Abstract:
:The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kolchanov NA,Ananko EA,Podkolodnaya OA,Ignatieva EV,Stepanenko IL,Kel-Margoulis OV,Kel AE,Merkulova TI,Goryachkovskaya TN,Busygina TV,Kolpakov FA,Podkolodny NL,Naumochkin AN,Romashchenko AGdoi
10.1093/nar/27.1.303subject
Has Abstractpub_date
1999-01-01 00:00:00pages
303-6issue
1eissn
0305-1048issn
1362-4962pii
gkc013journal_volume
27pub_type
杂志文章abstract::To achieve drug resistance Leishmania parasite alters gene copy number by using its repeated sequences widely distributed through the genome. Even though homologous recombination (HR) is ascribed to maintain genome stability, this eukaryote exploits this potent mechanism driven by the Rad51 recombinase to form benefic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv118
更新日期:2015-03-11 00:00:00
abstract::Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1074
更新日期:2012-01-01 00:00:00
abstract::ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1108
更新日期:2018-01-04 00:00:00
abstract::RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq531
更新日期:2010-07-01 00:00:00
abstract::An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw026
更新日期:2016-05-05 00:00:00
abstract::Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elemen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki486
更新日期:2005-07-01 00:00:00
abstract::Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1177
更新日期:2019-01-10 00:00:00
abstract::A single locus in the mouse, rat and chicken encodes both alkali myosin light chains, MLC1F and MLC3F. This gene has two distinct promoters and gives rise to two different primary transcripts, which are processed by alternative and different modes of splicing to form MLC1F and MLC3F mRNAs. The MLC1F/MLC3F gene is very...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.13.4623
更新日期:1985-07-11 00:00:00
abstract::The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, includin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.320
更新日期:2000-01-01 00:00:00
abstract::In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd(2+) due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv519
更新日期:2015-07-13 00:00:00
abstract::Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2633
更新日期:1993-06-11 00:00:00
abstract::Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa874
更新日期:2020-11-18 00:00:00
abstract::Purified UvrA, UvrB, UvrC, UvrD, PolA and Lig proteins from Escherichia coli have been used to assess the effect of nucleotide excision repair on the conformation of native negatively supercoiled plasmid DNA in an in vitro test system. The analysis of labeled reaction products on specific gel systems suggests that the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.24.10337
更新日期:1989-12-25 00:00:00
abstract::The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg017
更新日期:2003-01-01 00:00:00
abstract::Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational metho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki841
更新日期:2005-09-14 00:00:00
abstract::The cnjC gene from the protozoan Tetrahymena thermophila was completely sequenced. The deduced gene product was found to have significant sequence similarity to the yeast and prokaryotic RNA polymerase subunits involved with subunit assembly. Since cnjC is active only during the sexual stage (conjugation) of Tetrahyme...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2953
更新日期:1990-05-25 00:00:00
abstract::Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.23.6369
更新日期:1981-12-11 00:00:00
abstract::Sox proteins belong to the HMG box superfamily of DNA-binding proteins and are found throughout the animal kingdom. They are involved in the regulation of such diverse developmental processes as germ layer formation, organ development and cell type specifi-cation. Hence, deletion or mutation of Sox proteins often resu...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/27.6.1409
更新日期:1999-03-15 00:00:00
abstract::Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes an...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/27.5.1243
更新日期:1999-03-01 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::Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immun...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1343
更新日期:2015-01-01 00:00:00
abstract::There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.31
更新日期:1986-01-10 00:00:00
abstract::We previously reported the isolation of PRP28, a gene in Saccharomyces cerevisiae whose activity is required for the first step of nuclear mRNA splicing in vivo. Sequence analysis revealed that PRP28 is included in the 'DEAD-box' gene family, members of which are thought to function as ATP-dependent RNA helicases. Gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3187
更新日期:1994-08-11 00:00:00
abstract::The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast metho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv977
更新日期:2016-02-18 00:00:00
abstract::Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw620
更新日期:2016-11-02 00:00:00
abstract::Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular disea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa305
更新日期:2020-06-19 00:00:00
abstract::A synthetic gene encoding the Schizophyllum commune xylanase XynA was constructed by a novel PCR-based procedure. Three long oligonucleotides were synthesized and used in combination with flanking PCR primers to generate a 607 base pair gene which contained 31 unique locations for restriction enzyme cleavage. The amin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.21.4923
更新日期:1993-10-25 00:00:00
abstract::Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately isolated by phosphocellulose column chromatography (Ozaki et al., 1991 (2)). Here, the promoter selectivity of these three st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.257
更新日期:1992-01-25 00:00:00
abstract::UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustere...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1022
更新日期:2019-01-08 00:00:00
abstract::We have isolated the mouse MyoD1 gene flanked by its promoter region by screening a genomic library with synthetic oligonucleotides. The structural gene is interrupted by two G + C rich introns. Transfection of the cloned gene inserted into an expression vector converts fibroblasts to myoblasts. Sequence analysis of a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6433
更新日期:1991-12-11 00:00:00