ProteinsGenes encodeMutationsProteinGenomic SequenceChromosomeNanogAmino acidGenomeMotifGene expressionInsulinProliferationNucleotidePromoterEnhancerMotifsFamilySpecificGenesProteinsAmino acid sequencesDrosophilaProteinTranscription factorsHomology2002GenomicNucleotide sequenceComplexesEncodesEukaryoticDomainReference sequenceExpressionVirtuallyEpigeneticCopiesRegionMouseElementsCompletelyImportantPreviouslyAddress
Proteins9
- Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. (lookformedical.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)
- The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. (beds.ac.uk)
- Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. (embl.de)
- it has been known for forty years that the structures of proteins are determined by their amino acid sequences, but as recently as five or six years ago it was generally thought that the prediction problem was completely intractable as very little progress had been made. (bakerlab.org)
- this goal remained elusive for the first few years, but about a year and a half ago we made a breakthrough and found that we could make very accurate predictions for some proteins using a trick that involves folding not only the sequence of the protein of interest but also the sequences of a large number of evolutionarily related homologs. (bakerlab.org)
- so now, looking at David Kim's results and seeing that for quite a few proteins we are coming close to predicting structure from their amino acid sequences without any other information is pretty breathtaking. (bakerlab.org)
- Homeobox proteins are master regulators of develop-ment and control many cellular processes, including proliferation, apoptosis, cell shape, and cell migration. (123dok.net)
Genes encode3
- The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. (nih.gov)
- The HOX genes encode a family of homeodomain-containing transcription factors that play important roles in the early embryo, including the establishment of cell and tissue identity, and the regulation of cell proliferation, differentiation, and survival [ 12 ]. (biomedcentral.com)
- Background: HOX genes encode a family of homeodomain-containing transcription factors involved in the determination of cell fate and identity during embryonic development. (123dok.net)
Mutations4
- Mutations in the gene for the antennapedia homeodomain protein are associated with the conversion of antenna to leg or leg to antenna DROSOPHILA. (lookformedical.com)
- 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)
- Direct evidence for this model comes from the identification of heterozygous germline mutations in the homeodomain transcription factor PHOX2B , a regulator of sympathetic neuronal differentiation [3] - [8] . (prolekarniky.cz)
- Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
Protein6
- The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. (nih.gov)
- Antennapedia homeodomain protein. (lookformedical.com)
- Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)
- C. elegans homeobox protein ceh-14. (embl.de)
- C. elegans homeobox protein unc-97. (embl.de)
- however, this work did not achieve the goal of predicting structure accurately from the amino acid sequence of a protein alone as we had to resort to evolutionary information. (bakerlab.org)
Genomic Sequence1
- Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. (zfin.org)
Chromosome2
- This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. (nih.gov)
- In this study, we analyzed the gene structure and sequence characteristics of porcine NANOG and found that the porcine NANOG gene is localized on chromosome 5, while NANOG sequence on chromosome 1 is the processed pseudogene. (bvsalud.org)
Nanog1
- Nanog homeobox (NANOG) is the gateway to the pluripotent ground state in mouse embryonic stem cells and early embryos. (bvsalud.org)
Amino acid2
- 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)
- 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)
Genome1
- The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
Motif2
- The TIRF-PBM data used to generate the motif included only 96 sequences. (utoronto.ca)
- de novo generated motifs, by analyzing ChIP-seq/-exo sequences using a custom motif discovery pipeline (check the code at our repository ). (genereg.net)
Gene expression1
- We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. (preprints.org)
Insulin2
- When tested in vitro, IB1 bound specifically to the GTII cis element of the GLUT2 gene and to an homologous regulatory sequence of the insulin promoter termed RIPE3. (justia.com)
- This rat insulin promoter element 3 (RIPE3) is an important enhancer sequence sufficient to confer .beta. (justia.com)
Proliferation1
- WUS is a homeodomain transcription factor (TF) produced in the organizing center (OC) domain of apical meristems and is transported via plasmodesmata into the apical domain (called central zone, CZ) to promote proliferation of stem cells 3 . (nature.com)
Nucleotide2
- It is also called nucleotide sequence. (lookformedical.com)
- Highly repetitive sequences present in non-coding regions of crx and extended tetra-nucleotide repeats in intronic regions were associated with sequence variation between different strains. (zfin.org)
Promoter2
- In this study, by characterization of the dominant maize mutant Barren inflorescence3 ( Bif3 ) we identified a tandem-duplicated copy of ZmWUS1 whose expression is dramatically enhanced by the insertion of a short stretch of chimeric proximal promoter sequence. (nature.com)
- Important cis-regulatory sequences were identified within this promoter region including a functionally responsive PDX-1 element, a cyclic AMP responsive element, and three cis elements termed GTI, GTII and GTIII (3,36,53). (justia.com)
Enhancer1
- These stripes are regulated by a 300-bp enhancer (NEE) that contains high-affinity Dl-binding sites, Twist-binding sites, and "generic" E-box sequences that appear to bind ubiquitously distributed bHLH activators (Daughterless and Scute), which are present in the unfertilized egg. (sdbonline.org)
Motifs2
- There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)
- TF binding motifs may be used either to predict TFBSs on DNA sequences or as reference when annotating/comparing de novo motifs. (genereg.net)
Family1
- This gene belongs to the homeobox family of genes. (nih.gov)
Specific1
- PFMs can be transformed to probabilistic models to construct position weight matrices (PWMs) or position-specific scoring matrices (PSSMs), which then can be used to scan any DNA sequence and predict transcription factors binding sites (TFBSs). (genereg.net)
Genes14
- Four Pou-domain genes expressed in embryonic and adult mouse brain were cloned and sequenced: Brain-1, Brain-2, Brain-4, and Scip. (nih.gov)
- Putative genes that are regulated by NK-2 protein were cloned and were sequenced partially. (nih.gov)
- Cell Recognition and Synapse Formation Project Description Major Findings Mouse Homeobox Genes. (nih.gov)
- In collaboration with C. Kozak the Hox 1.11 gene was mapped to mouse chromosome 6, which contains the Hox-1 cluster of homeobox genes. (nih.gov)
- We described two tightly linked and nearly identical homeobox genes of the TGIF (TG-interacting factor)subclass called vismay and achintya that are essential for spermatogenesis in Drosophila . (biologists.com)
- Because Vismay and Achintya are likely to be sequence-specific DNA binding factors, these results suggest that they help to specify the spermatogenesis program by recruiting or stabilizing Always early and Cookie monster to specific target genes that need to be transcriptionally regulated during testes development. (biologists.com)
- The extremely high degree of sequence conservation in non-homeobox regions suggests that they might have important roles for the functions of Hox genes. (biomedcentral.com)
- During the course of studying DNA sequence divergence of Hox genes among different mammalian orders, we noticed that many ultraconserved regions exist in the protein coding regions outside the homeobox. (biomedcentral.com)
- Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. (lookformedical.com)
- The b380 deletion removes several known genes and expressed sequence tags, including dlx3 and dlx7 , two transcription factors that share a homoeobox domain similar in sequence to the Drosophila Distal-less gene. (silverchair.com)
- One is that the physical order of the genes in a complex is identical to the order in which the genes are expressed along the anteroposterior axis of the embryo during development. (ncse.ngo)
- Thus there is a colinear sequence between the genes on the chromosome and the structures along the anterior-posterior axis of the body that they affect (Graham, Papalopulu and Krumlauf, 1989. (ncse.ngo)
- The fact that body plans as diverse as a fruit fly and a mouse should be determined by an almost identical underlying system of regulatory genes was an entirely unexpected discovery! (ncse.ngo)
- We demonstrate that Lhx2 is the homeodomain transcription factor necessary to drive the expression of OR genes. (eneuro.org)
Proteins14
- Similar amino acid sequences were found in various regions of the proteins. (nih.gov)
- cDNA clones were obtained that encode 3 kinds of DNA binding proteins, each specific for a different novel mouse enhancer sequence were cloned. (nih.gov)
- Homeobox and Pou-domain proteins bind to DNA and regulate gene expression. (nih.gov)
- The amino acid sequence of the Hox-1.11 homeodomain is identical to that of Hox-2.8, which suggests that both homeobox proteins may bind to the same or similar nucleotide sequences in DNA. (nih.gov)
- Fifty seven of the 60 amino acid residues of mNK-1 homeodomain are identical to the amino acid residues of the Drosophila NK-1 homeodomain (95% homology), which suggests that mouse and Drosophila homeodomain proteins bind to similar nucleotide sequences in DNA. (nih.gov)
- One group of homeodomain proteins, called the TALE (for three amino acid loop extension) group, has an additional three amino acids separating the first and second alpha helices, resulting in a 63, instead of the more typical 60, amino acid homeodomain ( Burglin,1997 ). (biologists.com)
- Two TALE subgroups, MEIS and PBC, function as cofactors for the Hox homeodomain proteins ( Mann and Affolter,1998 ). (biologists.com)
- All Hox proteins contain a highly conserved homeodomain encoded by the homeobox motif, but the other regions are generally assumed to be less conserved. (biomedcentral.com)
- These proteins contain a domain called the homeodomain encoded by the homeobox motif. (biomedcentral.com)
- Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. (embl.de)
- Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL). (lookformedical.com)
- The active form can consist of a dimer of two identical proteins or a heterodimer of two related bone morphogenetic proteins. (lookformedical.com)
- Proteins containing a region of conserved sequence, about 200 amino acids long, which encodes a particular sequence specific DNA binding domain (the T-box domain). (lookformedical.com)
- Probe Set ID Ref Seq Protein ID Signal Strength Name Gene Symbol Species Function Swiss-Prot ID Amino Acid Sequence 1367452_at NP_598278 16.52 small ubiquitin-related modifier 2 precursor Sumo2 Rattus norvegicus " Ubiquitin-like protein that can be covalently attached to proteins as a monomer or as a lysine-linked polymer. (nih.gov)
Amino acid sequences1
- Comparison of the amino acid sequences of the mouse and Drosophila NK-1 revealed 95% homology. (nih.gov)
Drosophila1
- mNK-1 is the mouse equivalent of the Drosophila homeobox gene, NK-1, which we discovered previously. (nih.gov)
Protein6
- A nuclear protein was found that binds to a novel trinucleotide repeat sequence in the 5'-upstream region of a rat brain voltage-sensitive calcium channel a1 subunit that activates an enhancerless chloramphenicol acetyltransferase reporter gene. (nih.gov)
- The Hox-1.11 protein, 372 amino acid residues long, contains a conserved pentapeptide, a homeodomain, and an acidic region. (nih.gov)
- Although the consensus binding sequence is not present in the human insulin promoter, the A3 region is sufficiently similar for the protein to bind, at least in vitro, and stimulate reporter assays. (medscape.com)
- The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms a dimer with itself or with zinc fingers and homeoboxes family member 1. (nih.gov)
- C. elegans homeobox protein ceh-14. (embl.de)
- C. elegans homeobox protein unc-97. (embl.de)
Transcription factors1
- This creates the A4 site, [ 29 ] which is juxtaposed to A3 to generate an additional regulatory element that has been reported to bind other homeodomain transcription factors, some of which have been shown to affect transcription. (medscape.com)
Homology2
- Clear, though less well defined, asymmetrical homology of the other A box flanking regions to the human sequences is also apparent. (medscape.com)
- [ 73 ] Surprisingly, both the 5' and 3' flanking regions of each of the A4 TAAT sequences have higher homology to the human A3 region than rat insulin 1 A3, differing by only 1 bp. (medscape.com)
20022
Genomic3
- In collaboration with Y. Kim genomic DNA and cDNA for a novel mouse homeobox gene, mNK-1, were cloned and approximately 5.2 kb was sequenced. (nih.gov)
- Caenorhabditis elegans provides a powerful model to study such metazoan networks because its genome is completely sequenced and many functional genomic tools are available. (biomedcentral.com)
- All of those analyses utilized chromosomal tar get sequences that had been retrieved both by plasmid res cue from a heterogenous population of targeted cells or by PCR based methods making use of a restricted level of genomic DNA isolated from personal targeted clones grown on 96 properly plates. (plasignaling.com)
Nucleotide sequence2
- The nucleotide sequence of the DNA binding site for the NK-2 homeodomain was determined. (nih.gov)
- Epigenetic mechanisms are one of the essential regulators of gene expression which do not involve altering the primary nucleotide sequence. (bvsalud.org)
Complexes1
Encodes1
- This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. (nih.gov)
Eukaryotic1
- A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes. (lookformedical.com)
Domain1
- Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. (nih.gov)
Reference sequence2
Expression2
- Expression and prognostic significance of zinc fingers and homeoboxes family members in renal cell carcinoma. (nih.gov)
- 9 ]). The homeodomain (HD) TF OTX2 specifies the photoreceptor lineage by turning on the expression of cone rod homeobox (CRX) and its downstream TFs. (biomedcentral.com)
Virtually1
- The Dropsphila homeobox gene, NK-2, is expressed initially by virtually all cells in the ventral neurogenic anlage as the neuogenic anlage appears. (nih.gov)
Epigenetic2
- These non vital sequences can be susceptible to epigenetic silencing and in flip attenuate their transposition exercise. (plasignaling.com)
- This observation further implicates the feasible interac tion involving epigenetic silencing elements and the cis sequence of wild sort transposons, and for Tol2 in par ticular. (plasignaling.com)
Copies1
- 2nd, numerous copies of an identical plasmid have been typically obtained during the same tar geted clones, suggesting that most, if not all, inserts during the identical clones have been effectively recovered. (plasignaling.com)
Region1
- Methods The coding region of TBX20 was directly sequenced in 170 ASDII patients. (bmj.com)
Mouse1
Elements1
- The 3-bp flanking sequences have been shown to make an important contribution to the binding affinity of PDX-1 to TAAT core elements with a concomitant effect on activation. (medscape.com)
Completely1
- However, variations in these sequences are insufficient to completely explain differences in PDX-1 binding affinities. (medscape.com)
Important1
- One more important function of our practical piggyBac terminal sequences is that the vast majority of the activator sequences identified previously in D. melanogaster are excluded. (plasignaling.com)
Previously1
- In this respect, the micro PB may possibly poten tially be a safer cis piggyBac component as a mammalian genetic tool as compared towards the minimum piggyBac cis sequence identified previously. (plasignaling.com)
Address1
- In this study, we sought to address these questions using the retinal and disease relevant homeodomain TF CRX as a model. (biomedcentral.com)