Abstract:
:EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence analysis aimed at understanding gene regulation during erythropoiesis. New protocols have been developed for data integration and updating entries. Using a BLAST-based algorithm, we have grouped GenBank entries representing the same gene together. This sequence similarity protocol was also used to identify new entries to be included in EpoDB. We have recently implemented our database in Sybase (relational tables) in addition to SICStus Prolog to provide us with greater flexibility in asking complex queries that utilize information from multiple sources. New additions to the public web site (http://www.cbil.upenn.edu/epodb) for accessing EpoDB are the ability to retrieve groups of entries representing different variants of the same gene and to retrieve gene expression data. The BLAST query has been enhanced by incorporating BLASTView, an interactive and graphical display of BLAST results. We have also enhanced the queries for retrieving sequence from specified genes by the addition of MEME, a motif discovery tool, to the integrated analysis tools which include CLUSTALW and TESS.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Stoeckert CJ Jr,Salas F,Brunk B,Overton GCdoi
10.1093/nar/27.1.200subject
Has Abstractpub_date
1999-01-01 00:00:00pages
200-3issue
1eissn
0305-1048issn
1362-4962pii
gkc044journal_volume
27pub_type
杂志文章abstract::Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt718
更新日期:2013-11-01 00:00:00
abstract::The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.13.2999
更新日期:1980-07-11 00:00:00
abstract::The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh039
更新日期:2004-01-01 00:00:00
abstract::Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki087
更新日期:2005-01-01 00:00:00
abstract::We have analyzed multiple recombinant DNA clones containing ribosomal RNA repeat units of the silkmoth, Bombyx mori. In combination with genomic DNA blots, analysis of these clones indicated that the rDNA repeat of B. mori is 10.8 kilobase pair in length and tandemly repeated in the genome, as reported by Manning et a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.11.4703
更新日期:1984-06-11 00:00:00
abstract::Successful use and reliability of microarray technology is highly dependent on several factors, including surface chemistry parameters and accessibility of cDNA targets to the DNA probes fixed onto the surface. Here, we show that functionalisation of glass slides with homemade dendrimers allow production of more sensi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng088
更新日期:2003-08-15 00:00:00
abstract::The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.19.6837
更新日期:1983-10-11 00:00:00
abstract::Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl531
更新日期:2006-01-01 00:00:00
abstract::The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku314
更新日期:2014-06-01 00:00:00
abstract::The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in arch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4299
更新日期:2000-11-01 00:00:00
abstract::mRNA differential display RT-PCR has been extensively used for the isolation of genes differentially expressed between RNA populations. We have assessed its utility for the identification of developmentally regulated genes in plasmid cDNA libraries derived from individual tissues dissected from early mouse embryos. Us...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.19.4538
更新日期:1998-10-01 00:00:00
abstract::E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.22.7153
更新日期:1982-11-25 00:00:00
abstract::The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.4.1063
更新日期:1999-02-15 00:00:00
abstract::A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sourc...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/22.12.2183
更新日期:1994-06-25 00:00:00
abstract::Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3'-untranslated regions (3'-UTRs). PolyA_DB 2 contains p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl870
更新日期:2007-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx327
更新日期:2017-06-02 00:00:00
abstract::2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in y...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr896
更新日期:2012-03-01 00:00:00
abstract::The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv575
更新日期:2015-10-15 00:00:00
abstract::The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn530
更新日期:2008-10-01 00:00:00
abstract::In this article, we characterize histone demethylase activity of the entire family of JmjC+N proteins of Drosophila melanogaster. Our results show that Lid (little imaginal discs), which is structurally homologous to JARID1, demethylates H3K4me3. However, contrary to what would be inferred from its demethylase activit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn098
更新日期:2008-05-01 00:00:00
abstract::DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3872
更新日期:1995-10-11 00:00:00
abstract::The Protein Folding Database (PFD) is a publicly accessible repository of thermodynamic and kinetic protein folding data. Here we describe the first major revision of this work, featuring extensive restructuring that conforms to standards set out by the recently formed International Foldeomics Consortium. The database...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1007
更新日期:2007-01-01 00:00:00
abstract::A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr603
更新日期:2011-11-01 00:00:00
abstract::Affymetrix has recently developed whole-transcript GeneChips-'Gene' and 'Exon' arrays-which interrogate exons along the length of each gene. Although each probe on these arrays is intended to hybridize perfectly to only one transcriptional target, many probes match multiple transcripts located in different parts of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp853
更新日期:2010-01-01 00:00:00
abstract::A complete nucleotide sequence of human aldolase B mRNA was determined with a recombinant cDNA (pHABL120-3). The cDNA insert was composed of 1,652 bases excluding poly(A) tail and the sequence was consistent with the previous results reported by others. However, S1 nuclease mapping and subsequent genomic analysis allo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5055
更新日期:1985-07-25 00:00:00
abstract::Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx246
更新日期:2017-07-03 00:00:00
abstract::Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.16.3239
更新日期:1995-08-25 00:00:00
abstract::The pattern of preferential DNA repair of UV-induced pyrimidine dimers was studied in repair-deficient Chinese hamster ovary (CHO) cells transfected with the human excision repair gene, ERCC-1. Repair efficiency was measured in the active dihydrofolate reductase (DHFR) gene and in its flanking, non-transcribed sequenc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.15.7397
更新日期:1988-08-11 00:00:00
abstract::The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been auto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx790
更新日期:2018-01-04 00:00:00
abstract::Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7381
更新日期:1989-09-25 00:00:00