• genomes
  • Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq.Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region.As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. (nih.gov)
  • Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. (nih.gov)
  • Research to find all regulatory regions in the genomes of all sorts of organisms is under way. (wikipedia.org)
  • However, the question was raised, motivated by studies of viral genomes, how to define parameters for gene prediction in a rather short sequence that has no large genomic context. (wikipedia.org)
  • 3, 87-97 Schiex T, Gouzy J, Moisan A, de Oliveira Y. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. (wikipedia.org)
  • Borodovsky has made many contributions in the area of development of gene finding algorithms, notably the GeneMark program (1993) that made an impact in the field and was used for annotation of the first completely sequenced genomes of Haemophilus influenzae and Methanococcus jannaschii. (wikipedia.org)
  • Mark Borodovsky homepage at BME Mark Borodovsky research homepage Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training, Genome Research Gene identification in novel eukaryotic genomes by self-training algorithm, Nucleic Acids Research GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Nucleic Acids Research GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. (wikipedia.org)
  • genes
  • OCT4 directly binds Xite and Tsix, which encode two long noncoding RNAs (lncRNAs) that suppress the silencer lncRNA, Xist.Here we show that BRD4, a member of the BET protein subfamily, interacts with OCT4.BRD4 occupies the regulatory regions of pluripotent genes and the lncRNAs of XCI. (nih.gov)
  • A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. (nih.gov)
  • Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. (nih.gov)
  • While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. (nih.gov)
  • The two beta-lactamase genes of Streptomyces cacaoi, blaL and blaU, are under the control of the same regulatory system. (uliege.be)
  • It can thus be concluded that the S. cacaoi blaL and blaU genes are controlled by the same regulatory system. (uliege.be)
  • It also provides links to the evidence that supports the proposed TIS to be confirmed: PMID or external database links for IPT TIS, conserved domain search results for CDC-TIS and multiple N-terminal sequence alignments among orthologous genes for HSC TIS.Figure 1. (nih.gov)
  • A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. (wikipedia.org)
  • Since 2004 models built by the heuristic approach have been used in finding genes in metagenomic sequences. (wikipedia.org)
  • The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new TFBS recognition algorithms. (wikipedia.org)
  • Cis-regulatory module (CRM) is a stretch of DNA, usually 100-1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. (wikipedia.org)
  • One cis-regulatory element can regulate several genes, and conversely, one gene can have several cis-regulatory modules.Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given. (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)
  • In biology and research, short antisense molecules can interact with complementary strands of nucleic acids, modifying expression of genes. (wikipedia.org)
  • DNA strand 1: antisense strand (transcribed to)→ RNA strand (sense) DNA strand 2: sense strand Some regions within a double strand of DNA code for genes, which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites, noncoding introns, and other complicating details. (wikipedia.org)
  • 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
  • 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)
  • Regions
  • 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)
  • promoter
  • These include, but are not limited to: CACGTT sequence 20 bp upstream of the mouse Period2 (PER2) gene and regulates its expression CAGCTT sequence found within the MyoD core enhancer CACCTCGTGAC sequence in the proximal promoter region of human and rat APOE, which is a protein component of lipoproteins. (wikipedia.org)
  • The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
  • Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). (wikipedia.org)
  • bind
  • A DNA fragment Z + which contains the activator core sequence of the PGK(UAS) has been shown to bind RAP1. (hku.hk)
  • 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)
  • 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)
  • Surprisingly, these new elements are missing from the zebrafish and Fugu Hoxc8 early enhancer sequences. (zfin.org)
  • electrophoresis
  • 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)
  • Electrophoretic sequencing gels or capillary electrophoresis have been successful in analyzing footprinting of fluorescent tagged fragments. (wikipedia.org)
  • Analysis
  • 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)
  • upstream
  • Expression of the yeast phosphoglycerate kinase gene (PGK) requires the binding of RAP1 to the activator core sequence within the upstream activating sequence (UAS) of PGK. (hku.hk)
  • Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. (nih.gov)
  • characteristic
  • The BlaA DNA binding-site was further restricted to a 30-bp sequence containing a T-N11-A motif, a characteristic of LysR-type promoters. (uliege.be)
  • TESS also provides a program for the identification of cis-regulatory modules (CRMs, characteristic combinations of TFBSs), which uses TRANSFAC matrices. (wikipedia.org)
  • Depending
  • Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, junctions, bulges or internal loops. (wikipedia.org)
  • Unfortunately no available agents meet all of these standards, so an appropriate agent can be chosen, depending on your DNA sequence and ligand of interest. (wikipedia.org)
  • Expression
  • CFTR expression from a BAC carrying the complete human gene and associated regulatory elements. (nih.gov)
  • 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)
  • localization
  • This localization is mediated by isoform-specific 3'-untranslated sequences (zipcodes) and can be inhibited by antizipcode oligodeoxynucleotides (ODNs) (Kislauskis, E.H., X.-C. Zhu, and R.H. Singer. (umassmed.edu)
  • 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)