• genomic
  • One of the oligo probes which I am using is described as 'Universal', and it does indeed bind to yeast genomic DNA (as well as mitochondrial, I assume). (bio.net)
  • On the other hand, the percentage of Mn 2+ sites with at least one amino acid in the "beta strand-major binder-random coil" motif of secondary structure (77.88%) does not depend on genomic GC-content. (hindawi.com)
  • PMID
  • This conserved 9-amino acid motif ((V/A)P(I/L)AXXE(S/D)D) is required for ankyrin-G binding and functions to localise sodium channels to a variety of 'excitable' membrane domains both inside and outside of the nervous system [ PMID: 12716895 ]. (ebi.ac.uk)
  • KCNQ2/KCNQ3 channels are preferentially localised to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3 [ PMID: 16735477 ]. (ebi.ac.uk)
  • motif
  • Identification of a conserved ankyrin-binding motif in the family of sodium channel alpha subunits. (ebi.ac.uk)
  • Well-known EF-hand motif for Ca 2+ binding consists of two alpha helices and a loop between them [ 6 ]. (hindawi.com)
  • The aim of this study was to find out whether there is a secondary structural motif which is characteristic for relatively short parts of polypeptide chains around Mn 2+ binding amino acid residues. (hindawi.com)
  • Below is a non-exhaustive table of available databases: A collection of DNA binding sites, typically referred to as a DNA binding motif, can be represented by a consensus sequence. (wikipedia.org)
  • These matrices give information on the frequency of each base at each position of the DNA binding motif. (wikipedia.org)
  • An example is the N-glycosylation site motif: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro where the three-letter abbreviations are the conventional designations for amino acids (see genetic code). (wikipedia.org)
  • ribosomes
  • During protein synthesis, elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to the A-site of mRNA-programmed ribosomes in a GTP-dependent manner. (uleth.ca)
  • substrate
  • Boudker O et al (2007) Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. (springer.com)
  • mRNA
  • Translation of the mRNA produces 4 ribosomal protein products, one of which (S4) acts as a translational repressor by binding to the nested pseudoknot region. (wikipedia.org)
  • isoform
  • C7orf43 isoform 1 encodes a protein that is 580 amino acids long and only has one polyadenylation site. (wikipedia.org)
  • The inducible isoform, iNOS, is involved in immune response, binds calmodulin at physiologically relevant concentrations, and produces NO as an immune defense mechanism, as NO is a free radical with an unpaired electron. (wikipedia.org)
  • regulates
  • The RNA structure permits binding of PyrR protein which regulates pyrimidine biosynthesis in Bacillus subtilis. (wikipedia.org)
  • It encodes a type 1 membrane bound protease which is ubiquitously expressed and regulates cholesterol or lipid homeostasis via cleavage of substrates at non-basic residues. (wikipedia.org)
  • Identification
  • The identification of RBSs is used to determine the site of translation initiation in an unannotated sequence. (wikipedia.org)
  • However, the development of DNA microarrays and fast sequencing techniques has led to new, massively parallel methods for in-vivo identification of binding sites, such as ChIP-chip and ChIP-Seq. (wikipedia.org)
  • known
  • Known imprinting control regions (ICRs) contain unusual tandem arrays of DNA-binding sites for transcription factors, including YY1 for the Peg3, Gnas, and Xist/Tsix domains and CTCF for the H19/Igf2 domain. (mendeley.com)
  • These multiple DNA-binding sites are known to be the only functionally shared and evolutionarily selected feature among these ICRs. (mendeley.com)
  • Known substrates include sterol regulatory element-binding protein (SREBP)-1, SREBP-2 and forms of the transcriptional activator ATF6. (wikipedia.org)
  • strands
  • Beta strands near Mn 2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. (hindawi.com)
  • amino
  • There is some controversy in the results of in silico studies on amino acid preferences for Mn 2+ binding. (hindawi.com)
  • 1 ], there are three amino acid residues most frequently found in Mn 2+ binding sites: His, Asp, and Glu. (hindawi.com)
  • Histidine has the highest normalized frequency in binding sites, while glutamic acid has the lowest normalized frequency among those three amino acid residues [ 1 ]. (hindawi.com)
  • Regulation
  • The existence of something akin to DNA binding sites was suspected from the experiments on the biology of the bacteriophage lambda and the regulation of the Escherichia coli lac operon. (wikipedia.org)
  • data
  • This web site contains all the primary data reported in the paper, enhanced versions of figures, and additional figures and supplementary data not included in the published paper. (stanford.edu)
  • A Java application that reuires a local installation of a database that provides binding site information (eg the Public Transfac 6.0 data). (warwick.ac.uk)
  • We will see how to create prompts and validators, as well as bind data to controls in a compile-time checked manner. (codeproject.com)
  • demonstrate
  • This is a very simple model used to demonstrate how to can bind objects with associations. (codeproject.com)
  • In this workflow we demonstrate Bioconductor techniques for finding candidate TF binding sites in DNA sequence using the model organism Saccharomyces cerevisiae. (bioconductor.org)
  • start
  • The optimal distance between the RBS and the start codon is variable - it depends on the portion of the SD sequence encoded in the actual RBS and its distance to the start site of a consensus SD sequence. (wikipedia.org)
  • found
  • Blebs on apoptotic cells contain nearly all the autoantigens found in SLE, and phagocytes bind these apoptotic cells and phagocytose them. (wikipedia.org)
  • Several
  • Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. (pnas.org)
  • There are, however, several private and public databases devoted to compilation of experimentally reported, and sometimes computationally predicted, binding sites for different transcription factors in different organisms. (wikipedia.org)
  • CCDC82 has several predicted phosphorylation sites. (wikipedia.org)
  • techniques
  • DNA binding sites were finally confirmed in both systems with the advent of DNA sequencing techniques. (wikipedia.org)
  • Historically, the experimental techniques of choice to discover and analyze DNA binding sites have been the DNAse footprinting assay and the Electrophoretic Mobility Shift Assay (EMSA). (wikipedia.org)
  • Due to the diverse nature of the experimental techniques used in determining binding sites and to the patchy coverage of most organisms and transcription factors, there is no central database (akin to GenBank at the National Center for Biotechnology Information) for DNA binding sites. (wikipedia.org)
  • sequence
  • The optimal distance between the RBS and the start codon is variable - it depends on the portion of the SD sequence encoded in the actual RBS and its distance to the start site of a consensus SD sequence. (wikipedia.org)
  • The identification of RBSs is used to determine the site of translation initiation in an unannotated sequence. (wikipedia.org)
  • identification
  • However, the development of DNA microarrays and fast sequencing techniques has led to new, massively parallel methods for in-vivo identification of binding sites, such as ChIP-chip and ChIP-Seq. (wikipedia.org)
  • although
  • PSFM are usually conceived with the implicit assumption of positional independence (different positions at the DNA binding site contribute independently to the site function), although this assumption has been disputed for some DNA binding sites. (wikipedia.org)