Abstract:
:The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, including Spt7p, and a few false positives have been removed from the earlier version of HDB. Database contents include compilations of post-translational modifications for each of the core and linker histones, as well as genomic information in the form of map loci for the human histone gene complement, with the genetic loci linked to Online Mendelian Inheritance in Man (OMIM). Conflicts between similar sequence entries from a number of source databases are also documented. Newly added to the HDB are multiple sequence alignments in which predicted functions of histone fold amino acid residues are annotated. The database is freely accessible through the WWW at http://genome.nhgri.nih.gov/histones/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sullivan SA,Aravind L,Makalowska I,Baxevanis AD,Landsman Ddoi
10.1093/nar/28.1.320keywords:
subject
Has Abstractpub_date
2000-01-01 00:00:00pages
320-2issue
1eissn
0305-1048issn
1362-4962pii
gkd045journal_volume
28pub_type
杂志文章abstract::We have used heteroduplex analysis to investigate the sequences surrounding the germline C gamma 1 and C gamma 3 genes, and to compare them with those surrounding the C mu gene. We detected an inverted pseudogene 5' to the C gamma 3 gene and 50-65% homologous to it. A 400 bp region of the C gamma 1 and C gamma 3 3' fl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.23.5579
更新日期:1980-12-11 00:00:00
abstract::The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf523
更新日期:2002-09-15 00:00:00
abstract::The effect of several rifamycin derivatives on poly(A) synthesis in vitro was tested using purified rat liver mitochondrial poly(A) polymerase assayed with an exogenous primer. When used at a concentration of 300 mug/ml, derivatives AF/013, PR/19, AF/AETP, M/88 and AF/ABDP completely inhibited activity corresponding t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.11.1549
更新日期:1974-11-01 00:00:00
abstract::The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and sele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt197
更新日期:2013-07-01 00:00:00
abstract::Quantitative real-time PCR (qPCR) is the method of choice for specific and sensitive quantification of nucleic acids. However, data validation is still a major issue, partially due to the complex effect of PCR inhibition on the results. If undetected PCR inhibition may severely impair the accuracy and sensitivity of r...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr778
更新日期:2012-02-01 00:00:00
abstract::Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1230
更新日期:2010-05-01 00:00:00
abstract::The oncogene BMI1 encodes a polycomb group transcription factor that is required for embryonic development and self-renewal of stem cells. Despite these important functions little is known about the regulation of BMI1 expression. A cDNA microarray based search for target genes of E2F-1 in neuroblastoma cells expressin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl119
更新日期:2006-03-31 00:00:00
abstract::Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1141
更新日期:2014-02-01 00:00:00
abstract::The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1188
更新日期:2013-01-01 00:00:00
abstract::Alternative splicing has recently emerged as a major mechanism of regulation in the human genome, occurring in perhaps 40-60% of human genes. Thus, microarray studies of functional regulation could, in principle, be extended to detect not only the changes in the overall expression of a gene, but also changes in its sp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh173
更新日期:2004-12-14 00:00:00
abstract::Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj141
更新日期:2006-01-01 00:00:00
abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh441
更新日期:2004-07-01 00:00:00
abstract::The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1133
更新日期:2017-01-04 00:00:00
abstract::Eukaryotic cells use numerous pathways to regulate RNA production, localization and stability. Several of these pathways are controlled by ribonucleases. The essential ribonuclease, Dis3, plays important roles in distinct RNA metabolic pathways. Despite much progress in understanding general characteristics of the Dis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq295
更新日期:2010-09-01 00:00:00
abstract::Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication prob...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw344
更新日期:2016-06-20 00:00:00
abstract::Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.819
更新日期:1984-01-11 00:00:00
abstract::Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.5.1107
更新日期:2001-03-01 00:00:00
abstract::We have determined the complete nucleotide sequence of the regions of mouse ribosomal RNA transcription unit which separate mature rRNA genes. These internal transcribed spacers (ITS) are excised from rRNA precursor during ribosome biosynthesis. ITS 1, between 18S and 5.8S rRNA genes, is 999 nucleotides long. ITS 2, b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3375
更新日期:1983-05-25 00:00:00
abstract::The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.15.3138
更新日期:1999-08-01 00:00:00
abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky977
更新日期:2019-01-08 00:00:00
abstract::Self-cleaving ribozymes associated with the glmS genes of many Gram-positive bacteria are activated by binding to glucosamine-6-phosphate (GlcN6P). Representatives of the glmS ribozyme class function as metabolite-sensing riboswitches whose self-cleavage activities down-regulate the expression of GlmS enzymes that syn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl643
更新日期:2006-01-01 00:00:00
abstract::Microsatellites, such as (TG)n found at random throughout the genome, or as 3' extensions of Alu sequences are being increasingly used as genetic markers because of their pluriallelic character. The search for polymorphic microsatellites is time consuming, however, as it is necessary to sequence clones containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1333
更新日期:1992-03-25 00:00:00
abstract::The 4.5S rRNA was isolated from the chloroplast ribosomes from Dryopteris acuminata. The complete nucleotide sequence was determined to be: OHUAAGGUCACGGCAAGACGAGCCGUUUAUCACCACGAUAGGUGCUAAGUGGAGGUGCAGUAAUGUAUGCAGCUGAGGC AUCCUAAUAGACCGAGAGGUUUGAACOH. The 4.5S rRNA is composed of 103 nucleotides and shows strong homolog...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2257
更新日期:1982-04-10 00:00:00
abstract::Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3411
更新日期:1995-09-11 00:00:00
abstract::Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj058
更新日期:2006-01-01 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::MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1239
更新日期:2011-04-01 00:00:00
abstract::Although mobility of the phylogenetically widespread group I introns appears to be mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of the td and sunY introns are different from their eukaryotic counterparts. Most notably, they cleave at a distance from the intron insertion site...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3763
更新日期:1990-07-11 00:00:00
abstract::Fully protected diastereoisomers of deoxyguanylyl (3' leads to 5') deoxyadenosine stereospecifically labelled on phosphorus with oxygen-18 have been synthesized by oxidation of phosphite triester intermediates in the presence of 18O-labelled water. The diastereoisomers have been chromatographically separated and their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.20.7087
更新日期:1983-10-25 00:00:00
abstract::We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2318
更新日期:1994-06-25 00:00:00