Abstract:
:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes were previously known, and 110 of which remain unidentified despite literature and similarity searches. Seven new genes--arsE, arsF, arsG, treF, xylR, xylG, and xylH--were identified as well as the previously mapped pit and dctA genes. The arrangement of proposed genes relative to possible promoters and terminators suggests 90 potential transcription units. Other features include 19 REP elements, 95 computer-predicted bends, 50 Chi sites, and one grey hole. Thirty-one putative signal peptides were found, including those of thirteen known membrane or periplasmic proteins. One tRNA gene (proK) and two insertion sequences (IS5 and IS150) are located in this segment. The genes in this region are organized with equal numbers oriented with or against replication.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sofia HJ,Burland V,Daniels DL,Plunkett G 3rd,Blattner FRdoi
10.1093/nar/22.13.2576subject
Has Abstractpub_date
1994-07-11 00:00:00pages
2576-86issue
13eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg910
更新日期:2003-12-01 00:00:00
abstract::To develop structural modifications of dNTPs that are compatible with Taq DNA polymerase activity, we synthesized eight dUTP derivatives conjugated with Cy3 or Cy5 dye analogues that differed in charge and charge distribution throughout the fluorophore. These dUTP derivatives and commercial Cy3- and Cy5-dUTP were stud...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky247
更新日期:2018-07-06 00:00:00
abstract::A crucial component of the human mitochondrial DNA replisome is the ring-shaped helicase TWINKLE-a phage T7-gene 4-like protein expressed in the nucleus and localized in the human mitochondria. Our previous studies showed that despite being a helicase, TWINKLE has unique DNA annealing activity. At the time, the implic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw098
更新日期:2016-05-19 00:00:00
abstract::The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1010
更新日期:2021-01-08 00:00:00
abstract::This paper describes a method for predicting a supersecondary structural motif, beta-hairpins, in a protein sequence. The method was trained and tested on a set of 5102 hairpins and 5131 non-hairpins, obtained from a non-redundant dataset of 2880 proteins using the DSSP and PROMOTIF programs. Two machine-learning tech...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki588
更新日期:2005-07-01 00:00:00
abstract::Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.791
更新日期:1985-02-11 00:00:00
abstract::Several authors, including ourselves, have reported the existence of chromatosomes with DNA size larger than 166 bp in bird erythrocyte chromatin. It was tempting to correlate this increased DNA size with the presence of histone H5. In order to substantiate this hypothesis, we performed a micrococcal nuclease digestio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.15.3671
更新日期:1981-08-11 00:00:00
abstract::Translation initiation of eukaryotic mRNAs generally occurs by cap-dependent ribosome scanning. However, certain mRNAs contain internal ribosome entry sites (IRES) allowing cap-independent translation. Several of these IRES-competent transcripts and their corresponding proteins are involved in tumourigenesis. This stu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm096
更新日期:2007-01-01 00:00:00
abstract::We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.19.5935
更新日期:1982-10-11 00:00:00
abstract::We describe the structure (3840 bp) of a novel Euglena gracilis chloroplast ribosomal protein operon that encodes the five genes rpl16-rpl14-rpl5-rps8-rpl36. The gene organization resembles the spc and the 3'-end of the S10 ribosomal protein operons of E. coli. The rpl5 is a new chloroplast gene not previously reporte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.19.7591
更新日期:1989-10-11 00:00:00
abstract::OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa392
更新日期:2020-07-09 00:00:00
abstract::DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1500
更新日期:2002-04-01 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::The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public data...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj145
更新日期:2006-01-01 00:00:00
abstract::Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.18.8835
更新日期:1988-09-26 00:00:00
abstract::TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq837
更新日期:2011-02-01 00:00:00
abstract::The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by forming a covalent bond with the 6-position...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.10.2459
更新日期:1993-05-25 00:00:00
abstract::Significant differences are observed between the CD spectra of eu- and heterochromatin prepared by fractionating mechanically sheared rat liver chromatin on linear sucrose density gradients. Heterochromatin has a broad positive CD at 270--280 nm, a cross-over point at 256 nmn, and a negative shoulder at 248 nm. Euchro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1657
更新日期:1979-04-01 00:00:00
abstract::Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1099
更新日期:2020-12-16 00:00:00
abstract::We have detected a set of transcripts in Drosophila melanogaster cells which are homologous to repeating elements within the 'non-transcribed' spacer region of rDNA. The RNA molecules range from 240 to 1680 nucleotides, differing in length by an integral value of 240 nucleotides. We have sequenced several AluI fragmen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.1.11
更新日期:1983-01-11 00:00:00
abstract::We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1243
更新日期:1992-03-25 00:00:00
abstract::We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.24.7397
更新日期:1990-12-25 00:00:00
abstract::Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz181
更新日期:2019-05-21 00:00:00
abstract::MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.242
更新日期:1996-01-01 00:00:00
abstract::Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku667
更新日期:2014-09-01 00:00:00
abstract::A linear DNA plasmid, designated pLLE1, has been isolated from a mitochondrial fraction of a strain of Lentinus edodes. pLLE1(11.0 kbp) was sensitive to the 3'----5'-acting exonuclease III and resistant to the 5'----3'-acting lambda exonuclease. It showed no homology with mitochondrial and nuclear genomic DNAs of plas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1395
更新日期:1990-03-25 00:00:00
abstract::Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks887
更新日期:2012-11-01 00:00:00
abstract::Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs) are known, even in the well-characterized budding yeast. In silico prediction of protein-RNA interactions is therefore useful to guide experiments and to provide ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr160
更新日期:2011-08-01 00:00:00
abstract::RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.381
更新日期:1993-02-11 00:00:00
abstract::The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during veget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr792
更新日期:2012-02-01 00:00:00