Abstract:
:The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
He S,Liu C,Skogerbø G,Zhao H,Wang J,Liu T,Bai B,Zhao Y,Chen Rdoi
10.1093/nar/gkm1011subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D170-2issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm1011journal_volume
36pub_type
杂志文章abstract::The oligomerization state and mode of binding to DNA of the GIY-YIG endonuclease II (EndoII) from bacteriophage T4 was studied using gel filtration and electrophoretic mobility shift assays with a set of mutants previously found to have altered enzyme activity. At low enzyme/DNA ratios all mutants except one bound to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp652
更新日期:2009-10-01 00:00:00
abstract::We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1521
更新日期:1991-04-11 00:00:00
abstract::We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.14.2774
更新日期:1996-07-15 00:00:00
abstract::SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1277
更新日期:2017-04-20 00:00:00
abstract::In Trypanosoma brucei, the mutually exclusive expression of the major surface antigens, the variant surface glycoprotein (VSG) of the bloodstream form and procyclin of the procyclic form, is due to a stage-specific accumulation of the respective mRNAs. Through the targeting of a reporter construct in the procyclin pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.11.1862
更新日期:1995-06-11 00:00:00
abstract::Recombinant plasmids which contain EcoRI fragments of tobacco chloroplast DNA carrying tRNA genes were constructed. Plasmids pTC211 and pTC293 contain the base sequences for tRNAAsn in their 1.4 and 1.1 Md EcoRI fragments, respectively. These two tRNA sequences are identical and are; 5'-TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGC...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.21.5601
更新日期:1981-11-11 00:00:00
abstract::It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.11.3679
更新日期:1983-06-11 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.1043
更新日期:1979-10-25 00:00:00
abstract::The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw348
更新日期:2016-07-08 00:00:00
abstract::Toxic metals are part of our environment, and undue exposure to them leads to a variety of pathologies. In response, most organisms adapt their metabolism and have evolved systems to limit this toxicity and to acquire tolerance. Ribosome biosynthesis being central for protein synthesis, we analyzed in yeast the effect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt335
更新日期:2013-07-01 00:00:00
abstract::Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3497
更新日期:1997-09-01 00:00:00
abstract::This study describes a novel functional property of the eukaryotic transcription factor NF-kappa B in altering the DNA structure. We observed that the binding of purified NF-kappa B to DNA was facilitated by spermine and cations which are known to promote DNA bending, and by a nick in one position at the 3'-end of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.22.6497
更新日期:1990-11-25 00:00:00
abstract::Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage X174), whi...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/gkm688
更新日期:2007-01-01 00:00:00
abstract::Bacillus subtilis plasmid pGR71 is a promoter-probe shuttle vector derived from pUB110. The expression of the cat gene on pGR71 in B. subtilis requires the insertion of a Bacillus promoter and a ribosomal binding site (RBS) into the HindIII cloning site immediately upstream from the cat gene. A recombinant plasmid of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.4.739
更新日期:1990-02-25 00:00:00
abstract::RNA silencing is an evolutionarily conserved mechanism triggered by double-stranded RNA that is processed into 21- to 24-nt small interfering (si)RNA or micro (mi)RNA by RNaseIII-like enzymes called Dicers. Gene regulations by RNA silencing have fundamental implications in a large number of biological processes that i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku422
更新日期:2014-07-01 00:00:00
abstract::Southern blot analyses using reduced stringency hybridization conditions have been employed to search for sequence homologies between rodent VL30 genes and murine leukemia virus (MuLV) proviruses. These constitute two classes of transposon-like elements previously believed to be genetically unrelated. Our results demo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.2.305
更新日期:1983-01-25 00:00:00
abstract::Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj141
更新日期:2006-01-01 00:00:00
abstract::The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku314
更新日期:2014-06-01 00:00:00
abstract::The molecular organization of the dunce gene of Drosophila melanogaster has proved to be particularly complex, with two divergently transcribed genes, Sgs-4 and Pig-1, nested within its 79 kb intron (1). Here we report the identification and the molecular characterization of a third gene nested within the transcriptio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5837
更新日期:1990-10-11 00:00:00
abstract::Phosphorylation of the cellular single-stranded DNA-binding protein, replication protein A (RPA), occurs during normal mitotic cell cycle progression and also in response to genotoxic stress. In budding yeast, these reactions require the ATM homolog Mec1, a central regulator of the DNA replication and DNA damage check...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.23.4808
更新日期:2001-12-01 00:00:00
abstract::To screen multiple loci in small purified samples of diploid and aneuploid cells a PCR-based technique of whole genome amplification was adapted to the study of somatic lesions. DNA samples from different numbers of flow-sorted diploid and aneuploid cells from biopsies were amplified with a degenerate 15mer primer. Al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3488
更新日期:1995-09-11 00:00:00
abstract::Initially identified as a factor involved in tyrosine kinase receptor signaling, Grb10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5' cap-binding protein 4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. A curre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky198
更新日期:2018-06-20 00:00:00
abstract::Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl582
更新日期:2006-01-01 00:00:00
abstract::NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1159
更新日期:2017-01-25 00:00:00
abstract::Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkab034
更新日期:2021-01-27 00:00:00
abstract::A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku306
更新日期:2014-07-01 00:00:00
abstract::Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1149
更新日期:2020-12-16 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::Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky926
更新日期:2018-12-14 00:00:00