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 search for and identify gene families. The FGF output displays the results as visual phylogenetic trees including information on gene structure, chromosome position, duplication fate and selective pressure. It is particularly useful to identify pseudogenes and detect changes in gene structure. FGF is freely available on a web server at http://fgf.genomics.org.cn/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zheng H,Shi J,Fang X,Li Y,Vang S,Fan W,Wang J,Zhang Z,Wang W,Kristiansen K,Wang Jdoi
10.1093/nar/gkm426subject
Has Abstractpub_date
2007-07-01 00:00:00pages
W121-5issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkm426journal_volume
35pub_type
杂志文章abstract::Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer ac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg187
更新日期:2003-02-01 00:00:00
abstract::The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky368
更新日期:2018-07-06 00:00:00
abstract::The attachment of replicating DNA to a rapidly sedimenting nuclear structure was investigated by digestion with various nucleases. When DNA was gradually removed by DNase I, pulse label incorporated during either 1 min or during 1 hour in the presence of arabinosylcytosine, remained preferentially attached to the nucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.1.219
更新日期:1979-01-01 00:00:00
abstract::The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx096
更新日期:2017-05-05 00:00:00
abstract::We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.20.7515
更新日期:1985-10-25 00:00:00
abstract::WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz920
更新日期:2020-01-08 00:00:00
abstract::The swi4+ gene of Schizosaccharomyces pombe is involved in termination of copy-synthesis during mating-type switching. The gene was cloned by functional complementation of a swi4 mutant transformed with a genomic library. Determination of the nucleotide sequence revealed an open reading frame of 2979 nucleotides which...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2271
更新日期:1992-05-11 00:00:00
abstract::We analyzed the effects of site-directed mutations in the SUC2 promoter of Saccharomyces cerevisiae. Analyses were performed in wild-type as well as mig1 and tup1 mutant strains after the promoter mutants were reintroduced into the native SUC2 locus on the left arm of chromosome IX. Mutation of the two GC boxes reveal...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.4.1002
更新日期:1998-02-15 00:00:00
abstract::Reversion of T type cytoplasmic male sterility (cmsT) to fertility is correlated with sequence changes in a 1.5 kb AvaI fragment. This 1.5 kb AvaI fragment is composed of 5' flanking sequences of ATPase subunit 6, one complete open reading frame (ORF 13) and part of the another (ORF 25). The sequence of the 1.5 kb Ava...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.15.6091
更新日期:1987-08-11 00:00:00
abstract::In vivo footprinting experiments, augmented with gel shift and transfection analyses suggest that activation of the CYP1A1 gene by aryl hydrocarbons may be a multicomponent process. During the first 30 minutes of exposure to aryl hydrocarbon carcinogens and environmental contaminants, in vivo footprints appear at nine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1741
更新日期:1994-05-11 00:00:00
abstract::The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl994
更新日期:2007-01-01 00:00:00
abstract::We have examined the transcript levels of the Saccharomyces cerevisiae DNA repair gene RAD18 in UV irradiated cells, in the mitotic cell cycle, and during meiosis. Levels of RAD18 mRNA increased upon UV irradiation, but remained constant during the mitotic cell cycle. During meiosis, RAD18 mRNA levels rose about 4 fol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.4.893
更新日期:1991-02-25 00:00:00
abstract::The pyrrole-imidazole (Py-Im) triamide-cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf486
更新日期:2002-09-01 00:00:00
abstract::Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq769
更新日期:2011-01-01 00:00:00
abstract::The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg449
更新日期:2003-07-15 00:00:00
abstract::Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz697
更新日期:2019-09-26 00:00:00
abstract::The DNA damage checkpoint halts cell cycle progression in G2 in response to genotoxic insults. Central to the execution of cell cycle arrest is the checkpoint-induced stabilization of securin-separase complex (yeast Pds1-Esp1). The checkpoint kinases Chk1 and Chk2 (yeast Chk1 and Rad53) are thought to critically contr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa355
更新日期:2020-06-19 00:00:00
abstract::Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years of investigation, remains a challenging and unsolved problem. Manual inspection still plays a key role in domain decomp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg189
更新日期:2003-02-01 00:00:00
abstract::PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki479
更新日期:2005-07-01 00:00:00
abstract::A database (http://perso.curie.fr/tsoussi ) is described, in which over 1000 mutations in the human APC gene of tumors (colon cancer predominantly) are compiled from the literature. It includes both molecular information about the mutations and clinical data about the patients. Software has been designed to analyse al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.269
更新日期:1998-01-01 00:00:00
abstract::Initiation of bacterial DNA replication at oriC is mediated by primosomal proteins that act cooperatively to melt an AT-rich region where the replicative helicase is loaded prior to the assembly of the replication fork. In Bacillus subtilis, the dnaD, dnaB and dnaI genes are essential for initiation of DNA replication...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1236
更新日期:2010-05-01 00:00:00
abstract::The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6457
更新日期:1991-12-11 00:00:00
abstract::Phage display technology involves the display of proteins or peptides, as coat protein fusions, on the surface of a phage or phagemid particles. Using standard technology, helper phage are essential for the replication and assembly of phagemid particles, during library production and biopanning. We have eliminated the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl772
更新日期:2006-01-01 00:00:00
abstract::A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3681
更新日期:1982-06-25 00:00:00
abstract::The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm965
更新日期:2008-01-01 00:00:00
abstract::Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh910
更新日期:2004-10-28 00:00:00
abstract::Using peptide arrays and binding to native histone proteins, we show that the ADD domain of Dnmt3a specifically interacts with the H3 histone 1-19 tail. Binding is disrupted by di- and trimethylation of K4, phosphorylation of T3, S10 or T11 and acetylation of K4. We did not observe binding to the H4 1-19 tail. The ADD...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq147
更新日期:2010-07-01 00:00:00
abstract::PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1266
更新日期:2019-03-18 00:00:00
abstract::Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp362
更新日期:2009-07-01 00:00:00
abstract::The intragenic control regions of a eukaryotic tRNA gene have been examined by transcribing mutant forms of a Drosophila tRNAArg gene either by injection into the nucleus of Xenopus oocytes or in extracts prepared from isolated oocyte nuclei. These experiments demonstrate that the selection of the transcription initia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.24.8677
更新日期:1983-12-20 00:00:00