Abstract:
:The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Skrzypek MS,Nash RS,Wong ED,MacPherson KA,Hellerstedt ST,Engel SR,Karra K,Weng S,Sheppard TK,Binkley G,Simison M,Miyasato SR,Cherry JMdoi
10.1093/nar/gkx1112subject
Has Abstractpub_date
2018-01-04 00:00:00pages
D736-D742issue
D1eissn
0305-1048issn
1362-4962pii
4616877journal_volume
46pub_type
杂志文章abstract::The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.1
更新日期:1998-01-01 00:00:00
abstract::p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn414
更新日期:2008-08-01 00:00:00
abstract::Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a hig...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky321
更新日期:2018-07-02 00:00:00
abstract::Interleukin 2 (IL2) mRNA has a short half-life in the cytoplasm of T lymphocytes, relative to most mRNA. We have discovered a candidate ribonuclease to account for the rapid turnover of IL2 mRNA in the cytosol of the human T lymphocyte cell line Jurkat. In partially purified form, this RNase is about 7 times as active...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.1.155
更新日期:1993-01-11 00:00:00
abstract::Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, repr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa106
更新日期:2020-05-07 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::In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq993
更新日期:2011-03-01 00:00:00
abstract::Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-sup...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.169
更新日期:2001-01-01 00:00:00
abstract::High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng015
更新日期:2003-02-15 00:00:00
abstract::S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.372
更新日期:2002-01-01 00:00:00
abstract::Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4279
更新日期:1982-07-24 00:00:00
abstract::We show how to speed up sequence alignment algorithms of the type introduced by Needleman and Wunsch (and generalized by Sellers and others). Faster alignment algorithms have been introduced, but always at the cost of possibly getting sub-optimal alignments. Our modification results in the optimal alignment still bein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part1.175
更新日期:1984-01-11 00:00:00
abstract::The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2741
更新日期:1981-06-25 00:00:00
abstract::G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa442
更新日期:2020-07-09 00:00:00
abstract::The isolation and characterization of deletion mutants of the bacteriocinogenic plasmid Clo DF13 is described. To construct these deletion mutants, DNA of Clo DF13::Tn901 and Clo DF13-rep3::Tn901 plasmids was digested with restriction endonucleases, ligated with T4 ligase and introduced by transformation into Escheric...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.6.1801
更新日期:1978-06-01 00:00:00
abstract::Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1084
更新日期:2019-01-08 00:00:00
abstract::The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixe...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkaa135
更新日期:2020-04-17 00:00:00
abstract::Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few metho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt451
更新日期:2013-07-01 00:00:00
abstract::Replication Protein A (RPA) is a critical complex that acts in replication and promotes homologous recombination by allowing recombinase recruitment to processed DSB ends. Most organisms possess three RPA subunits (RPA1, RPA2, RPA3) that form a trimeric complex critical for viability. The Caenorhabditis elegans genome...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1293
更新日期:2021-01-21 00:00:00
abstract::The erbAalpha gene encodes two alpha-thyroid hormone receptor isoforms, TRalpha1 and TRalpha2, which arise from alternatively processed mRNAs, erbAalpha1 (alpha1) and erb alpha2 (alpha2). The splicing and alternative polyadenylation patterns of these mRNAs resemble that of mRNAs encoding different forms of immunoglobu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.21.4296
更新日期:1997-11-01 00:00:00
abstract::In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Ut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1172
更新日期:2011-01-01 00:00:00
abstract::Substantial amounts of DNA (at least 25 microgram per cm2) can be stably bound to diazobenzyloxymethyl (DBM)-paper. Complementary RNA will hybridize to the DNA paper almost completely in 24 hours. Using several different conditions of hybridization and washing, the background of RNA bound non-specifically is very low ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.1.195
更新日期:1979-01-01 00:00:00
abstract::UMSBP is a CCHC-type zinc finger protein, which functions during replication initiation of kinetoplast DNA minicircles and the segregation of kinetoplast DNA networks. Interactions of UMSBP with origin sequences, as well as the protein oligomerization, are affected by its redox state. Reduction yields UMSBP monomers a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn927
更新日期:2009-01-01 00:00:00
abstract::Initial steps in the synthesis of functional tRNAs require 5'- and 3'-processing of precursor tRNAs (pre-tRNAs), which in yeast mitochondria are achieved by two endonucleases, RNase P and RNase Z. In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr941
更新日期:2012-02-01 00:00:00
abstract::Transcript of the rbpA1 gene in Anabaena variabilis accumulates significantly at low growth temperatures below 28 degreesC. This accumulation was maximal at 16 degreesC. Accumulation of the rbpA1 transcript was completely abolished by rifampicin, but not by chloramphenicol. Photosynthesis was not required for this col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.9.2192
更新日期:1998-05-01 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::UV-irradiation (lambda = 254 nm) of liquid aqueous solutions of deoxyguanosine in the presence of oxygen at pH less than 7 causes an intensive degradation of nucleoside. The quantum yield estimated from A254 decrease for the reaction mixture was found to be 1.5X10(-4) at doses to 150 E/mole. The rate of A254 decrease ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.4.955
更新日期:1977-04-01 00:00:00
abstract::The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3097
更新日期:1977-09-01 00:00:00
abstract::Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.766
更新日期:2002-02-01 00:00:00
abstract::The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.11.4481
更新日期:1987-06-11 00:00:00