The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.

Abstract:

:The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and other genome features as well as heritable phenotypes and quantitative trait loci. The genome feature catalog is generated by the integration of computational and manual genome annotations generated by NCBI, Ensembl and Vega/HAVANA. MGD curates and maintains the comprehensive listing of functional annotations for mouse genes using the Gene Ontology, and MGD curates and integrates comprehensive phenotype annotations including associations of mouse models with human diseases. Recent improvements include integration of the latest mouse genome build (GRCm38), improved access to comparative and functional annotations for mouse genes with expanded representation of comparative vertebrate genomes and new loads of phenotype data from high-throughput phenotyping projects. All MGD resources are freely available to the research community.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Blake JA,Bult CJ,Eppig JT,Kadin JA,Richardson JE,Mouse Genome Database Group.

doi

10.1093/nar/gkt1225

subject

Has Abstract

pub_date

2014-01-01 00:00:00

pages

D810-7

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gkt1225

journal_volume

42

pub_type

杂志文章
  • The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription.

    abstract::KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1142

    authors: Cogoi S,Ferino A,Miglietta G,Pedersen EB,Xodo LE

    更新日期:2018-01-25 00:00:00

  • Analysis of the gene encoding the RNA subunit of ribonuclease P from cyanobacteria.

    abstract::The genes encoding the RNA subunit of ribonuclease P from the unicellular cyanobacterium Synechocystis sp. PCC 6803, and from the heterocyst-forming strains Anabaena sp. PCC 7120 and Calothrix sp. PCC 7601 were cloned using the homologous gene from Anacystis nidulans (Synechococcus sp. PCC 6301) as a probe. The genes ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.23.6331

    authors: Vioque A

    更新日期:1992-12-11 00:00:00

  • The C/ebp-Atf response element (CARE) location reveals two distinct Atf4-dependent, elongation-mediated mechanisms for transcriptional induction of aminoacyl-tRNA synthetase genes in response to amino acid limitation.

    abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw667

    authors: Shan J,Zhang F,Sharkey J,Tang TA,Örd T,Kilberg MS

    更新日期:2016-11-16 00:00:00

  • Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation.

    abstract::The ability of histone chaperone Anti-silencing factor 1 (Asf1) to direct acetylation of lysine 56 of histone H3 (H3K56ac) represents an important regulatory step in genome replication and DNA repair. In Saccharomyces cerevisiae, Asf1 interacts functionally with a second chaperone, Vps75, and the lysine acetyltransfer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz508

    authors: Cote JM,Kuo YM,Henry RA,Scherman H,Krzizike DD,Andrews AJ

    更新日期:2019-08-22 00:00:00

  • A mathematical model and a computerized simulation of PCR using complex templates.

    abstract::A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.18.3538

    authors: Rubin E,Levy AA

    更新日期:1996-09-15 00:00:00

  • Construction of an expression vector for the fission yeast Schizosaccharomyces pombe.

    abstract::We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.17.8603

    authors: Kudla B,Persuy MA,Gaillardin C,Heslot H

    更新日期:1988-09-12 00:00:00

  • Phylogenetic relationships and altered genome structures among Tetrahymena mitochondrial DNAs.

    abstract::Tetrahymena thermophila mitochondrial DNA is a linear molecule with two tRNAs, large subunit beta (LSU beta) rRNA (21S rRNA) and LSU alpha rRNA (5.8S-like RNA) encoded near each terminus. The DNA sequence of approximately 550 bp of this region was determined in six species of Tetrahymena. In three species the LSU beta...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.1.327

    authors: Morin GB,Cech TR

    更新日期:1988-01-11 00:00:00

  • Construction of yeast artificial chromosome libraries with large inserts using fractionation by pulsed-field gel electrophoresis.

    abstract::A method for constructing yeast artificial chromosome (YAC) libraries with large insert sizes is reported. High molecular weight human DNA was partially digested with EcoRI and cloned in the vector pYAC4. When unfractionated DNA was used, the mean YAC size was 120kb. Fractionation by pulsed-field gel electrophoresis u...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.9.3425

    authors: Anand R,Villasante A,Tyler-Smith C

    更新日期:1989-05-11 00:00:00

  • Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.

    abstract::The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution fol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1349

    authors: Jordán-Pla A,Gupta I,de Miguel-Jiménez L,Steinmetz LM,Chávez S,Pelechano V,Pérez-Ortín JE

    更新日期:2015-01-01 00:00:00

  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences.

    abstract::Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq487

    authors: Chikkagoudar S,Livesay DR,Roshan U

    更新日期:2010-07-01 00:00:00

  • The interaction of high mobility proteins HMG14 and 17 with nucleosomes.

    abstract::The interaction of the high mobility group proteins, HMG14 and HMG17, with nucleosome core particles has been studied. The results show that two molecules of HMG14/17 can be bound tightly but reversibly to each core particle and that their affinity for core particles is greater than their affinity for histone-free DNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.17.3757

    authors: Sandeen G,Wood WI,Felsenfeld G

    更新日期:1980-09-11 00:00:00

  • Activated levels of rRNA synthesis in fission yeast are driven by an intergenic rDNA region positioned over 2500 nucleotides upstream of the initiation site.

    abstract::RNA polymerase I-catalyzed synthesis of the Schizosaccharomyces pombe approximately 37S pre-rRNAs was shown to be sensitive to regulatory sequences located several kilobases upstream of the initiation site for the rRNA gene. An in vitro transcription system for RNA polymerase I-catalyzed RNA synthesis was established ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.3.659

    authors: Liu Z,Zhao A,Chen L,Pape L

    更新日期:1997-02-01 00:00:00

  • Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21.

    abstract::In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.14.2950

    authors: Blom D,Burg Jv,Breek CK,Speijer D,Muijsers AO,Benne R

    更新日期:2001-07-15 00:00:00

  • Molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V(D)J recombination.

    abstract::The somatic V(D)J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences (Rss) and the V(D)J recombinase. A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly(A)+ RNA, using the Rss as a ligand. The deduced amino acid sequence ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.22.5067

    authors: Wu LC,Mak CH,Dear N,Boehm T,Foroni L,Rabbitts TH

    更新日期:1993-11-11 00:00:00

  • Altered cleavage of DNA sequences by bleomycin and its deglycosylated derivative in the presence of actinomycin.

    abstract::The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.8.1516

    authors: Bailly C,Kénani A,Waring MJ

    更新日期:1997-04-15 00:00:00

  • Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes.

    abstract::Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindere...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp248

    authors: Zhang S,Xu M,Li S,Su Z

    更新日期:2009-06-01 00:00:00

  • The cell line A-to-I RNA editing catalogue.

    abstract::Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular disea...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa305

    authors: Schaffer AA,Kopel E,Hendel A,Picardi E,Levanon EY,Eisenberg E

    更新日期:2020-06-19 00:00:00

  • Nuclear RNA transcripts from Drosophila melanogaster ribosomal RNA genes containing introns.

    abstract::The transcription of ribosomal genes in a cell line (Kc) derived from female D.melanogaster, has been investigated using hybridization probes prepared from restriction fragments of a cloned rDNA repeat with a 5 kb type I [Wellauer et al. (1978) Cell 14, 269-278] intron. Gels, of nuclear RNA that have been transferred ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.1.67

    authors: Jolly DJ,Thomas CA Jr

    更新日期:1980-01-11 00:00:00

  • In vitro transcription analysis of the region of Saccharomyces cerevisiae mitochondrial DNA containing the tRNA(fMet) gene.

    abstract::Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.21.5937

    authors: Biswas TK

    更新日期:1991-11-11 00:00:00

  • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

    abstract::Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This pote...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg874

    authors: Cerdeño-Tárraga AM,Efstratiou A,Dover LG,Holden MT,Pallen M,Bentley SD,Besra GS,Churcher C,James KD,De Zoysa A,Chillingworth T,Cronin A,Dowd L,Feltwell T,Hamlin N,Holroyd S,Jagels K,Moule S,Quail MA,Rabbinowitsch E

    更新日期:2003-11-15 00:00:00

  • Compilation of tRNA sequences and sequences of tRNA genes.

    abstract::Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.1.148

    authors: Sprinzl M,Horn C,Brown M,Ioudovitch A,Steinberg S

    更新日期:1998-01-01 00:00:00

  • Large scale chromosomal mapping of human microRNA structural clusters.

    abstract::MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt112

    authors: Mathelier A,Carbone A

    更新日期:2013-04-01 00:00:00

  • DEG: a database of essential genes.

    abstract::Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are con...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh024

    authors: Zhang R,Ou HY,Zhang CT

    更新日期:2004-01-01 00:00:00

  • Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.

    abstract::Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome's subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1253

    authors: Scheunemann AE,Graham WD,Vendeix FA,Agris PF

    更新日期:2010-05-01 00:00:00

  • The k-junction motif in RNA structure.

    abstract::The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP ribosw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku144

    authors: Wang J,Daldrop P,Huang L,Lilley DM

    更新日期:2014-04-01 00:00:00

  • A new telomerase RNA element that is critical for telomere elongation.

    abstract::The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro, telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo, additional proteins are required. Telomerase RNAs of different species vary in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt514

    authors: Laterreur N,Eschbach SH,Lafontaine DA,Wellinger RJ

    更新日期:2013-09-01 00:00:00

  • Cellular uptake mediated by epidermal growth factor receptor facilitates the intracellular activity of phosphorothioate-modified antisense oligonucleotides.

    abstract::Chemically modified antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages have been extensively studied as research and therapeutic agents. PS-ASOs can enter the cell and trigger cleavage of complementary RNA by RNase H1 even in the absence of transfection reagent. A number of cell surface proteins hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky145

    authors: Wang S,Allen N,Vickers TA,Revenko AS,Sun H,Liang XH,Crooke ST

    更新日期:2018-04-20 00:00:00

  • Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine.

    abstract::A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn797

    authors: Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

    更新日期:2008-12-01 00:00:00

  • Proton magnetic resonance studies of ultraviolet-irradiated apurinic acid.

    abstract::In apurinic acid, a single-stranded polydeoxyribonucleotide easily obtained upon depurination of DNA, the proton resonances arising from thymine and cytosine are readily observable in aqueous solution of 25 degrees C. Two methyl thymine resonances, centered at 1.88 ppm and separated by 0.045 ppm, are observed. We attr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/1.8.999

    authors: Rahn RO,Schleich T

    更新日期:1974-08-01 00:00:00

  • Correlation of thermodynamic and genetic properties in the Tn10 encoded TET gene control region.

    abstract::The thermal stability of the Tn10 encoded tetracycline resistance (TET) gene control region is investigated by melting studies using purified DNA restriction fragments containing various amounts of flanking sequences. In order to study the thermodynamic properties of this control region under conditions, where enough ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.8.2685

    authors: Hillen W,Unger B

    更新日期:1982-04-24 00:00:00