GenBank.

Abstract:

:The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Rapp BA,Wheeler DL

doi

10.1093/nar/28.1.15

keywords:

subject

Has Abstract

pub_date

2000-01-01 00:00:00

pages

15-8

issue

1

eissn

0305-1048

issn

1362-4962

pii

gkd071

journal_volume

28

pub_type

杂志文章
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    abstract::MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...

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    更新日期:2018-06-20 00:00:00

  • The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization.

    abstract::More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...

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    authors: Matunis MJ,Xing J,Dreyfuss G

    更新日期:1994-03-25 00:00:00

  • The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea.

    abstract::Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-bindin...

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    pub_type: 杂志文章

    doi:10.1093/nar/gkr283

    authors: Hsu CH,Wang AH

    更新日期:2011-08-01 00:00:00

  • FragGeneScan: predicting genes in short and error-prone reads.

    abstract::The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...

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    authors: Rho M,Tang H,Ye Y

    更新日期:2010-11-01 00:00:00

  • Increased removal of 3-alkyladenine reduces the frequencies of hprt mutations induced by methyl- and ethylmethanesulfonate in Chinese hamster fibroblast cells.

    abstract::We have previously reported the isolation of mammalian cell lines expressing the 3-methyladenine DNA glycosylase I (tag) gene from E. coli. These cells are 2-5 fold more resistant to the toxic effects of methylating agents than normal cells (15). Kinetic measurements of 3-methyladenine removal from the genome in situ ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.9.1670

    authors: Klungland A,Bjørås M,Hoff E,Seeberg E

    更新日期:1994-05-11 00:00:00

  • DEAD-box RNA helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and RNA duplex recognition.

    abstract::DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku747

    authors: Samatanga B,Klostermeier D

    更新日期:2014-01-01 00:00:00

  • Carrier detection in haemophilia B using two further intragenic restriction fragment length polymorphisms.

    abstract::A normal human population has been screened for the existence of further restriction fragment length polymorphisms (RFLPs) in the clotting factor IX gene in addition to the TaqI polymorphism already characterised (1,2). Two polymorphic loci were found, both within 6 Kb of the TaqI polymorphism within the body of the f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.23.8861

    authors: Winship PR,Anson DS,Rizza CR,Brownlee GG

    更新日期:1984-12-11 00:00:00

  • Regulatory modules function in a non-autonomous manner to control transcription of the mbp gene.

    abstract::Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1160

    authors: Dib S,Denarier E,Dionne N,Beaudoin M,Friedman HH,Peterson AC

    更新日期:2011-04-01 00:00:00

  • EK3D: an E. coli K antigen 3-dimensional structure database.

    abstract::A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1313

    authors: Kunduru BR,Nair SA,Rathinavelan T

    更新日期:2016-01-04 00:00:00

  • Flow cytometry assay for the detection of single-copy DNA in human lymphocytes.

    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

    authors: Uno N,Kaku N,Morinaga Y,Hasegawa H,Yanagihara K

    更新日期:2020-09-04 00:00:00

  • Molecular modelling of the 3-D structure of RNA tetraloops with different nucleotide sequences.

    abstract::One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.19.4556

    authors: Kajava A,Rüterjans H

    更新日期:1993-09-25 00:00:00

  • HIV-1 LTR as a target for synthetic ribozyme-mediated inhibition of gene expression: site selection and inhibition in cell culture.

    abstract::A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed agai...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.21.4059

    authors: Bramlage B,Luzi E,Eckstein F

    更新日期:2000-11-01 00:00:00

  • Defective chromatin recruitment and retention of NHEJ core components in human tumor cells expressing a Cyclin E fragment.

    abstract::Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt812

    authors: Chatterjee P,Plesca D,Mazumder S,Boutros J,Yannone SM,Almasan A

    更新日期:2013-12-01 00:00:00

  • JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

    abstract::A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl329

    authors: Scheer M,Klawonn F,Münch R,Grote A,Hiller K,Choi C,Koch I,Schobert M,Härtig E,Klages U,Jahn D

    更新日期:2006-07-01 00:00:00

  • Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

    abstract::Loss-of-function (LOF) methods such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing provide unparalleled power for studying the biological function of genes of interest. However, a major concern is non-specific targeting, which involves depletion of transcripts other than those in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky437

    authors: Stojic L,Lun ATL,Mangei J,Mascalchi P,Quarantotti V,Barr AR,Bakal C,Marioni JC,Gergely F,Odom DT

    更新日期:2018-07-06 00:00:00

  • Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides.

    abstract::High performance liquid chromatography analysis of imidazole open ring 7-methylguanine, 2-6 diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G), showed two well-separated peaks (fI and fII) of the same magnitude. Rechromatography of each isolated component indicated that they are slowly interconverted to give a 1:...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.13.5429

    authors: Boiteux S,Belleney J,Roques BP,Laval J

    更新日期:1984-07-11 00:00:00

  • GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.

    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 gra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn330

    authors: Martinez-Guerrero CE,Ciria R,Abreu-Goodger C,Moreno-Hagelsieb G,Merino E

    更新日期:2008-07-01 00:00:00

  • Demonstration of a word design strategy for DNA computing on surfaces.

    abstract::A strategy for DNA computing on surfaces using linked sets of 'DNA words' that are short oligonucleotides (16mers) is proposed. The 16mer words have the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in 8 variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.23.4748

    authors: Frutos AG,Liu Q,Thiel AJ,Sanner AM,Condon AE,Smith LM,Corn RM

    更新日期:1997-12-01 00:00:00

  • In vivo cleavage rules and target repertoire of RNase III in Escherichia coli.

    abstract::Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky684

    authors: Altuvia Y,Bar A,Reiss N,Karavani E,Argaman L,Margalit H

    更新日期:2018-11-02 00:00:00

  • Real-time analysis of single influenza virus replication complexes reveals large promoter-dependent differences in initiation dynamics.

    abstract::The viral RNA (vRNA) genome of influenza viruses is replicated by the RNA-dependent RNA polymerase (RNAP) via a complementary RNA (cRNA) intermediate. The vRNA promoter can adopt multiple conformations when bound by the RNAP. However, the dynamics, determinants, and biological role of these conformations are unknown; ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz313

    authors: Robb NC,Te Velthuis AJW,Fodor E,Kapanidis AN

    更新日期:2019-07-09 00:00:00

  • Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit.

    abstract::The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the si...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.8.2369

    authors: Singer J,Roberts-Ems J,Luthardt FW,Riggs AD

    更新日期:1979-12-20 00:00:00

  • EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

    abstract::The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mappi...

    journal_title:Nucleic acids research

    pub_type: 历史文章,杂志文章

    doi:10.1093/nar/gkj146

    authors: Schmid CD,Perier R,Praz V,Bucher P

    更新日期:2006-01-01 00:00:00

  • A periodic pattern of mRNA secondary structure created by the genetic code.

    abstract::Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl287

    authors: Shabalina SA,Ogurtsov AY,Spiridonov NA

    更新日期:2006-05-08 00:00:00

  • A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand.

    abstract::Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.21.4249

    authors: Ikehara K,Amada F,Yoshida S,Mikata Y,Tanaka A

    更新日期:1996-11-01 00:00:00

  • Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions.

    abstract::Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz368

    authors: Roy AA,Dhawanjewar AS,Sharma P,Singh G,Madhusudhan MS

    更新日期:2019-07-02 00:00:00

  • Phylogenetic evidence for tertiary interactions in 16S-like ribosomal RNA.

    abstract::Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.6.2215

    authors: Haselman T,Camp DG,Fox GE

    更新日期:1989-03-25 00:00:00

  • Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants.

    abstract::enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the mol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm173

    authors: Gultyaev AP,Roussis A

    更新日期:2007-01-01 00:00:00

  • miROrtho: computational survey of microRNA genes.

    abstract::MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn707

    authors: Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

    更新日期:2009-01-01 00:00:00

  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences.

    abstract::Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq487

    authors: Chikkagoudar S,Livesay DR,Roshan U

    更新日期:2010-07-01 00:00:00

  • Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide.

    abstract::The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.23.6167

    authors: Xu R,Birke S,Carberry SE,Geacintov NE,Swenberg CE,Harvey RG

    更新日期:1992-12-11 00:00:00