Abstract:
:To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wiwatwattana N,Kumar Adoi
10.1093/nar/gki071keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
D598-604issue
Database issueeissn
0305-1048issn
1362-4962pii
33/suppl_1/D598journal_volume
33pub_type
杂志文章abstract::1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5689
更新日期:1991-10-25 00:00:00
abstract::Three Rat1/Xrn2 homologues exist in Arabidopsis thaliana: nuclear AtXRN2 and AtXRN3, and cytoplasmic AtXRN4. The latter has a role in degrading 3' products of miRNA-mediated mRNA cleavage, whereas all three proteins act as endogenous post-transcriptional gene silencing suppressors. Here we show that, similar to yeast ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq172
更新日期:2010-07-01 00:00:00
abstract::We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.16.3269
更新日期:1997-08-15 00:00:00
abstract::Ribosome-inactivating proteins (RIP) are a family of plant enzymes for which a unique activity was determined: rRNAN-glycosidase at a specific universally conserved position, A4324in the case of rat ribosomes. Recently we have shown that the RIP from Saponaria officinalis have a much wider substrate specificity: they ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.3.518
更新日期:1997-02-01 00:00:00
abstract::The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.307
更新日期:1991-01-25 00:00:00
abstract::Aging research is a multi-disciplinary field encompassing knowledge from many areas of basic, applied and clinical research. Age-related processes occur on molecular, cellular, tissue, organ, system, organismal and even psychological levels, trigger the onset of multiple debilitating diseases and lead to a loss of fun...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1287
更新日期:2016-01-04 00:00:00
abstract::Heat shock genes are activated by the binding of the heat shock transcription factor (HSF) to heat shock elements (HSEs), consisting of arrays of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.2.167
更新日期:1994-01-25 00:00:00
abstract::With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Further...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv677
更新日期:2015-09-03 00:00:00
abstract::Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg751
更新日期:2003-09-15 00:00:00
abstract::Gene duplication is an important process in evolution. The availability of genome sequences of a number of organisms has made it possible to conduct comprehensive searches for duplicated genes enabling informative studies of their evolution. We have established the FGF (Fishing Gene Family) program to efficiently sear...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm426
更新日期:2007-07-01 00:00:00
abstract::The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1164
更新日期:2013-01-01 00:00:00
abstract::Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng066
更新日期:2003-06-01 00:00:00
abstract::In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn629
更新日期:2008-11-01 00:00:00
abstract::Heptadecaoligodeoxyribonucleotides containing one or more of the bases, 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), and hypoxanthine (I) and combinations of P with K and I have been synthesised on a DNA synthesiser. The stability of duplexes containing these basemodified ol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.19.5149
更新日期:1992-10-11 00:00:00
abstract::DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr053
更新日期:2011-05-01 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::Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1036
更新日期:2014-11-10 00:00:00
abstract::Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx920
更新日期:2018-01-04 00:00:00
abstract::The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.17.3483
更新日期:1994-09-01 00:00:00
abstract::Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4945
更新日期:1987-06-25 00:00:00
abstract::HOX11 is a homeobox-containing oncogene of specific T-cell leukemias. We determined the DNA binding specificity of the Hox11 protein by using a novel technique of random oligonucleotide selection developed in this study. The optimal Hox11 binding sequence, GGCGGTAAGTGG, contained a core TAAGTG motif that is consistent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.11.1928
更新日期:1995-06-11 00:00:00
abstract::The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg237
更新日期:2003-03-01 00:00:00
abstract::Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.19.3899
更新日期:1999-10-01 00:00:00
abstract::The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm689
更新日期:2007-01-01 00:00:00
abstract::Multi-modal interactions are frequently observed in intrinsically disordered regions (IDRs) of proteins upon binding to their partners. In many cases, post-translational modifications in IDRs are accompanied by coupled folding and binding. From both molecular simulations and biochemical experiments with mutational stu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1297
更新日期:2018-03-16 00:00:00
abstract::DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw993
更新日期:2017-01-04 00:00:00
abstract::The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.789
更新日期:1978-03-01 00:00:00
abstract::Conformations of 8-bromo-2'-[unk]-triisopropylbenzenesulfonyladenosine ([unk]) and its 3'-[unk]-isomer ([unk]) in solution have been determined by the use of intramolecular nuclear Overhauser effects in (1)H NMR spectroscopy. Compound [unk] has been proved to have a conformation in which the adenosine and benzene ring...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.6.823
更新日期:1974-06-01 00:00:00
abstract::This is a study of the effect of total and partial deuteration of solvent on critical temperatures and profiles of all four reactions occurring in poly(A) x n poly(U) (n = 1 or 2) aqueous systems. The study was done at observational times not longer than hydrogen exchange times at base pairs in helically ordered struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.18.4283
更新日期:1980-09-25 00:00:00
abstract::Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky828
更新日期:2018-10-12 00:00:00