Abstract:
:The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the initiation codon (-20, +10); c) the length, 'G+C%' of the third position of codons (GC3), the 'codon adaptation index' (CAI) and the 'effective number of codons' statistic (Nc); d) summary tables for each organism including total codon usage, stop codon and tetranucleotide stop-signal usage, and matrices tallying base frequencies at each position around the initiation and termination codons. The data are arranged to facilitate investigation of the relationships between the three phases of protein synthesis. The database is available electronically from EMBL.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Brown CM,Stockwell PA,Dalphin ME,Tate WPdoi
10.1093/nar/22.17.3620subject
Has Abstractpub_date
1994-09-01 00:00:00pages
3620-4issue
17eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::The rates of acid-catalyzed hydrolysis of a hypermodified nucleoside, wyosine and its 5'-monophosphate were determined at various pH, temperature and buffer concentrations. The results show that despite distinct differences in structure and the glycosyl bond stability, the hydrolysis of wyosine proceeds via cleavage o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.7.2443
更新日期:1985-04-11 00:00:00
abstract::Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.7.1362
更新日期:1997-04-01 00:00:00
abstract::Staphylococcus aureus plasmid pT181 is thought to replicate via an asymmetric rolling-circle mechanism. By studying pulse labeled replicative intermediates, here we report that pT181 replication involves: (1) a post-replicative hypersupercoiled monomer and (2) a partially replicated intermediate which lacks superhelic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.2897
更新日期:1988-04-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8181
更新日期:1984-11-12 00:00:00
abstract::Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.10.2103
更新日期:2002-05-15 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::Molecular beacons (MBs) have the potential to provide a powerful tool for rapid RNA detection in living cells, as well as monitoring the dynamics of RNA expression in response to external stimuli. To exploit this potential, it is necessary to distinguish true signal from background signal due to non-specific interacti...
journal_title:Nucleic acids research
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更新日期:2010-05-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.13.5071
更新日期:1989-07-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.1081
更新日期:1979-10-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.2.261
更新日期:1990-01-25 00:00:00
abstract::An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx710
更新日期:2017-10-13 00:00:00
abstract::After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.9.1960
更新日期:2001-05-01 00:00:00
abstract::Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog page...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp953
更新日期:2010-01-01 00:00:00
abstract::The Saccharomyces cerevisiae Sgs1p helicase localizes to the nucleolus and is required to maintain the integrity of the rDNA repeats. Sgs1p is a member of the RecQ DNA helicase family, which also includes Schizo-saccharomyces pombe Rqh1, and the human BLM and WRN genes. These genes encode proteins which are essential ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.9.1978
更新日期:1999-05-01 00:00:00
abstract::A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1613
更新日期:1990-03-25 00:00:00
abstract::This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/15.23.9985
更新日期:1987-12-10 00:00:00
abstract::The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to imp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm352
更新日期:2007-07-01 00:00:00
abstract::Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn391
更新日期:2008-08-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6341
更新日期:1982-10-25 00:00:00
abstract::Effective drug discovery and optimization can be accelerated by techniques capable of deconvoluting the complexities often present in targeted biological systems. We report a single-molecule approach to study the binding of an alternative splicing regulator, muscleblind-like 1 protein (MBNL1), to (CUG)n = 4,6 and the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt330
更新日期:2013-07-01 00:00:00
abstract::Au (III) reacts with DNA at pH 5.6 to form a complex which is sensitive to mid-UV radiation. Cyclobutane pyrimidine dimers are produced at some 15 to 30 times the rate that they are in untreated DNA. The mechanism of photosensitization appears to involve energy absorption by Au-urine and Au-cytosine adducts which can ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.10.3731
更新日期:1978-10-01 00:00:00
abstract::The UAS (upstream activator sequence) of the yeast PGK gene contains a transcriptional activator domain located between bases -479 and -402 upstream from the initiating ATG. This region of the UAS contains three direct repeats of the sequence 5'CTTCC3'. The roles in transcriptional activation of these repeats and othe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.17.8245
更新日期:1988-09-12 00:00:00
abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1613
更新日期:1994-05-11 00:00:00
abstract::The cDNA encoding Chinese hamster O6-alkylguanine-DNA-alkyltransferase (ATase) has been isolated from a library prepared from RNA isolated from V79 lung fibroblasts which had an upregulated level of this repair activity following stepwise selection with a chloroethylating agent (1, 2). Expression of the cDNA in E. col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.8.1891
更新日期:1992-04-25 00:00:00
abstract::Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the sign...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1253
更新日期:2021-01-25 00:00:00
abstract::Human minisatellite probes cross-hybridize to mouse DNA and detect multiple variable loci. The resulting DNA "fingerprints" vary substantially between inbred strains but relatively little within an inbred strain. By studying the segregation of variable DNA fragments in BXD recombinant inbred strains of mice, at least ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.7.2823
更新日期:1987-04-10 00:00:00
abstract::The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to s...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2020-07-09 00:00:00
abstract::We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4145
更新日期:1989-06-12 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1239
更新日期:2010-04-01 00:00:00
abstract::Accumulation of replicative intermediates of the bacteriophage phi X174 was observed in E. coli C infected cells when phage DNA methylation has been inhibited by nicotinamide or when cells were infected with a temperature-sensitive mutant in gene A. Analysis of the accumulating replicative intermediates by electron mi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.10.3483
更新日期:1977-10-01 00:00:00