Abstract:
:FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIKEN's Mouse Gene Encyclopedia Project aims to collect full-length enriched cDNA clones from various mouse tissues, determine the full-length nucleotide sequences, infer their chromosomal locations by computer and characterize gene expression patterns. FANTOM DB has been developed to facilitate this work and to facilitate functional genomic studies such as positional candidate cloning, cDNA microarrays and protein interaction analyses. FANTOM DB contains 21 076 full-length cDNA sequences with rich functional annotations and is publicly available. FANTOM DB thus provides curated functional annotation to RIKEN full-length enriched mouse clones, and has links to other public resources. FANTOM DB can be accessed at http://fantom.gsc.riken.go.jp/db/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bono H,Kasukawa T,Furuno M,Hayashizaki Y,Okazaki Ydoi
10.1093/nar/30.1.116keywords:
subject
Has Abstractpub_date
2002-01-01 00:00:00pages
116-8issue
1eissn
0305-1048issn
1362-4962journal_volume
30pub_type
杂志文章abstract::Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki640
更新日期:2005-06-08 00:00:00
abstract::Methods for increasing the transient level of expression of transfected DNA in cultured Drosophila cells have been examined. Here we show that cells exposed to the steroid hormone 20-hydroxyecdysone for 48h prior to transfection show an 4 to 5 fold increase in the levels of expression of transfected DNA. By analysis, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9255
更新日期:1987-11-25 00:00:00
abstract::We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky024
更新日期:2018-02-28 00:00:00
abstract::Human papillomavirus 16 (HPV-16), which is involved in genital carcinogenesis, contains an enhancer of transcription that is activated by cellular factors rather than by the viral E2 proteins. The activity resides on a 232 bp segment with 5 binding sites for nuclear factor 1 (NF1), 2 for AP1, and 1 for steroid recepto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.3.465
更新日期:1990-02-11 00:00:00
abstract::Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl058
更新日期:2006-03-14 00:00:00
abstract::EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1235
更新日期:2013-01-01 00:00:00
abstract::When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.19.3951
更新日期:1994-09-25 00:00:00
abstract::Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr201
更新日期:2011-07-01 00:00:00
abstract::Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg400
更新日期:2003-06-01 00:00:00
abstract::By introduction of recombinant plasmids into monkey CV1 cells, we have unambiguously demonstrated that sequences entirely within the 72 bp repeat, which is located upstream of the SV40 early region, are crucial for T-antigen expression in vivo. We have also shown that a DNA fragment containing the 72 bp repeat, insert...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.22.6047
更新日期:1981-11-25 00:00:00
abstract::Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky800
更新日期:2018-10-12 00:00:00
abstract::In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr080
更新日期:2011-07-01 00:00:00
abstract::The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.20.4072
更新日期:1997-10-15 00:00:00
abstract::To investigate the mechanism of N4-aminocytidine-induced mutagenesis, N'-alkyl-N4-aminocytidines and N4-alkyl-N4-aminocytidines were prepared and their mutagenicity on bacteria were assayed. N'-Methyl-N4-aminocytidine, N'-(2-hydroxyethyl)-N4-aminocytidine and N',N'-dimethyl-N4-aminocytidine showed direct-acting mutage...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.24.8893
更新日期:1985-12-20 00:00:00
abstract::HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa527
更新日期:2020-11-18 00:00:00
abstract::Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3769
更新日期:1982-06-25 00:00:00
abstract::The TWIST1 bHLH transcription factor controls embryonic development and cancer processes. Although molecular and genetic analyses have provided a wealth of data on the role of bHLH transcription factors, very little is known on the molecular mechanisms underlying their binding affinity to the E-box sequence of the pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw334
更新日期:2016-06-20 00:00:00
abstract::The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3563
更新日期:1995-09-11 00:00:00
abstract::The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1280
更新日期:2014-03-01 00:00:00
abstract::We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2387
更新日期:1982-04-10 00:00:00
abstract::The oncoprotein c-Myc plays an important role in cell proliferation, transformation, inhibition of differentiation and apoptosis. These functions most likely result from the transcription factor activity of c-Myc. As a heterodimer with Max, the c-Myc protein binds to the E-box sequence (CACGTG), which is also recogniz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1493
更新日期:1997-04-15 00:00:00
abstract::The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1152
更新日期:2015-01-01 00:00:00
abstract::Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1059
更新日期:2012-03-01 00:00:00
abstract::Signals setting the level of transcription of the tRNA-tufB operon have been studied by deletion mapping. TufB transcription was measured in vivo with plasmid-borne tRNA-tufB:galk operon fusions. Removal of the sequences from -133 to -58 with respect to the transcription start point, results in a 90% decrease of tufB ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9515
更新日期:1987-11-25 00:00:00
abstract::Modified nucleosides in natural RNA molecules are essential for their functions. Non-natural nucleoside analogues have been introduced into RNA to manipulate its structure and function. We have recently developed a new strategy for the in situ modification of RNA based on the functionality transfer reaction between an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku538
更新日期:2014-07-01 00:00:00
abstract::We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz905
更新日期:2019-12-02 00:00:00
abstract::Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh045
更新日期:2004-03-05 00:00:00
abstract::Spectroscopic studies of the complexes of double-stranded (ds) DNA with the polymethylene-amine linked heterodimers thiazole orange-thiazole blue, thiazole orange-ethidium, and fluorescein-ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson, S.C., Singh, P. and Glazer, A.N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5720
更新日期:1993-12-11 00:00:00
abstract::The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.563
更新日期:1992-02-11 00:00:00
abstract::We have previously isolated two different aFGF cDNA clones from kidney and brain. The two corresponding mRNA, designated aFGF 1.A and 1.B, are the predominant species in kidney and brain, respectively. During the characterization of aFGF mRNA in glioblastoma cells, we demonstrated that aFGF mRNA in U1242MG and D65MG g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.489
更新日期:1993-02-11 00:00:00