Abstract:
:PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecular and phenotypic annotations, through to the display of genome-wide high-throughput studies. Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates. Both in-house curators and community researchers provide manually curated data to PomBase. The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
McDowall MD,Harris MA,Lock A,Rutherford K,Staines DM,Bähler J,Kersey PJ,Oliver SG,Wood Vdoi
10.1093/nar/gku1040subject
Has Abstractpub_date
2015-01-01 00:00:00pages
D656-61issue
Database issueeissn
0305-1048issn
1362-4962pii
gku1040journal_volume
43pub_type
杂志文章abstract::The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.8.2357
更新日期:1979-12-20 00:00:00
abstract::The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.16.3347
更新日期:1994-08-25 00:00:00
abstract::Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.921
更新日期:1987-02-11 00:00:00
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
更新日期:1988-09-12 00:00:00
abstract::Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq913
更新日期:2011-04-01 00:00:00
abstract::BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We dete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky784
更新日期:2018-11-02 00:00:00
abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt713
更新日期:2013-11-01 00:00:00
abstract::CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa705
更新日期:2020-09-25 00:00:00
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp814
更新日期:2010-01-01 00:00:00
abstract::SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1277
更新日期:2017-04-20 00:00:00
abstract::Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH deg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm865
更新日期:2007-01-01 00:00:00
abstract::Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz838
更新日期:2019-11-18 00:00:00
abstract::PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz424
更新日期:2019-07-02 00:00:00
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
更新日期:2001-07-15 00:00:00
abstract::The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.563
更新日期:1992-02-11 00:00:00
abstract::The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1070
更新日期:2013-12-01 00:00:00
abstract::Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gk...
journal_title:Nucleic acids research
pub_type:
doi:10.1093/nar/27.1.1
更新日期:1999-01-01 00:00:00
abstract::Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Span...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx338
更新日期:2017-07-27 00:00:00
abstract::Simian cells have been transformed with SV40 origin-defective recombinant plasmids containing the tsA209 T-antigen gene. These plasmids contain deletions of either 5 or 52 nucleotides that include the BglI site at the SV40 ori, are defective for replication in COS-1 cells but retain a functional SV40 early promoter. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.7913
更新日期:1985-11-25 00:00:00
abstract::Approximately 2% of the Dictyostelium discoideum genome consists of multiple copies of a retrotransposable element termed DRE (Dictyostelium Repetitive Element). These elements have always been found integrated in a position and orientation-specific manner 50 +/- 4 nucleotides upstream of the coding region of tRNA gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.23.6247
更新日期:1992-12-11 00:00:00
abstract::Transcriptional co-activator LEDGF/p75 is the major cellular interactor of HIV-1 integrase (IN), critical to efficient viral replication. In this work, a series of INs from the Betaretrovirus, Gammaretrovirus, Deltaretrovirus, Spumavirus and Lentivirus retroviral genera were tested for interaction with the host factor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl885
更新日期:2007-01-01 00:00:00
abstract::We examined the mechanism regulating the cellular levels of PNKP, the major kinase/phosphatase involved in the repair of oxidative DNA damage, and find that it is controlled by ATM phosphorylation and ubiquitylation-dependent proteasomal degradation. We discovered that ATM-dependent phosphorylation of PNKP at serines ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks909
更新日期:2012-12-01 00:00:00
abstract::Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm088
更新日期:2007-01-01 00:00:00
abstract::Chicken conalbumin double-stranded cDNA (con-dscDNA) was synthesized from a laying hen oviduct mRNA preparation enriched for conalbumin mRNA (con-mRNA). The dscDNA was inserted by blunt-end ligation into the Sal I site of plasmid pBR322 which had been repaired with DNA polymerase I to create Taq I sites on each side o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2435
更新日期:1979-06-11 00:00:00
abstract::We have constructed vectors from bacteriophage lambda and from plasmid pBR322 having a single EcoRI restriction site which is immediately downstream from the lac UV5 promotor. Each vector allows the fusion of a cloned gene to the lac Z gene in a different phase relative to the translation initiation codon of the lac Z...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.12.4479
更新日期:1978-12-01 00:00:00
abstract::Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku580
更新日期:2014-07-01 00:00:00
abstract::We have identified and sequenced two members of a chicken middle repetitive DNA sequence family. By reassociation kinetics, members of this family (termed CRl) are estimated to be present in 1500-7000 copies per chicken haploid genome. The first family member sequenced (CRlUla) is located approximately 2 kb upstream f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5383
更新日期:1981-10-24 00:00:00
abstract::The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa479
更新日期:2020-07-09 00:00:00
abstract::The C (pifC) protein of miniF represses transcription of its own gene by binding to the pif operator (pifO); it is also needed for replication initiated from the miniF primary origin (ori-1). We have determined the nucleotide sequence of the C gene. The gene has been inserted into an expression vector under Ptrp contr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.24.9699
更新日期:1986-12-22 00:00:00