimidine) . poly(purine) tracts have been discovered in the 5'-flanking regions of many eucaryotic genes. They may be involved in the regulation of expression since they can be mapped to the nuclease-sensitive sites of active chromatin. We have found that poly(pyrimidine) . poly(purine) DNAs which contain 5-met...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.16.6603
更新日期:1984-08-24 00:00:00
abstract::Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm543
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abstract::The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4283
更新日期:1992-08-25 00:00:00
abstract::Gene duplications are a major source of evolutionary innovations. Understanding the functional divergence of duplicates and their role in genetic robustness is an important challenge in biology. Previously, analyses of genetic robustness were primarily focused on duplicates essentiality and epistasis in several labora...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1200
更新日期:2014-02-01 00:00:00
abstract::We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl170
更新日期:2006-07-01 00:00:00
abstract::The alpha/beta-hydrolase fold is characterized by a beta-sheet core of five to eight strands connected by alpha-helices to form a alpha/beta/alpha sandwich. In most of the family members the beta-strands are parallels, but some show an inversion in the order of the first strands, resulting in antiparallel orientation....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh141
更新日期:2004-01-01 00:00:00
abstract::We have used paired-end sequencing of yeast nucleosomal DNA to obtain accurate genomic maps of nucleosome positions and occupancies in control cells and cells treated with 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. In control cells, 3AT-inducible genes exhibit a series of distinct nucleos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr643
更新日期:2011-12-01 00:00:00
abstract::A C-->U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold inc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh860
更新日期:2004-10-11 00:00:00
abstract::We present RADAR--a rigorously annotated database of A-to-I RNA editing (available at http://RNAedit.com). The identification of A-to-I RNA editing sites has been dramatically accelerated in the past few years by high-throughput RNA sequencing studies. RADAR includes a comprehensive collection of A-to-I RNA editing si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt996
更新日期:2014-01-01 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::The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.9087
更新日期:1989-11-25 00:00:00
abstract::We previously reported that O4-alkyl dTTPs could replace, for short times, dTTP in polymer synthesis [Singer et al., PNAS 83, 26-32, 1986]. The reasons for such early termination of synthesis could be either proofreading or the eventual formation of weakly paired primer termini. Utilizing the known 3'----5' exonucleol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.16.6735
更新日期:1986-08-26 00:00:00
abstract::Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh400
更新日期:2004-07-01 00:00:00
abstract::MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. Only few databases report protein-polysaccharide interactions and, to the best of our knowledge, there is no other database of extracellular interactions. MatrixDB takes ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq830
更新日期:2011-01-01 00:00:00
abstract::Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2-MSH3 heterodimer) is required in mice for on-go...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks810
更新日期:2012-11-01 00:00:00
abstract::Homologous recombination (HR) is a highly accurate mechanism of DNA repair that can be exploited for homology-directed gene targeting. Since in most cell types HR occurs very infrequently (approximately 10(-6) to 10(-8)), its practical application has been largely restricted to specific experimental systems that allow...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp643
更新日期:2009-09-01 00:00:00
abstract::MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku458
更新日期:2014-07-01 00:00:00
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journal_title:Nucleic acids research
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更新日期:2018-04-20 00:00:00
abstract::CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1165
更新日期:2019-02-20 00:00:00
abstract::SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp281
更新日期:2009-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks396
更新日期:2012-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh359
更新日期:2004-07-01 00:00:00
abstract::Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki685
更新日期:2005-06-30 00:00:00
abstract::To synchronize SV40 replicons, simian cells infected with a tsA mutant were restricted at 40 degrees, to complete ongoing replication and returned to 32 degrees, to activate new replicons in the presence of the DNA chain elongation inhibitor aphidicolin. Upon further incubation at 40 degrees without the drug, 3H-dT wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.2.763
更新日期:1982-01-22 00:00:00
abstract::We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.6205
更新日期:1988-07-11 00:00:00
abstract::The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.24.5163
更新日期:2001-12-15 00:00:00