*  http://ufdc.ufl.edu/UFE0021436/00001
Both of the proteins. bind to the EE motif located in the promoter of the TOC1 gene, a positive element, and repress. TOC1 ... dCLK-CYC complex binds to a specific sequence in PER and TI2~promoters known as the E-. box motif, a consensus hexanucleotide ... that are within one of the core loops of the oscillator (Roenneberg and Merrow, 1998).. The molecular basis of circadian clocks ... an organism. The first, entrainment, is the manner in which the clocks are set to 'local' time by. environmental cues such as ...
  http://ufdc.ufl.edu/UFE0021436/00001
*  DNA-binding domain - Wikipedia
HMG-box domains are found in high mobility group proteins which are involved in a variety of DNA-dependent processes like ... pyogenes can be programmed to direct both activation and repression to natural and artificial eukaryotic promoters through the ... Originally discovered in bacteria, the helix-turn-helix motif is commonly found in repressor proteins and is about 20 amino ... "reviewed:yes AND organism:"Homo sapiens (Human) [9606]" AND proteome:up000005640 in UniProtKB". www.uniprot.org. Retrieved 2017 ...
  https://en.wikipedia.org/wiki/DNA-binding_domain
*  CLOCK - Circadian locomoter output cycles protein kaput - Homo sapiens (Human) - CLOCK gene & protein
... harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are ... The CLOCK-ARNTL/BMAL1 heterodimer also recognizes the non-canonical E-box motifs 5'-AACGTGA-3' and 5'-CATGTGA-3' (PubMed: ... Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating ... The preferred binding motif for the CLOCK-ARNTL/BMAL1 heterodimer is 5'-CACGTGA-3', which contains a flanking Ala residue in ...
  http://www.uniprot.org/uniprot/O15516
*  The organization, expression, function and evolution of some essential genes from the hyperthermophilic eubacterium thermotoga...
The N protein binds to a helical box B sequence that is adjacent to box A on X transcripts. Together, these RNA motifs ... The sequence elements that control transcription and their positions in eukaryotic genes are complex. For the Pol II promoters ... 2. Recent data indicate that the organism used to clone these ribosomal protein genes was actually S. acidocaldarius and not S ... and the protein is likely to be in substantial excess over the amount of core RNA polymerase. Thus, it is possible that the ...
  https://open.library.ubc.ca/cIRcle/collections/ubctheses/831/items/1.0098821
*  PER2 - Period circadian protein homolog 2 - Homo sapiens (Human) - PER2 gene & protein
... harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are ... Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating ... PER1 and PER2 proteins transport CRY1 and CRY2 into the nucleus with appropriate circadian timing, but also contribute directly ... Second, brings H3K9 methyltransferases such as SUV39H1 and SUV39H2 to the E-box elements of the circadian target genes, like ...
  http://www.uniprot.org/uniprot/O15055
*  Conservation and implications of eukaryote transcriptional regulatory regions across multiple species | BMC Genomics | Full Text
Abeel T, Saeys Y, Bonnet E, Rouze P, Peer Van de Y: Generic eukaryotic core promoter prediction using structural features of ... Other motifs, such as CAAT box-like motifs, can also be found in the tuple-pair dictionary (out of the top 100 ranks; not shown ... and they are regulated by regions with core parts similar to those core TRRs for protein-coding transcripts [19, 45, 46, 69-71 ... we show that the core TRRs are conserved among genes, not only in one organism, but also across species. ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-623
*  Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in...
The second family is found in the eukaryotic Med13 protein, one of four protein components of the repressive CDK8 subcomplex of ... Seila AC, Core LJ, Lis JT, Sharp PA: Divergent transcription: a new feature of active promoters. Cell Cycle. 2009, 8: 2557-2564 ... organism abbreviation, and gi number for a representative protein. Characteristic C-rich and helical regions of the DinG-type ... The small green box immediately upstream of the MID domain represents the conserved, small "linker" domain. Other unlabeled ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-8-13
*  Cis-regulatory element - Wikipedia
... the TATA box, a TFIIB recognition site, an initiator, and the downstream core promoter element. It has been found that a single ... "A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs". Rna. 2 (4): 367-79. ... Tighter or looser binding of regulatory proteins will lead to up- or down-regulated transcription. An example of a cis-acting ... The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product ...
  https://en.wikipedia.org/wiki/Cis-regulatory_element
*  DNA-binding protein - Wikipedia
Iftode C, Daniely Y, Borowiec J (1999). "Replication protein A (RPA): the eukaryotic SSB". Crit Rev Biochem Mol Biol. 34 (3): ... Luger K, Mäder A, Richmond R, Sargent D, Richmond T (1997). "Crystal structure of the nucleosome core particle at 2.8 A ... Wong KC, Chan TM, Peng C., Li Y., and Zhang Z. "DNA Motif Elucidation using belief propagation" Nucleic Acids Research Advanced ... These DNA targets can occur throughout an organism's genome. Thus, changes in the activity of one type of transcription factor ...
  https://en.wikipedia.org/wiki/DNA-binding_protein
*  IJMS | Free Full-Text | Characterization of a Gene Encoding Clathrin Heavy Chain in Maize Up-Regulated by Salicylic Acid,...
ZmCHC1 encodes a 1693-amino acid-protein including 29 exons and 28 introns, and ZmCHC2 encodes a 1746-amino acid-protein ... in the promoter sequence of ZmCHC1, the expression of ZmCHC1 instead of ZmCHC2 in maize roots is significantly up-regulated by ... The high similarities of gene structure, protein sequences and 3D models among ZmCHC1, and Arabidopsis AtCHC1 and AtCHC2 ... in eukaryotic cells. In this study, the genes ZmCHC1 and ZmCHC2 encoding clathrin heavy chain in maize were cloned and ...
  http://www.mdpi.com/1422-0067/14/7/15179/htm
*  Polyepitope carrier protein - Patent # 6855321 - PatentGenius
The carrier proteins are use useful as components of vaccines that can elicit a T-cell dependent immune response. These ... The invention relates to polyepitope carrier proteins that comprise at least five CD4+ T cell epitopes, for conjugation to ... The TATA box is thought todirect RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also ... hepatitis B nuclear core protein, H influenzae matrix protein, H. influenzaehaemagglutinin, diphtheria toxoid, diphtheria ...
  http://www.patentgenius.com/patent/6855321.html
*  Protocols and Video Articles Authored by Steve A. Kay
A Modified Yeast-one Hybrid System for Heteromeric Protein Complex-DNA Interaction Studies' ... and F-box and leucine-rich repeat protein 3 (FBXL3), modulate the stability of closely linked core clock proteins period (PER) ... An analysis of promoter elements of genes regulated in this way identified conserved promoter motifs potentially important in ... suitable for in vivo screens targeting the core clock mechanism that take into account the complexity of an intact organism. ...
  https://www.jove.com/author/Steve++A._Kay
*  Antievolution.org Discussion Board [Powered by Ikonboard]
Histidine Kinases and Eukaryotic Protein Kinases Homology or Analogy?. A distance-based phylogenetic analysis of proteins ... This organism lacks a cell wall but has a membrane-bound internal cytoskeleton, composed primarily of a unique 59 kDa protein, ... 1999 ; Dutta, Qin, and Inouye 1999 ). Further variability in His-acceptor domains is seen in the Spo0B protein, whose H-box ... Subunits move down the hollow core and are polymerized at the tip of the flagellum. The V. parahaemolyticus polar organelle is ...
  http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=5a645b6dd642305a
*  Eif4a3 - Eukaryotic initiation factor 4A-III - Rattus norvegicus (Rat) - Eif4a3 gene & protein
The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors ... The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core ... Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed. Involved in ... thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the ...
  http://www.uniprot.org/uniprot/Q3B8Q2
*  Antievolution.org - Antievolution.org Discussion Board -Topic::Evolution of prokaryote flagella
Histidine Kinases and Eukaryotic Protein Kinases Homology or Analogy?. A distance-based phylogenetic analysis of proteins ... This organism lacks a cell wall but has a membrane-bound internal cytoskeleton, composed primarily of a unique 59 kDa protein, ... 1999 ; Dutta, Qin, and Inouye 1999 ). Further variability in His-acceptor domains is seen in the Spo0B protein, whose H-box ... structurally similar region covers virtually the entire conserved core of both folds but is circularly permuted in the protein ...
  http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=59ee8ea0a0c2eb29
*  Multiple Epidermal Growth Factor-like Domains 8 - Wikipedia
... and TBP-dependent core promoter element for RNA polymerase II transcription from TATA-less promoters Chorion-specific ... ß propeller tertiary structure of the protein. Leucine Zipper: A motif found in regulatory proteins, as predicted by PSORT II ... Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation ... GC-Box factors SP1/GC Estrogen response elements KRAB domain zinc finger protein 57 Neuron-specific olfactory factor (2 sites) ...
  https://en.wikipedia.org/wiki/Multiple_Epidermal_Growth_Factor-like_Domains_8
*  Transfer RNA - Wikipedia
... or A box), and the 3'-ICR (T-control region or B box) inside tRNA genes. The first promoter begins at +8 of mature tRNAs and ... Eukaryotic pre-tRNA contains bulge-helix-bulge (BHB) structure motif that is important for recognition and precise splicing of ... However, the existence of the P/I site in eukaryotic or archaeal ribosomes has not yet been confirmed. The P-site protein L27 ... Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA. Because the ...
  https://en.wikipedia.org/wiki/Transfer_RNA
*  Transcription factor - Wikipedia
Cofactors are interchangeable between specific gene promoters; the protein complex that occupies the promoter DNA and the amino ... homeo domain plus zinc finger motifs 3.2 Class: Paired box 3.2.1 Family: Paired plus homeo domain 3.2.2 Family: Paired domain ... They are ubiquitous and interact with the core promoter region surrounding the transcription start site(s) of all class II ... Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics. 34: 77-137. doi:10.1146 ...
  https://en.wikipedia.org/wiki/Transcription_factor
*  DNA - Wikipedia
In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend ... Within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide ... DNA packaging and its influence on gene expression can also occur by covalent modifications of the histone protein core around ... Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that ...
  https://en.wikipedia.org/wiki/DNA
*  Sandwalk: June 2007
Most eukaryotic protein-encoding genes are interrupted. The coding regions are divided into numerous blocks called "exons" and ... boxes). (Solid boxes on transcripts) Untranslated sequences, (open boxes) translated sequences.. This isn't much different from ... There is no correlation between the exons and any protein domains or motifs. (It used to be thought that exons corresponded to ... It may be that development in the near future will reveal the importance for our organism of copper concerning oxidation and of ...
  http://sandwalk.blogspot.de/2007/06/
*  S)-dihydroorotate:NAD+ oxidoreductase - WikiVisually
... to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the ... the secondary structure shares many of the motifs of SDR, including a Rossman fold for strong NADPH binding. The protein exists ... The C-terminal domain is the larger of the two and folds into a conserved α/β-barrel structure with a core of eight parallel β- ... Eukaryotic DECR exists in both the mitochondria and the peroxisome, the enzymes from each organelle are homologous and part of ...
  https://wikivisually.com/wiki/%28S%29-dihydroorotate%3ANAD%2B_oxidoreductase
*  YBX1 - Nuclease-sensitive element-binding protein 1 - Homo sapiens (Human) - YBX1 gene & protein
Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA ... Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors ( ... Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro. ... Organism-specific databases. Human Protein Atlas. More...HPAi. ... European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. UniProt is an ELIXIR core ...
  https://www.uniprot.org/uniprot/P67809
*  Steroidal Ligands and Their Use in Gene Switch Modulation - Patent application
... non-glycosylated core protein product. Expression in yeast can produce a glycosylated product. Expression in eukaryotic cells ... 0229]The DBD is characterized by the presence of two cysteine zinc fingers between which are two amino acid motifs, the P-box ... viral promoters, bacterial promoters, animal promoters, mammalian promoters, synthetic promoters, constitutive promoters, ... organism or a eukaryotic organism. In another specific embodiment, the non-human organism is an invertebrate organism or a ...
  http://www.patentsencyclopedia.com/app/20090298175
*  calcium - How intracellular Calcium signaling, gradient and its role as a universal intracellular regulator points to design
17 The growing number of proteins containing various Ca2+-binding motifs supports the importance of Ca2+, which controls ... throughout evolution, but in plants a calmoldulin-like domain is integrated into protein kinase molecules. The eukaryotic cell ... The 10 transmembrane domains of the pump are numbered and indicated by red boxes. Splice sites "A" (first cytosolic loop) and " ... But how could and would evolution produce it, if it had no use in the organism by its own ? The Regulation of a Cell's Ca 2+ ...
  http://reasonandscience.heavenforum.org/t2448-howintracellular-calcium-signaling-gradient-and-its-role-as-a-universal-intracellular-regulator-points-to-design?highlight=calcium