Consensus sequence is ccaat. Medical search. Frequent questions

These show a different consensus sequence than normal phosphate backbone CCAAT/enhancer binding protein recognition sites for NF-IL6. (utmb.edu)
Computer analysis reveals 10 consensus sequences for Sp1, six for activating protein 1 (AP-1), six for polyoma enhancer A3 (PEA3), 12 for AP-2 and five CCAAT boxes. (uea.ac.uk)
CCAAT/enhancer-binding protein beta (Cebpb) is a key factor of Runx2 expression and our previous study has reported two CCD signs including hyperdontia and elongated coronoid process of the mandible in Cebpb deficient mice. (biomedcentral.com)
This segment included the direct repeat sequence and an adjacent GC-rich region of about 20 nucleotides defined in studies of Moloney murine sarcoma virus enhancer-promoter function (L. A. Laimins, P. Gruss, R. Pozzatti, and G. Khoury, J. Virol. (temple.edu)
Thus, although sequences outside the enhancer region are minor determinants of disease specificity when the enhancer is derived entirely from either Friend or Moloney virus, they can play a significant role when the enhancer is of mixed origin. (temple.edu)
CCAAT/enhancer-binding protein β (C/EBPβ), is a member of a family of transcription factors consisting of six structurally related basic leucine-zipper DNA-binding proteins. (biomedcentral.com)
It has been identified as a protein up-regulated by inflammatory stimuli in myeloid (THP-1) cells, and also as an oncogene that inactivates the transcription factor C/EBPalpha (CCAAT/enhancer-binding protein alpha) and causes acute myelogenous leukemia. (antibodypedia.com)
DYRK1B inhibits the Sonic Hedgehog and WNT pathways, increasing the expression of master adipogenic transcription factors CCAAT/enhancer binding protein (C/EBP-alpha) and peroxisome proliferator-activated receptor gamma (PPAR-gamma) [ 2 ]. (biomedcentral.com)

These proteins are known as CCAAT box binding proteins/CCAAT box binding factors. (wikipedia.org)
However, the full effect of the internal sequence may be greater, since the large 3-galactosidase fusion proteins studied here have been shown to be unstable. (le.ac.uk)
However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex - there should be a single motif for all four proteins, containing CCAAT. (utoronto.ca)
Histone H2B gene transcription during Xenopus early development requires functional cooperation between proteins bound to the CCAAT and octamer motifs. (wikigenes.org)
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. (biomedcentral.com)

Protein specific binding is required for the CCAAT box activation. (wikipedia.org)
We used ligation-mediated polymerase chain reaction (PCR) for a genomic sequencing study in which 450 bp of the human PGK-1 promoter region was analyzed for the presence of in vivo protein footprints and cytosine methylation at all CpG sites. (oregonstate.edu)
The other regions include potential binding sites for transcription factors ATF, NF1, and a CCAAT-binding protein. (oregonstate.edu)
Unlike the wild-type 10-mer sequences, which bind 1 protein dimer/duplex, these 22-mer thiophosphate aptamers bind with a stoichiometry of 2 dimers/duplex. (utmb.edu)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
Binding of the CCAAT-displacement protein/Cux to the untranslated exon 1 sequence. (nih.gov)
These mice express tamoxifen-induced Cre recombinase (Mer-cre-Mer) that enzymatically removes a stop codon flanked by lox sequences (floxed) on a reporter gene such as green fluorescent protein or yellow fluorescent protein, thus resulting in traceable fluorescence on the cells of interest. (musculoskeletalkey.com)
The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. (lookformedical.com)

Firstly, sequence located between -161 and -120bp (possibly spanning -120) relative to the transcript start site is essential for expression, thus demonstrating that the putative core promoter, including potential TATA and CCAAT boxes, and a pyrimidine rich region, is not alone sufficient to enable expression. (le.ac.uk)
untranslated region, lacked TATA and CCAAT boxes, and had multiple transcriptional start sites. (eurekamag.com)
Also it is curious that there is no TATA sequence in the logo. (utoronto.ca)
The murine S100{dollar}\beta{dollar} gene contains a TATA box (AATAA) and a reverse CCAAT box (ATTGG) located at 30 nucleotides and 92 nucleotides upstream of the transcription start site, respectively. (umaryland.edu)
A 149 bp DNA fragment ({dollar}-{dollar}157/{dollar}-{dollar}9) spanning the TATA box and reverse CCAAT box functions as a promoter. (umaryland.edu)

The transcriptional activator NF-Y is a heterotrimeric complex made up of NF-YA, NF-YB, and NF-YC, which specifically binds the CCAAT consensus within about 30% of eukaryotic promoters. (irjs.info)
The AhR is activated by binding to ligands, including dioxins, translocates from the cytoplasm to the nucleus and then binds to the consensus sequence known as XRE (xenobiotic responsive element) [ 7 ]. (biomedcentral.com)

In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. (biomedcentral.com)
De novo motif discovery, i.e. discovery of potentially novel motifs from a set of DNA sequences, can work well for input sequences with high motif content, like from ChIP-Seq experiments. (biomedcentral.com)
This makes them hard to discover with de novo motif discovery methods since the signal-to-noise ratio can be quite low when searching for motifs embedded in long background sequences. (biomedcentral.com)
Hence, groups of motifs for co-operating factors will often occur in close proximity to each other in the DNA sequence, and such "composite motifs", or cis -regulatory modules (CRM), can provide a stronger signal than individual motifs. (biomedcentral.com)
Signal search analysis is an ancient method (published in 1984) to analyse sequence motifs that occur at characteristic distances upstream or downstream from a functional site in a nucleic acid sequence. (expasy.org)
They are likely to have conserved DNA sequence elements, called transcription factor binding motifs (TFBMs), in their promoter regions. (biomedcentral.com)

Both of these consensus sequences belong to the regulatory promoter. (wikipedia.org)
In an experiment done with core binding factors (CBF) and DNA complexes, researchers were able to determine the preferential sequences of the promoter in a region over and immediately adjacent to the CAAT box, and two regions on either side of the CAAT box. (wikipedia.org)
For sequences that flanked the ATTGG motif with two adenine residues (AA) on its 5' end and G(A/G) on its 3' end, seems to have inhibited formation of the CBF-DNA complex and subsequently occurred in only 1% of the promoter sequences. (wikipedia.org)
In another experiment performed with the major late promoter (MLP) of adenoviruses from a variety of host species, it was shown that the mutation of the CAAT box and CCAAT sequence, which is thought to play a pivotal role in the (MLP) of subgroup C human adenoviruses, in species with a deficient CAAT sequence. (wikipedia.org)
In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. (oregonstate.edu)
Analyse the positional distributions of the CCAAT-box like signals in the non-redundant insect and plant promoter subsets. (expasy.org)
This page allows you to extract promoter sequence segments around transcription initiation sites You can use this tool to select all promoters (leaving all 'Optional criterias' blank) or them based on all or some of their genomic contexes (such as presence of core promoter elements) or expression levels. (expasy.org)
A comparison of this sequence to known promoter elements has revealed the presence of an octamer AAGCAAAT (-131 to -124), with a seven out of eight base pair match to the consensus octamer sequence ATGCAAAT characterized as being essential for the expression of several higher eukaryotic genes. (le.ac.uk)
Analysis of the mouse C3 promoter showed that it is directly regulated by C/EBPβ through a C/EBPβ consensus site located at position −616/-599 of the gene. (biomedcentral.com)

We compared the genomic sequences of susceptible and resistant isolates without mutations in cyp51A (non- cyp51A ) and found mutations in hmg1 and erg6 involved in ergosterol biosynthesis. (cdc.gov)

Experiments in many laboratories have shown that mutations to the CCAAT motif that cause a loss of CBF binding also decreases transcriptional activity in these promoters, suggesting that CBF-CCAAT complexes are essential for optimum transcriptional activity. (wikipedia.org)
Previous studies showed that sequences encompassing the viral transcriptional signals in U3 are the primary determinant of this phenotype in recombinants between these two viruses. (temple.edu)
The organization, sequence and transcriptional regulation of the murine S100{dollar}\beta{dollar} gene have been studied. (umaryland.edu)

Expressed sequence tag (EST) analysis and developmental polymerase chain reaction (PCR) studies demonstrated that Ov-phy-1 was expressed in L3 and adult parasites. (embl.de)

Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)

In molecular biology, a CCAAT box (also sometimes abbreviated a CAAT box or CAT box) is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occur upstream by 60-100 bases to the initial transcription site. (wikipedia.org)
Secondly, the surrounding nucleotides in plants do not match the consensus sequence above determined by Bi et al. (wikipedia.org)
This was shown using an oligonucleotide sequence (R1) which contained 27 random nucleotides, flanked by a defined 20 nucleotide sequence on each side. (wikipedia.org)
While no single nucleotide was selected in every clone on either side of the ATTGG motif (CCAAT in the complementary strand), there were several nucleotides in positions selected with high frequency. (wikipedia.org)
This same experiment also yielded the same sequence as shown above when using a different oligonucleotide (R2) that contained an ATTGG core and flanked by 12 5' random nucleotides and 10 3' random nucleotides. (wikipedia.org)
The direct repeats of Friend and Moloney viruses are identical in a central core sequence of 32 nucleotides but have sequence differences on either side of this core as well as in their GC-rich segments. (temple.edu)

There, one wants to find a motif present in all or a statistically significant proportion of input sequences. (expasy.org)

By using PCR-mediated random binding selection process, researchers were able to show that the sequence "3' - (T/C)G ATTGG (T/C)(T/C)(A/G) - 5'" immediately flanking the ATTGG region (CCAAT in the complementary strand) was preferentially selected on the coding strand (opposite of the template strand). (wikipedia.org)
Most notably from the sequence above was the G residue towards the 5' end of the ATTGG. (wikipedia.org)

Furthermore, sequence located between -638 and -488bp, and including an eight bp consensus element TGAGGTGT common to the four cloned A.nidulans glycolytic genes, has been shown to modulate expression: increasing activity about 1.5-fold on gluconeogenic compared to glycolytic carbon sources. (le.ac.uk)
A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3′ coding region. (biomedcentral.com)

Whilst the octamer containing sequence contributes almost a residual 40% of the maximum expression recorded, a second region encompassing codons 14 to 183 and including the two introns of pgk has been shown to account for over 30% of the total activity. (le.ac.uk)

It is also called nucleotide sequence. (lookformedical.com)

It is an invariant DNA sequence at about minus 70 base pairs from the origin of transcription in many eukaryotic promoters. (wikipedia.org)
The CCAAT-box is another signal reported to occur frequently in the upstream region of eukaryotic promoters. (expasy.org)

this fragment contains 1718 bp 5' flanking sequences, exon 1, a 929 bp intron 1 and part of exon 2. (uea.ac.uk)

Produce a signal occurrence profile for the pentamer sequence CCAAT. (expasy.org)

Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis -regulatory modules. (biomedcentral.com)
All six members of this family exhibit a high sequence similarity in their C-terminal DNA binding domain and a more diverge regulatory N-terminus [ 1 , 2 ]. (biomedcentral.com)

The derived amino acid sequence of Ov-phy-1 encoded a peptide that was most similar to the two Caenorhabditis elegans prolyl 4-hydroxylase homologues and to the isoform II enzymes of vertebrates. (embl.de)

Prokaryotic messenger RNAs contain a so-called Shine-Dalgarno interaction region upstream of the initiation codon, containing a sequence motif that is complementary to the highly conserved 3'-terminus of the 16s ribosomal RNA (see for instance A14565 ). (expasy.org)

Therefore, we searched for DYRK1B variants in the exome sequencing data derived from 968 unrelated individuals (509 with type 2 diabetes) belonging to the DMS1 SIGMA-cohort (ExAC) [ 4 ], focusing on variants classified by Variant Effect Predictor (VEP) as deleterious and damaging to confirm their co-segregation with AOMS3. (biomedcentral.com)

It is essential to the transcription that these core binding factors (also referred to as nuclear factor Y or NF-Y) are able to bind to the CCAAT motif. (wikipedia.org)
This factor can specifically bind to a 17 bp DNA fragment ({dollar}-{dollar}1513/{dollar}-{dollar}1497) which contains a consensus silencer element. (umaryland.edu)

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

Bone marrow & Lymphoid tissues Brain Breast and female reproductive system Connective & Soft tissue Endocrine tissues Eye Gastrointestinal tract Kidney & Urinary bladder Liver & Gallbladder Lymphoid Male reproductive system Muscle tissues Myeloid Pancreas Proximal digestive tract Respiratory system Skin * nTPM: Normalized TPM levels represent consensus gene expression calculated using two data sets. (antibodypedia.com)

The CAAT box signals the binding site for the RNA transcription factor, and is typically accompanied by a conserved consensus sequence. (wikipedia.org)

We found that disease specificity, in particular the ability of Friend virus sequence to confer erythroleukemogenicity on Moloney virus, is encoded throughout the region in at least three separable segments: the 5' and 3' halves of the direct repeat and the GC-rich segment. (temple.edu)

In signal search analysis, the input is a list of experimentally defined functional sites, for instance transcription initiation sites, given as pointers to positions in nucleotide database sequences (The sequences are stored somewhere else on the computer). (expasy.org)
The analysis of transformed strains in which single copies of lacZ fusions have been targeted to the qutE locus has identified three constitutive positively acting sequence elements in the pgk gene. (le.ac.uk)
PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)

Four of the footprints contained the consensus sequence of the binding site for transcription factor Sp1. (oregonstate.edu)

Both these sequences are very similar and confirmed in multiple experiments. (wikipedia.org)

As mentioned before, SSA programs typically do not use sequences as input but lists of computer-readable pointers to sequence positions in a database. (expasy.org)

The Xi did not show any specifically protected sequences, and with the exception of four hyperreactive sites, the in vivo DMS reactivity profile of Xi DNA was very similar to that of purified, linear Xi DNA. (oregonstate.edu)

In a separate exercise, the native pgk gene has been replaced with disrupted sequence to generate a pgk mutant strain of A.nidulans. (le.ac.uk)
The TIRF-PBM data used to generate the motif included only 96 sequences. (utoronto.ca)

Within metazoa (animal kingdom), the core binding factor (CBF)-DNA complex retains a high degree of conservation within the CCAAT binding motif, as well as the sequences flanking this pentameric motif. (wikipedia.org)

A recent study showed that HapE forms a CCAAT binding complex, which plays a role in the negative regulation of cyp51A expression. (cdc.gov)

A CCAAT box is a feature frequently found before eukaryote coding regions, but is not found in prokaryotes. (wikipedia.org)

Using a 22-nucleotide-long duplex random library, nanomolar binding, specific 22-mer thiophosphate backbone substitution sequences (at dA positions only) were selected. (utmb.edu)

On the left side under the header Sequence input make sure that the checkbox "Transcription initiation sites" is activated. (expasy.org)
On the right side under the header Signal description make sure that the checkbox "Consensus sequence" is activated. (expasy.org)

To more precisely identify the sequences responsible, we constructed additional recombinants, within U3, between Friend and Moloney viruses and assayed these recombinants for for their disease specificity. (temple.edu)

All PCR solutions were cloned utilizing pGEM T simple and sequenced with Major Dye Terminator chemistry and the ABI 3730 automated sequencer, each delivered by. (alkpathway.com)

Anatomy13

Organisms11

Diseases1

Chemicals and Drugs95

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Psychiatry and Psychology1

Phenomena and Processes101

Disciplines and Occupations1

Anthropology, Education, Sociology and Social Phenomena1

Information Science9

Health Care3

Enhancer8

Proteins7

Protein9

TATA5

Binds2

Motifs6

Promoter9

Genomic1

Transcriptional3

Polymerase chain re1

Nucleic2

Nucleotides6

Input sequences1

ATTGG2

Genes2

Octamer1

Nucleotide sequence1

Eukaryotic2

Exon1

Occurrence1

Regulatory2

Peptide1

Complementary1

Variants1

Bind2

Amino1

Gene expression1

Signals1

Region1

Analysis3

Binding site1

Experiments1

Typically1

Show1

Generate2

High1

Complex1

Coding regions1

Positions1

Side2

Identify1

Simple1