Abstract:
:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog mapping and mining of information about orthologs in common genetic model species; reagent-centric resources that help researchers identify RNAi and CRISPR sgRNA reagents or designs; and data-centric resources that facilitate visualization and mining of transcriptomics data, protein modification data, protein interactions, and more. Here, we discuss updated and new features that help biological and biomedical researchers efficiently identify, visualize, analyze, and integrate information and data for Drosophila and other species. Together, these resources facilitate multiple steps in functional genomics workflows, from building gene and reagent lists to management, analysis, and integration of data.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hu Y,Comjean A,Rodiger J,Liu Y,Gao Y,Chung V,Zirin J,Perrimon N,Mohr SEdoi
10.1093/nar/gkaa936subject
Has Abstractpub_date
2021-01-08 00:00:00pages
D908-D915issue
D1eissn
0305-1048issn
1362-4962pii
5940514journal_volume
49pub_type
杂志文章abstract::KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh991
更新日期:2004-12-15 00:00:00
abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2483
更新日期:1979-06-11 00:00:00
abstract::Transcription factor IIIA (TFIIIA) and p43 zinc finger protein form distinct complexes with 5S ribosomal RNA in Xenopus oocytes. Additionally, TFIIIA binds the internal promoter of the 5S RNA gene and supports assembly of a transcription initiation complex. Both proteins have nine tandemly repeated zinc fingers with a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.703
更新日期:1998-02-01 00:00:00
abstract::During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw172
更新日期:2016-05-19 00:00:00
abstract::An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1941
更新日期:1993-04-25 00:00:00
abstract::A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of ol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.24.5156
更新日期:1994-12-11 00:00:00
abstract::The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA dama...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa127
更新日期:2020-05-07 00:00:00
abstract::A microchip method has been developed for massive and parallel thermodynamic analyses of DNA duplexes. Fluorescently labeled oligonucleotides were hybridized with oligonucleotides immobilized in the 100 x 100 x 20 mum gel pads of the microchips. The equilibrium melting curves for all microchip duplexes were measured i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.6.1515
更新日期:1998-03-15 00:00:00
abstract::Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg457
更新日期:2003-07-15 00:00:00
abstract::Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm513
更新日期:2007-01-01 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.10.2331
更新日期:1993-05-25 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
abstract::We have constructed a complete, five-enzyme restriction map of the genome of the archaeon Halobacterium sp. GRB, based on a set of 84 overlapping cosmid clones. Fewer than 30 kbp, in three gaps, remain uncloned. The genome consists of five replicons: a chromosome (2038 kbp) and four plasmids (305, 90, 37, and 1.8 kbp)...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.8.1476
更新日期:1994-04-25 00:00:00
abstract::On the tandemly linked ribosomal genes of Xenopus laevis, the RNA polymerase transcribes past the 3' end of the 40S coding region and terminates at T3 just upstream of the gene promoter. The close proximity of T3 to the gene promoter, and the functional interdependence of these two elements, has led to the suggestion ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.373
更新日期:1989-01-11 00:00:00
abstract::The contacts of phosphate groups in mRNAs with ribosomes were studied. Two mRNAs were used: one mRNA contained in the middle two defined codons to construct the pre- and the post-translocational states, the other was a sequence around the initiation site of the natural cro-mRNA. Phosphorothioate nucleotides were rando...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2228
更新日期:1996-06-15 00:00:00
abstract::Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky084
更新日期:2018-04-06 00:00:00
abstract::Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.143
更新日期:1999-01-01 00:00:00
abstract::Cyclic AMP response element binding protein (CREB) activates transcription of cAMP response element (CRE)-containing promoters following an elevation of intracellular cAMP. Here we show that CREB and the highly related protein ATF-1 are also potent transcription inhibitors. Strikingly, CREB inhibits transcription of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2907
更新日期:1993-06-25 00:00:00
abstract::A DNA region of 2750 base pairs encompassing the genes III, VI and I of bacteriophage M13 has been sequenced by the Maxam-Gilbert procedure. By establishing the nucleotide changes introduced by several amber mutations, the coding region and the regulatory signals of each gene have been deduced. The genes appear to spa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2799
更新日期:1979-06-25 00:00:00
abstract::Two different genomic genes for the COUP-transcription factor, COUP-TF I and COUP-TF II, have been isolated from a human cosmid genomic library using a [32P]-labeled cDNA probe. Data obtained from Southern blot analysis of these cosmid clones indicated that two closely related genes exist in the human genome and have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6857
更新日期:1990-12-11 00:00:00
abstract::The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.5.2259
更新日期:1984-03-12 00:00:00
abstract::The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into DNA in vitro. To determine the effects of this incorporation on DNA structure and function, the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides containing dFdC were made using automated sol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1763
更新日期:1992-04-11 00:00:00
abstract::Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2407
更新日期:1977-07-01 00:00:00
abstract::Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl287
更新日期:2006-05-08 00:00:00
abstract::We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.19.5935
更新日期:1982-10-11 00:00:00
abstract::Large-scale cooperative helix opening has been previously observed in A + T rich sequences contained in supercoiled DNA molecules at elevated temperatures. Since it is well known that helix melting of linear DNA is suppressed by addition of salt, we have investigated the effects of added salts on opening transitions i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.2042
更新日期:1994-06-11 00:00:00
abstract::Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm057
更新日期:2007-01-01 00:00:00
abstract::Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj470
更新日期:2006-02-02 00:00:00
abstract::Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vec...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr436
更新日期:2011-08-01 00:00:00