Abstract：
:In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1,956,826 entries or 1,741,313,111 bases. The released data include approximately 90,000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse GSS. In addition to the data collection, we have indexed the submitted data to the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org) to classify the entries into research projects behind data submissions. They are expected to be useful to the data submitters and users for enhancing the data submission, retrieval and systematic data analyses at INSDC. The results of indexing also allow one to grasp research projects in life sciences that promoted and produced the DNA sequences submitted to INSDC.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Okubo K,Sugawara H,Gojobori T,Tateno Ydoi
10.1093/nar/gkj111keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D6-9issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D6journal_volume
34pub_type
杂志文章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
abstract：:We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq275
更新日期：2010-07-01 00:00:00
abstract：:In this study, we demonstrate that the lack of retinoic acid-related orphan receptor (ROR) γ or α expression in mice significantly reduced the peak expression level of Cry1, Bmal1, E4bp4, Rev-Erbα and Per2 in an ROR isotype- and tissue-selective manner without affecting the phase of their rhythmic expression. Analysis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks630
更新日期：2012-09-01 00:00:00
abstract：:We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn524
更新日期：2008-10-01 00:00:00
abstract：:Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.7.1410
更新日期：2001-04-01 00:00:00
abstract：:We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.15.6307
更新日期：1984-08-10 00:00:00
abstract：:We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf647
更新日期：2002-12-01 00:00:00
abstract：:The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.10.1855
更新日期：1994-05-25 00:00:00
abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.16.4467
更新日期：1991-08-25 00:00:00
abstract：:Human telomerase RNA (hTR) contains several guanine tracts at its 5'-end that can form a G4-quadruplex structure. Previous evidence suggests that a G4-quadruplex within this region disrupts the formation of an important structure within hTR known as the P1 helix, a critical element in defining the template boundary fo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1306
更新日期：2012-05-01 00:00:00
abstract：:The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1163
更新日期：2015-01-01 00:00:00
abstract：:The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1012
更新日期：2014-01-01 00:00:00
abstract：:Alternative splicing constitutes a major mechanism creating protein diversity in humans. This diversity can result from the alternative skipping of entire exons or by alternative selection of the 5' or 3' splice sites that define the exon boundaries. In this study, we analyze the sequence and evolutionary characterist...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm603
更新日期：2007-01-01 00:00:00
abstract：:Synthesis and antisense activity of oligonucleotides modified with 2'-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2'-O-DMAOE) are described. The 2'-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide 'gapmers', with 2'-O-DMAOE- modified nucleoside residues at t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh220
更新日期：2004-02-03 00:00:00
abstract：:To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1138
更新日期：2008-03-01 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：:The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh236
更新日期：2004-02-11 00:00:00
abstract：:Constitutive expression of major histocompatibility complex class II (MHC II) antigens normally occurs in B-lymphocytes and antigen presenting cells of the monocyte/macrophage lineage. However, many malignant tumours and transformed cells express these proteins aberrantly. We demonstrate here that the MHC II DR alpha ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4881
更新日期：1992-09-25 00:00:00
abstract：:The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1010
更新日期：2010-01-01 00:00:00
abstract：:The genome stability is maintained by coordinated action of DNA repairs and checkpoints, which delay progression through the cell cycle in response to DNA damage. Rad9 is conserved from yeast to human and functions in cell cycle checkpoint controls. Here, a regulatory mechanism for Rad9 function is reported. In this s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1264
更新日期：2011-06-01 00:00:00
abstract：:7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique Pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku711
更新日期：2014-09-01 00:00:00
abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5423
更新日期：1992-10-25 00:00:00
abstract：:A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.20.8007
更新日期：1986-10-24 00:00:00
abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.9.2951
更新日期：1982-05-11 00:00:00
abstract：:G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1613
更新日期：1998-04-01 00:00:00
abstract：:The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1170
更新日期：2020-02-20 00:00:00
abstract：:Observation and tracking of fluorescently labeled molecules and particles in living cells reveals detailed information about intracellular processes on the molecular level. Whereas light microscopic particle observation is usually limited to two-dimensional projections of short trajectory segments, we report here imag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1194
更新日期：2015-01-01 00:00:00
abstract：:HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3' terminal AU-rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh282
更新日期：2004-02-19 00:00:00
abstract：:Use of the polymerase chain reaction (PCR) to amplify variable numbers of tandem repeat (VNTR) loci has become widely used in genetic typing. Unfortunately, preferential amplification of small allelic products relative to large allelic products may result in incorrect or ambiguous typing in a heterozygous sample. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.15.3050
更新日期：1995-08-11 00:00:00
abstract：:The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.24.9729
更新日期：1986-12-22 00:00:00
