Abstract:
:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield Mdoi
10.1093/nar/gkaa1010subject
Has Abstractpub_date
2021-01-08 00:00:00pages
D1058-D1064issue
D1eissn
0305-1048issn
1362-4962pii
5973440journal_volume
49pub_type
杂志文章abstract::NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn202
更新日期:2008-07-01 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::Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are classed as either processed pseudogenes (made by reverse transcription from an mRNA) or duplicated pseudogenes, arising from ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg169
更新日期:2003-02-01 00:00:00
abstract::DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm334
更新日期:2007-07-01 00:00:00
abstract::The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw796
更新日期:2017-01-04 00:00:00
abstract::The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh123
更新日期:2004-01-01 00:00:00
abstract::The mutations of 76 haemophilia B patients representing the whole population registered with the Malmö haemophilia centre (42) and referrals from the UK, were characterised. RFLP haplotype analysis of the defective genes indicated that 51 single base pair substitutions were definitely of independent origin and 27 of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3227
更新日期:1990-06-11 00:00:00
abstract::In an RNase III-deficient strain of E. coli 23S pre-rRNA accumulates unprocessed in 50S ribosomes and in polysomes. These ribosomes provide a substrate for the analysis of rRNA maturation in vitro. S1 nuclease protection analysis of the products obtained in in vitro processing reactions demonstrates that 23S rRNA proc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5041
更新日期:1985-07-25 00:00:00
abstract::Thermally induced structural transition in the d(TTTTATAATAAA) d(TTTATTATAAAA) heteroduplex is characterized by UV-spectroscopy and differential scanning calorimetry. At low salt (less than 0.1 M) the occurrence of a cooperative transition in the lower temperature range, followed by a broad transition connected with s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.7.3245
更新日期:1984-04-11 00:00:00
abstract::Ubiquitin mRNA was found to be an abundant transcript which was induced by heat shock (HS), and certain other stresses in mammalian cells. In Chinese hamster cells, the 2 major ubiquitin transcripts of 2.6 kb and 1.7 kb were induced coordinately, while a minor ubiquitin transcript of 0.8 kb was not induced; the respon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.3.1215
更新日期:1989-02-11 00:00:00
abstract::The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid resid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2707
更新日期:1986-03-25 00:00:00
abstract::The eukaryotic mismatch repair protein Msh6 shares five domains in common with other MutS members. However, it also contains several hundred additional residues at its N-terminus. A few of these residues bind to PCNA, but the functions of the other amino acids in the N-terminal region (NTR) are unknown. Here we demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm409
更新日期:2007-01-01 00:00:00
abstract::We have generated a codon usage table for Pseudomonas aeruginosa. Codon usage in P. aeruginosa is extremely biased. In contrast to E. coli and yeast, P. aeruginosa preferentially uses those codons within a synonymous codon group with the strongest predicted codon-anticodon interaction. We were unable to correlate a pa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.19.9323
更新日期:1988-10-11 00:00:00
abstract::DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq173
更新日期:2010-07-01 00:00:00
abstract::Cellular ribonucleic acid (RNA) plays a crucial role in the initial conversion of cellular prion protein PrP(C) to infectious PrP(Sc) or scrapie. The nature of this RNA remains elusive. Previously, RNA aptamers against PrP(C) have been isolated and found to form G-quadruplexes (G4s). PrP(C) binding to G4 RNAs destabil...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku559
更新日期:2014-08-01 00:00:00
abstract::siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq961
更新日期:2011-03-01 00:00:00
abstract::USF is a helix-loop-helix transcription factor that, like Myc, recognizes the DNA binding motif CACGTG. Two different forms of USF, characterized by apparent molecular weights of 43,000 and 44,000, were originally identified in HeLa cells by biochemical analysis. Clones for the 43-kDa USF were first characterized, but...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.3.427
更新日期:1994-02-11 00:00:00
abstract::The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1235
更新日期:2011-01-01 00:00:00
abstract::Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh976
更新日期:2004-12-01 00:00:00
abstract::The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer [d(GCGATTCGC)]2, containing a central T.T mismatch, has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics and molecular dynamics computations including relaxati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.20.4706
更新日期:1998-10-15 00:00:00
abstract::The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the lin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3703
更新日期:1987-05-11 00:00:00
abstract::Three new proteins which selectively bind to UV-damaged DNA were identified and purified to near homogeneity from UV-irradiated Drosophila melanogaster embryos through several column chromatographies. These proteins, tentatively designated as D-DDB P1, P2 and P3, can be identified as different complex bands in a gel s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2600
更新日期:1995-07-25 00:00:00
abstract::A simple and rapid procedure to isolate clones carrying sequences from a specific region of the polytene chromosome of Drosophila is demonstrated. The procedure involves microdissection of the region of interest, amplification of the DNA by PCR using a primer designed to prime the synthesis nonspecifically, labeling o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.3.599
更新日期:1990-02-11 00:00:00
abstract::Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn922
更新日期:2009-02-01 00:00:00
abstract::Here we examined the role of cellular vitamin C in genotoxicity of carcinogenic chromium(VI) that requires reduction to induce DNA damage. In the presence of ascorbate (Asc), low 0.2-2 microM doses of Cr(VI) caused 10-15 times more chromosomal breakage in primary human bronchial epithelial cells or lung fibroblasts. D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1069
更新日期:2007-01-01 00:00:00
abstract::A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3813
更新日期:1990-07-11 00:00:00
abstract::DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By takin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv501
更新日期:2015-07-13 00:00:00
abstract::Nucleoside 3'-phosphoramidite and chlorophosphite reagents have been found to react with the lactam function of guanine. This reaction caused unsatisfactory results when oligodeoxyribonucleotides containing a large number of guanine bases were prepared in an automated solid phase synthesizer. The guanine modification ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.18.6447
更新日期:1985-09-25 00:00:00
abstract::The role of the enzyme poly(adenosine diphosphate-ribose) polymerase (PADPRP) in DNA repair at the level of the gene was investigated with human HeLa cells in which PADPRP antisense transcripts are inducible with dexamethasone. After such induction, the cellular content of PADPRP is reduced by 90%. DNA damage and its ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.22.4620
更新日期:1994-11-11 00:00:00
abstract::Long-range enhancers of transcription are a key component of the genomic regulatory architecture. Recent studies have identified bi-directionally transcribed RNAs emanating from these enhancers known as eRNAs. However, it remains unclear how tightly coupled eRNA production is with enhancer activity. Through our system...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1018
更新日期:2014-11-10 00:00:00