Abstract:
:EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhou J,Rudd KEdoi
10.1093/nar/gks1235subject
Has Abstractpub_date
2013-01-01 00:00:00pages
D613-24issue
Database issueeissn
0305-1048issn
1362-4962pii
gks1235journal_volume
41pub_type
杂志文章abstract::For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.4.727
更新日期:1991-02-25 00:00:00
abstract::We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq130
更新日期:2010-07-01 00:00:00
abstract::For sophisticated gene targeting procedures requiring two sequential selective steps to operate efficiently it is essential that the marker genes used are not prone to position effects. The double replacement gene targeting procedure, to produce mice with subtle gene alterations, is based on the use of hypoxanthine ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.19.3937
更新日期:1997-10-01 00:00:00
abstract::Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripalu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.22.4699
更新日期:2001-11-15 00:00:00
abstract::Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni118
更新日期:2005-07-26 00:00:00
abstract::X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 368 entries from 318 unrelated families showing 228 unique molecular events. In addi...
journal_title:Nucleic acids research
pub_type: 杂志文章,多中心研究
doi:10.1093/nar/25.1.166
更新日期:1997-01-01 00:00:00
abstract::IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku939
更新日期:2014-11-10 00:00:00
abstract::We have isolated a second gene (MLS1), which in addition to DAL7, encodes malate synthase from S. cerevisiae. Expression of the two genes is specific for their physiological roles in carbon and nitrogen metabolism. Expression of MLS1, which participates in the utilization of non-fermentable carbon sources, is sensitiv...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.21.5677
更新日期:1992-11-11 00:00:00
abstract::We present the complete nucleotide sequence of the larval beta I-globin gene of Xenopus laevis including 240 nucleotides of the 5' flanking region and 594 nucleotides beyond the polyadenylation site. The site of transcription initiation was mapped by S1 nuclease, and the site of polyadenylation was determined by compa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.20.7705
更新日期:1984-10-25 00:00:00
abstract::Three different types of repetitive Eco RI fragments, which comigrate within a visible band of approximately 500 bp at gel electrophoresis of Xenopus laevis DNA Eco RI digests have been cloned and sequenced. These sequences are designated as Repetitive Eco RI Monomers: REM 1, REM 2 and REM 3. The sequences contain dir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.12.4921
更新日期:1984-06-25 00:00:00
abstract::Transposable elements are found throughout the genomes of all organisms. Repressive marks such as DNA methylation and histone H3 lysine 9 (H3K9) methylation silence these elements and maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid the silencing of genes remains unclear. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv958
更新日期:2016-01-29 00:00:00
abstract::mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic processes in vivo is difficult due to the paucity of methods capable of direct measurements. We present a highly sensitive and ver...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw596
更新日期:2016-10-14 00:00:00
abstract::Transfer RNAGlu4 was isolated from Drosophila melanogaster by affinity chromatography. The tRNA was iodinated "in vitro" with Na[25I] and hybridized "in situ" to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAGlu4 to the right arm of the second chro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.5.1465
更新日期:1978-05-01 00:00:00
abstract::The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa969
更新日期:2021-01-08 00:00:00
abstract::Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt492
更新日期:2013-08-01 00:00:00
abstract::Mitochondrial DNA (mtDNA) contains high levels of oxidative damage relative to nuclear DNA. A full, functional DNA base excision repair (BER) pathway is present in mitochondria, to repair oxidative DNA lesions. However, little is known about the organization of this pathway within mitochondria. Here, we provide eviden...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki683
更新日期:2005-07-08 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::Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh788
更新日期:2004-09-01 00:00:00
abstract::Real-time PCR is being used increasingly as the method of choice for mRNA quantification, allowing rapid analysis of gene expression from low quantities of starting template. Despite a wide range of approaches, the same principles underlie all data analysis, with standard approaches broadly classified as either absolu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng073
更新日期:2003-07-15 00:00:00
abstract::The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp419
更新日期:2009-07-01 00:00:00
abstract::To examine the influence of thyrotropin (TSH) on the thyroglobulin (Tgb) mRNA content, the latter was evaluated in the cytoplasm of hog thyroid cells cultured in the absence (control cells) or presence of TSH. The Tgb mRNA levels were determined by, (i) kinetics of hybridization to sheep Tgb cDNA, (ii) capacity of cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.10.3353
更新日期:1979-07-25 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 inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1124
更新日期:2008-03-01 00:00:00
abstract::To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw782
更新日期:2016-12-15 00:00:00
abstract::Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.5.2213
更新日期:1987-03-11 00:00:00
abstract::Eukaryotic cellular mRNAs contain a cap at their 5'-ends, but some viral and cellular mRNAs bypass the cap-dependent mechanism of translation initiation in favor of internal entry of ribosomes at specific RNA sequences. Cap-dependent initiation requires intact initiation factor eIF4G (formerly eIF-4gamma, eIF-4Fgamma ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.2.395
更新日期:1997-01-15 00:00:00
abstract::Recently, a cDNA from the hepatitis C virus (HCV) RNA genome has been isolated in the USA from a chronically infected chimpanzee. In order to isolate HCV cDNA derived from human material, RNA was extracted from plasma of a Japanese blood donor implicated in post-transfusion non-A, non-B hepatitis and HCV cDNA was synt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.24.10367
更新日期:1989-12-25 00:00:00
abstract::Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn584
更新日期:2008-10-01 00:00:00
abstract::Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gk...
journal_title:Nucleic acids research
pub_type:
doi:10.1093/nar/27.1.1
更新日期:1999-01-01 00:00:00
abstract::Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn470
更新日期:2008-09-01 00:00:00