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  • Genetic
  • Yeast repressor activator protein 1 (RAP1) binds in vitro to specific DNA sequences that are found in diverse genetic elements. (hku.hk)
  • 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)
  • A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. (wikipedia.org)
  • Genome
  • Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. (nih.gov)
  • Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome sequences, which may have limited their power. (nih.gov)
  • Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of Methanococcus jannaschii. (wikipedia.org)
  • These algorithms are currently in use in many research labs in the US and abroad as well as at the major sequencing and annotation centers, such as the Broad Institute, DOE Joint Genome Institute and NIH National Center for Biotechnology Information. (wikipedia.org)
  • Both Watson and Crick strands can be either sense or antisense strands depending on the gene whose sequences are displayed in the genome sequence database. (wikipedia.org)
  • nucleotide
  • Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. (nih.gov)
  • A) and B) display the pairwise nucleotide and predicted amino acid differences among orders regressed against tmrca, respectively. (nih.gov)
  • Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is recognized and bound by transcription factors to initiate gene transcription. (wikipedia.org)
  • Cumulative data shows that Pur-alpha preferentially binds to the sequence (G2-4N1-3)n, where N is not G. N denotes a nucleotide, and n denotes the number of repeats of this small sequence. (wikipedia.org)
  • In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. (wikipedia.org)
  • The degree of complementarity between two nucleic acid strands may vary, from complete complementarity (each nucleotide is across from its opposite) to no complementarity (each nucleotide is not across from its opposite) and determines the stability of the sequences to be together. (wikipedia.org)
  • In the absence of L-histidine and divalent metal ions or both, HutP does not bind to the hut mRNA, thus allowing the formation of a stem loop terminator structure within the nucleotide sequence located between the hutP and structural genes. (wikipedia.org)
  • genomic
  • We built a random forest classifier to predict methylation levels at CpG site resolution using features including neighboring CpG site methylation levels and genomic distance, co-localization with coding regions, CpG islands (CGIs), and regulatory elements from the ENCODE project. (nih.gov)
  • Colors represent different types of features: neighbors in red, genomic position in green, sequence properties in blue and CREs in black. (nih.gov)
  • Genomic sequence is highly predictive of local nucleosome depletion. (nih.gov)
  • Binding of a TF to a genomic site is documented by specifying the localization of the site, its sequence and the experimental method applied. (wikipedia.org)
  • Regions
  • This new approach has significantly improved the prediction accuracy.Regulatory elements are enriched in low N-score regions.While our model is derived from yeast data, the N-score pattern computed from this model agrees well with recent high-resolution protein-binding data in human. (nih.gov)
  • Regulatory elements are enriched in low N-score regions. (nih.gov)
  • Previous studies have demonstrated an association between polymorphisms in the regulatory regions of Cyclophilin A (CypA) and susceptibility to both HIV-1 infection and disease progression. (nih.gov)
  • We screened participants of the ACS for the C1604G and A1650G polymorphisms in the regulatory regions of CypA. (nih.gov)
  • We postulate that extensive restructuring and remodeling of Hox cis-regulatory regions occurring in different taxa lead to relatively different Hox expression patterns, which in turn may act as a driving force in generating diverse axial morphologies. (zfin.org)
  • Conserved non-coding sequences often contain regulatory regions, and so they are often the subject of these analyses. (wikipedia.org)
  • However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. (wikipedia.org)
  • zebrafish
  • The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny. (nih.gov)
  • Finally, we demonstrate that the regulatory sequences of zebrafish hoxa3a are divergent with respect to the mouse ortholog Hoxa3, or the paralog hoxb3a. (zfin.org)
  • Surprisingly, these new elements are missing from the zebrafish and Fugu Hoxc8 early enhancer sequences. (zfin.org)
  • bind
  • A DNA fragment Z + which contains the activator core sequence of the PGK(UAS) has been shown to bind RAP1. (hku.hk)
  • analysis
  • Western analysis and immunohistochemistry were used to detect and confirm the protein expression, and hyaluronic acid substrate gel electrophoresis analyzed its hyaluronidase activity. (nih.gov)
  • Here we describe four additional cis-acting elements (F-I) within the 200 bp Hoxc8 early enhancer region identified by comparative regulatory analysis and transgene-mutation studies. (zfin.org)
  • Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique. (wikipedia.org)
  • Consensus Sequence
  • See also consensus sequence. (wikipedia.org)
  • Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
  • enhancer
  • Significant divergence between mammalian and fish Hoxc8 early enhancer sequences and activities suggested additional cis-acting elements. (zfin.org)
  • Factor
  • Following the identification of a Pur factor, which specifically bound a purine-rich sequence in the control region of the c-MYC gene, the gene, PURA, encoding the protein, Pur-alpha, was cloned and sequenced for both human and mouse (GenBank U02098.1). (wikipedia.org)
  • Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. (wikipedia.org)
  • expression
  • Then, associations between sequence features and meta-expression values were inferred by structure learning of Bayesian networks. (nih.gov)
  • organisms
  • This evolutionary conservation means that the specific sequence of this domain is important for the survival of most species throughout the spectrum of living organisms. (wikipedia.org)