Abstract:
:The Exon/Intron Database (ExInt) stores information of all GenBank eukaryotic entries containing an annotated intron sequence. Data are available through a retrieval system, as flat-files and as a MySQL dump file. In this report we discuss several implementations added to ExInt, which is accessible at http://intron.bic.nus.edu.sg/exint/newexint/exint.html.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sakharkar M,Passetti F,de Souza JE,Long M,de Souza SJdoi
10.1093/nar/30.1.191keywords:
subject
Has Abstractpub_date
2002-01-01 00:00:00pages
191-4issue
1eissn
0305-1048issn
1362-4962journal_volume
30pub_type
杂志文章abstract::Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt636
更新日期:2013-10-01 00:00:00
abstract::The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa018
更新日期:2020-03-18 00:00:00
abstract::Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1985-12-09 00:00:00
abstract::In addition to the cap-dependent mechanism, eukaryotic initiation of translation can occur by a cap-independent mechanism which directs ribosomes to defined start codons enabled by internal ribosome entry site (IRES) elements. IRES elements from poliovirus and encephalomyocarditis virus are often used to construct bi-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.16.3327
更新日期:2001-08-15 00:00:00
abstract::IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1088
更新日期:2012-01-01 00:00:00
abstract::Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cyto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1345
更新日期:2016-04-07 00:00:00
abstract::Transgenic mice have proven to be an effective expression system for studying developmental control of the human fetal and adult beta-globin genes. In the current work we are interested in developing the transgenic mouse system for the study of the human embryonic beta-globin gene, epsilon. An epsilon-globin gene cons...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp603
更新日期:2009-11-01 00:00:00
abstract::The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2000-12-01 00:00:00
abstract::We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1984-08-10 00:00:00
abstract::Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, makin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp680
更新日期:2009-10-01 00:00:00
abstract::In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv934
更新日期:2015-12-15 00:00:00
abstract::Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm760
更新日期:2007-01-01 00:00:00
abstract::Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw095
更新日期:2016-06-02 00:00:00
abstract::Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks842
更新日期:2012-11-01 00:00:00
abstract::Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl812
更新日期:2007-01-01 00:00:00
abstract::The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.10.3871
更新日期:1978-10-01 00:00:00
abstract:UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3287
更新日期:1990-06-11 00:00:00
abstract::PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.19.4070
更新日期:2001-10-01 00:00:00
abstract::The DNA sequences at and around the junctions between viral and cellular DNA in the polyoma virus transformed mouse cell line, TS-A-3T3, have been determined. No common sequence specificity or structural features at the joins have been observed. The sequence indicates that the 94K truncated large T antigen found in TS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.15.4515
更新日期:1982-08-11 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::Transcription is the first step in gene expression, and it is the step at which most of the regulation of expression occurs. Although sequenced prokaryotic genomes provide a wealth of information, transcriptional regulatory networks are still poorly understood using the available genomic information, largely because a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr795
更新日期:2012-02-01 00:00:00
abstract::Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.12.3611
更新日期:1990-06-25 00:00:00
abstract::Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa915
更新日期:2021-01-08 00:00:00
abstract::We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.18.6341
更新日期:1983-09-24 00:00:00
abstract::High-throughput sequencing technologies enable direct approaches to catalog and analyze snapshots of the total small RNA content of living cells. Characterization of high-throughput sequencing data requires bioinformatic tools offering a wide perspective of the small RNA transcriptome. Here we present SeqBuster, a hig...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1127
更新日期:2010-03-01 00:00:00
abstract::We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.11.2011
更新日期:1996-06-01 00:00:00
abstract::Recently, a cDNA from the hepatitis C virus (HCV) RNA genome has been isolated in the USA from a chronically infected chimpanzee. In order to isolate HCV cDNA derived from human material, RNA was extracted from plasma of a Japanese blood donor implicated in post-transfusion non-A, non-B hepatitis and HCV cDNA was synt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.24.10367
更新日期:1989-12-25 00:00:00
abstract::The human beta-globin LCR plays a key role in the transcriptional regulation of the beta-globin locus and comprises four erythroid specific DNase I hypersensitive sites, designated 5'HS1-4. We have now isolated genomic clones containing 5'HS3 and 5'HS4 of the mouse beta-globin LCR. 5'HS3 and 5'HS4 are located 15 kb an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.21.5797
更新日期:1992-11-11 00:00:00
abstract::Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq119
更新日期:2010-05-01 00:00:00