• All members of the Iroquois (IRO) family of proteins share two highly conserved features, encoding both a homeodomain and a characteristic IRO sequence motif. (wikipedia.org)
  • The IRO motif is a region downstream of the homeodomain that is found only in members of the Iroquois-class homeodomain proteins, though its function is poorly understood. (wikipedia.org)
  • IRX1 is one of six members of the Iroquois-class homeodomain proteins found in humans: IRX2, IRX3, IRX4, IRX5, and IRX6. (wikipedia.org)
  • We focus our attention on three families of transcription factors that are known to have roles in vertebrate chondrogenesis: Sox and the Ant- and Prd- class families of the homeodomain proteins. (europa.eu)
  • Both predicted proteins are highly conserved with other known homologous sequences, with the exception of two small domains present only in the Sof-RXR. (europa.eu)
  • The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.com)
  • Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL). (lookformedical.com)
  • The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS. (lookformedical.com)
  • As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. (biomedcentral.com)
  • Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. (biomedcentral.com)
  • DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. (lookformedical.com)
  • The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. (embl-heidelberg.de)
  • The KH repeat is an ancient RNA binding motif found in proteins from diverse organisms. (nsf.gov)
  • A superfamily of proteins that share a highly conserved MADS domain sequence motif. (bvsalud.org)
  • Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). (bvsalud.org)
  • Members of the zinc-finger homeodomain (ZF-HD) family play a key role in the control of plant growth and development, which are involved in plant responses to stress. (ashs.org)
  • Based on previous phylogenetic analyses in arabidopsis ( Arabidopsis thaliana ), our results showed that some tomato SL-ZH ( S. lycopersicum zinc-finger homeodomain) genes cluster into the same neighbor-joining (NJ) branch as arabidopsis, indicating that these genes may share similar structures and functions in these plants. (ashs.org)
  • Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. (embl.de)
  • A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. (biomedcentral.com)
  • The absence of genomic resources renders the search for paralogous cuttlefish genes dependent upon the presence of highly conserved protein motifs within genes of interest, thus we used a degenerate primer strategy to isolate partial coding sequence from the conserved domains specific to these families. (europa.eu)
  • Spatial expression analysis of both genes revealed that Sof-RXR is expressed ubiquitously in all cells of the embryo, including the chondrocytes, whereas Sof-ALDH was expressed only in a sub-set of epithelial cells and no expression at the level of chondrocytes was observed. (europa.eu)
  • Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
  • Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
  • TFs contain motifs for activation or repression of target genes through direct binding to gene regulatory elements or motifs. (ashs.org)
  • Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. (lookformedical.com)
  • C) DAVID clustering analysis shows enrichment for developmental (dev) terms in all Smad2/3-associated genes and for genes that have stable Smad2/3 binding when E2a is depleted (red box in B) but not other subcategories of Smad2/3 binding. (xenbase.org)
  • The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. (gao-lab.org)
  • Genetic analysis of early development in the Drosophila embryo has revealed that embryonic pattern formation depends on both maternal and zygotic genes. (silverchair.com)
  • Mutant analysis revealed complex genetic interactions between FLK and several major SA pathway genes. (nsf.gov)
  • RNA sequencing experiments indicated that >7000 genes are mis‐expressed in the Mting2‐1 mutant, consistent with its strong mutant phenotypes. (nsf.gov)
  • A BLAST search revealed that IRX1 contains two highly conserved domains: a homeodomain and a characteristic IRO motif of unknown function. (wikipedia.org)
  • HD-Zip protein usually contain two highly conserved domains: homeodomain (HD) and leucine zipper (LZ) [ 1 ]. (biomedcentral.com)
  • This gene encodes a basic motif-leucine zipper transcription factor of the Maf subfamily. (en-academic.com)
  • 1992). "A conserved retina-specific gene encodes a basic motif/leucine zipper domain" . (en-academic.com)
  • 2000). "The leucine zipper of NRL interacts with the CRX homeodomain. (en-academic.com)
  • These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. (biomedcentral.com)
  • A homeobox (HB) encodes a protein domain, the homeodomain (HD), which is a conserved 60-amino acid motif present in transcription factors found in all the eukaryotic organisms. (gao-lab.org)
  • A comparative study based on four fully sequenced eukaryotic genomes has revealed profound differences in the sets of transcription factors used by plants, fungi and animals. (biomedcentral.com)
  • With the completed genome sequences of Saccharomyces cerevisiae (budding yeast), Caenorhabditis elegans and Drosophila melanogaster , complete proteomes from representatives of three eukaryotic kingdoms (plants, fungi and animals) are now available for comprehensive comparative studies. (biomedcentral.com)
  • The presence of this well characterized homeodomain strongly suggests that IRX1 acts as a transcription factor. (wikipedia.org)
  • HD-Zip transcription factors belong to the Homeodomain (HD) transcription factor superfamily and are only found in plants. (biomedcentral.com)
  • A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)
  • PWMs are a useful way to represent binding specificities and provide a statistical framework for searching for novel instances of the motif in genome sequences (Berman, 2002). (sdbonline.org)
  • Gene identity was determined initially based upon BLAST similarity and confirmed by phylogenetic analysis. (europa.eu)
  • Relative levels of gene expression throughout development were determined by quantitative polymerase chain reaction (PCR) analysis and in cases where sufficient specific gene sequence was acquired, ribonucleic acid (RNA) probes were generated to evaluate the spatial expression patterns during the period of organogenesis. (europa.eu)
  • The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental processes in plants, such as embryonic patterning, stem-cell maintenance and organ formation. (gao-lab.org)
  • Transcription factors (TFs), which bind to specific nucleotide sequences, have been shown to play important roles in the regulatory networks of numerous developmental processes in plants. (ashs.org)
  • 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)
  • It is also called nucleotide sequence. (lookformedical.com)
  • Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO. (lookformedical.com)
  • Iroquois-class homeodomain protein IRX-1, also known as Iroquois homeobox protein 1, is a protein that in humans is encoded by the IRX1 gene. (wikipedia.org)
  • Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)
  • The entire protein is more fully conserved through vertebrate species, while only the homeodomain and IRO motif are conserved in more distant homologs.Homologous sequences were found in species as distantly related to humans as the pig roundworm Ascaris suum, from the family Ascarididae, using BLAST and the ALIGN tool through the San Diego Super Computer Biology Workbench. (wikipedia.org)
  • The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. (lookformedical.com)
  • Recently, we described the characterisation of a parasite gene (TashAT2), whose polypeptide product bears AT hook DNA-binding motifs and may be transported from the parasite to the host nucleus. (lookformedical.com)
  • The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger . (embl-heidelberg.de)
  • Ubiquitination and degradation of homeodomain-interacting protein kinase 2 by WD40 repeat/SOCS box protein WSB-1. (nih.gov)
  • The recent completion of the Arabidopsis thaliana genome sequence allowed the first prediction of a full plant proteome. (biomedcentral.com)
  • Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. (biomedcentral.com)
  • Some LIM domains bind protein partners via tyrosine-containing motifs. (embl.de)
  • They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)
  • In addition to these two characteristic domains, IRX1 contains a third domain from the HARE-HTH superfamily fused to the C-terminal end of the homeodomain. (wikipedia.org)
  • This 60-amino acid sequence folds into a characteristic three-helix structure that is able to interact specifically with DNA. (gao-lab.org)
  • In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. (bvsalud.org)
  • The MtING2 PHD finger bound H3K4me2/3 peptides weakly in vitro , but analysis of gene‐edited mutants indicated that it was dispensable to MtING2 function in wild‐type plants. (nsf.gov)
  • Loss of function analysis using Xenopus tropicalis embryos (A) Sequence alignment of MOs and mRNAs. (xenbase.org)
  • Human DNMT1o mRNA is detectable in mature oocytes and early fertilized embryos but not in any somatic tissues analysed. (biomedcentral.com)
  • Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)
  • Given that we previously defined the viral np9 gene, which is aberrantly activated in human leukemia, as a potent oncogene [ 1 ], we next attempted to search for cellular homologs of the viral oncogene np9 in NCBI database by performing alignment using Np9 protein sequence. (aging-us.com)
  • The reverse activity transcribes the ZAR2 mRNA with 966 nt coding sequence which codes for a 321 amino acid protein. (biomedcentral.com)
  • Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. (biomedcentral.com)
  • PHD: plant homeodomain fingers or LAP domains. (atlasgeneticsoncology.org)
  • HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. (biomedcentral.com)
  • The physiological analysis and dissection of floral induction were made by introducing an experimental system based on the understanding that an external controllable stimulus can cause flowering when applied to a specific plant. (jabonline.in)
  • While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. (bvsalud.org)
  • Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. (bvsalud.org)
  • Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. (biomedcentral.com)
  • Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes. (bvsalud.org)
  • The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. (lookformedical.com)
  • They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. (embl.de)
  • They consist of positively charged sequences of nine amino acids centered on the invariant tripeptide glycine-arginine-proline. (lookformedical.com)
  • Recent global analyses of gene transcripts revealed that specific transcription factors (TFs) and their networking systems physiologically correspond to the onset of human diseases, including cancer. (intechopen.com)
  • Using Western blot analysis, the affinity-purified polyclonal VCY2 antibody gave a single specific band of approximately 14 kDa in size, corresponding to the expected size of VCY2 in all the collected human testicular biopsy specimens with normal spermatogenesis. (bioone.org)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • And the arrangement of the three helices determines the difference in the specific binding of homeodomain to DNA. (biomedcentral.com)
  • Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl.de)
  • The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cells. (bvsalud.org)
  • The binding sequences for each factor were aligned by using the motif-assembly program, and the binding specificities of each factor were modeled with position weight matrices (PWMs). (sdbonline.org)
  • The homeodomain belongs to the TALE (three amino acid loop extension) class of homeodomains, and is characterized by the addition of three extra amino acids between the first and second helix of three alpha helices that comprise the domain. (wikipedia.org)
  • FLIM-FRET analysis of protein-protein interactions showed that PLIN5 S155 phosphorylation regulates PLIN5 interaction with adipose triglyceride lipase at the lipid droplet, but not with α-β hydrolase domain-containing 5. (uci.edu)
  • The KDM5A (JARID1A) sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain. (atlasgeneticsoncology.org)
  • The homeodomain domain is generally composed of about 60 amino acids encoded homeobox, which form three alpha helices. (biomedcentral.com)
  • The sequence variant rs2106261 is an intronic SNP located in the ZFHX3 gene, also called AT motif-binding factor 1 ( ATBF1 ), on chromosome 16q22, and was highly associated with AF in a Chinese GeneID study [ 8 ]. (e-arrhythmia.org)
  • Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. (bvsalud.org)
  • Along with the core binding motif, the flanking sequence context can play a role in DNA-TF recognition. (bvsalud.org)
  • Promoter analysis was performed using El Dorado through the Genomatix software page. (wikipedia.org)
  • Promoter analysis with the El Dorado program from Genomatix predicted that IRX1 expression is regulated by factors that include E2F cell cycle regulators, NRF1, and ZF5, and brachyury. (wikipedia.org)
  • A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. (lookformedical.com)
  • b) Loss- of-function analysis in X. tropicalis. (xenbase.org)
  • c) Gain-of-function analysis in X. laevis. (xenbase.org)
  • We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. (bvsalud.org)
  • Here we report the expression and functional analysis of cnd-1 , a C. elegans NeuroD homolog. (biologists.com)
  • molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)