Genomic sequences analyses homeodomain sequences. Medical search. Frequent questions

Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.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)
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)
The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS. (lookformedical.com)
Using SVS software for their statistical analysis for genetic association as well as haplotype association, the team used the results of their study to provide evidence of genetic association of widely used SNV's in both genes with PCOS in this Tunisian population, suggesting they are good markers for PCOS in this region of the world. (goldenhelix.com)
SVS was used to filter and prioritize candidate genes in their WES analysis, which was based on the Human Genome annotation, GRCh37/hg19. (goldenhelix.com)
Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines. (zfin.org)
The ms4 locus was fine mapped to a 216 kb region, which contains 23 protein-coding genes including Glyma.02G243200 , an ortholog of Arabidopsis MALE MEIOCYTE DEATH 1 ( MMD1 ), which is a Plant Homeodomain (PHD) protein involved in male fertility. (biomedcentral.com)
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)
Target genes are analysed by bidirectional automated DNA sequencing. (chl.co.nz)
The decision as to which gene or genes are to be analysed is dependent on either the clinical details provided or the specific test request. (chl.co.nz)
NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
Mutational analysis of two positional candidate susceptibility genes for bipolar disorder on chromosome 12q23-q24: phenylalanine hydroxylase and human LIM-homeobox LHX5. (wikigenes.org)
Gene transcription is mainly regulated by transcription factors (TFs) that bind to specific DNA sequences (called motifs) located in the promoter regions of genes [ 1 ]. (biomedcentral.com)
Expression analysis of several Hox genes in human embryos. (cnr.it)
Isolation of the murine homologs of the otd and ems homeobox containing genes and analysis of their expression during brain development. (cnr.it)
Most of these hearing loss genes have been detected using classical genetic methods, typically starting with linkage analysis in large families with hereditary hearing loss. (biomedcentral.com)
Eighty known hearing loss genes were selected and simultaneously sequenced by targeted next-generation sequencing (NGS) in 8 Korean families with autosomal dominant non-syndromic sensorineural hearing loss. (biomedcentral.com)
However, there are 54 candidate chromosomal loci at which causative genes have not yet been identified, although classical genetic studies such as linkage analysis have predicted that these loci contain novel hearing loss-associated genes (Hereditary Hearing loss Homepage, http://hereditaryhearingloss.org ). (biomedcentral.com)
Due to the limitation of the Sanger sequencing method, which is highly expensive and time-consuming, it has been difficult to sequence the hundreds of genes in these candidate chromosomal loci. (biomedcentral.com)
However, there have been no reports of the detection of pathogenic mutations by screening candidate hearing loss genes in small families without using linkage analysis. (biomedcentral.com)
Therefore, based on the hypothesis that causative mutations of hearing loss are more likely to exist in known hearing loss associated-genes than in novel genes, we performed exon capture and resequencing using Illumina library generation and Solexa sequencing methods. (biomedcentral.com)

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)
Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL). (lookformedical.com)
The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.com)
The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc. (embl.de)
Protein interactions of homeodomain proteins. (embl.de)
Homeodomain proteins are conserved DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. (embl.de)
Many homeodomain proteins require additional cofactors to bind with high affinity and specificity to their DNA sites. (embl.de)
The recent structural determinations and biochemical analysis of several multimeric complexes have provided a better understanding of how protein interactions influence the DNA-binding activity of homeodomain proteins. (embl.de)
Homeodomain proteins play key roles in development and gene regulation in eukaryotes. (embl.de)
Chromosome Architecture and Gene Regulation by Chromatin Insulators, Epigenetic Gene Regulation by Polycomb-group Proteins, and Cooperative DNA binding by Sequence-specific Transcription Factors. (jefferson.edu)

With no known attempts to investigate the heritable factors using next generation sequencing (NGS) and whole exome sequencing (WES), a research team from Mexico endeavored to better understand the genetic basis of the defect in a family with a recurrence of gastroschisis. (goldenhelix.com)
performed whole-exome sequencing in a Palestinian family with hereditary hearing loss and identified a novel mutation in the gene, GPSM2 , which had been hidden in the autosomal recessive hearing loss locus (DFNB32) first identified by Masmoudi et al. (biomedcentral.com)

BACKGROUND: Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. (bvsalud.org)
The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. (bvsalud.org)
SHORT CONCLUSION: This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. (bvsalud.org)
Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis. (bvsalud.org)
PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)
Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. (zfin.org)

molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
Australian researchers performed a pilot study to test the value of whole genome sequencing (WGS) intended to aid in embryo selection in high-risk couples engaged in in vitro fertilization (IVF) treatment. (goldenhelix.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)
Reference Genome == '''Nucleotide View''' When zoomed in, the DNA sequence of the Release 6 (R6) [http://flybase.org/reports/FBrf0227719.html (Hoskins et al, 2015)] genome is shown as color-coded blocks, G-orange, A-green, T-red, C-blue. (flybase.org)

Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. (oist.jp)
In addition, we use bioinformatic analysis across twelve Drosophila genomes to identify putative cis-regulatory sequences that may be capable of facilitating specific promoter-enhancer interactions at the bithorax complex and propose a model for their molecular function during development. (nih.gov)

PHD: plant homeodomain fingers or LAP domains. (atlasgeneticsoncology.org)

Gene identity was determined initially based upon BLAST similarity and confirmed by phylogenetic analysis. (europa.eu)
Phylogenetic analyses confirmed the actual positioning of the selected 3D structures and showed these docked structures belonged to their usual classes due to the extremely close distances found in each docked subtype compared with its corresponding non-docked structures. (bvsalud.org)
Phylogenetic analysis showed presence of a homolog protein (MS4_homolog) encoded by the Glyma.14G212300 gene. (biomedcentral.com)

2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences" . (en-academic.com)
We first identified the transcription start site of cNANOG by 5′-rapid amplification of cDNA ends PCR analysis. (biomedcentral.com)

Muenke craniosynostosis, caused by FGFR3 P250R, represents the most common human transversion known whilst Boston-type craniosynostosis, caused by a P148H substitution occurring at position 7 of the highly conserved homeodomain of MSX2, is uncommon. (chl.co.nz)

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)
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)

The full-length p200 isoform contains four DNA binding motifs, three CUT repeats, and a homeodomain. (nature.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)
Repeat region''' Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner [http://{{flybaseorg}}/reports/FBrf0194515.html (Smith, et al. (flybase.org)

Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. (xenbase.org)
Our findings establish Sox17 as a tissue -specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/β-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and β-catenin/Tcf transcriptional complexes. (xenbase.org)
Hypermethylation at CpG websites inside the minimal transcriptional regulatory area was proven in HeLa R1-11 cells as in contrast with the parental PCFT-competent HeLa cells, utilizing bisulfite conversion and sequence evaluation. (inacj.com)

Although a controversial topic, the team intends to take advantage of recent advancements in next generation sequencing to assist with selecting embryos for implantation to prevent early life fatal genetic conditions which adversely affect the quality of life of the afflicted individuals and their families. (goldenhelix.com)
Our understanding of the landscape of pediatric cancer genomics has improved markedly in the past 20 years with the advent of next generation sequencing and other high throughput genetic sequencing. (medscape.com)
Linkage analysis used DNA from mapping panels of single homozygous mutant animals with mixed genetic backgrounds. (zfin.org)
CONCLUSIONS: Despite the presence of sequence variations in their respective genetic backgrounds, within each line the sequence of crx was identical. (zfin.org)
We are analyzing how long-range repression and activation occur over an entire genetic locus, even skipped ( eve ), and its genomic neighborhood, through the regulation of chromatin structure. (jefferson.edu)
However, these classical strategies are not well suited for mutation analysis in smaller families who have insufficient genetic information. (biomedcentral.com)
In a candidate gene study aiming at identifying genetic determinants of breast cancer susceptibility, we undertook the full sequencing of the NBN gene in our cohort of 97 high-risk non- BRCA1 and - BRCA2 breast cancer families, along with 74 healthy unrelated controls, also from the French Canadian population. (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)

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)
Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. (zfin.org)
Therefore, it has been nearly impossible to identify the precise pathogenic mutations in affected individuals from small families who cannot be examined either through linkage analysis or standard capillary sequencing analysis. (biomedcentral.com)

Using a small number of IVF couples and their IVF embryos, the team obtained trophectoderm cell biopsy samples from the embryos and genomic DNA from the blood of the parents to detect inherited pathogenic and high-risk de novo variations in a first of its kind study design. (goldenhelix.com)
METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). (zfin.org)
Isolation and expression analysis both in invertebrate and vertebrate embryos of a new homeobox containing gene named Orthopedia (Otp). (cnr.it)
Isolation and expression analysis in murine embryos of Dlx5 and Dlx6, two murine homologues of the Drosophila Distal-less gene. (cnr.it)

Isolation and sequencing of Glyma.02G243200 from the ms4 mutant line showed a single base insertion in the 3rd exon causing a premature stop codon resulting in truncated protein production. (biomedcentral.com)
This analysis will not detect variants located within intronic regions, except at the intron-exon boundaries. (chl.co.nz)
The KDM5A (JARID1A) sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain. (atlasgeneticsoncology.org)
We've got studied this uncommon exon definition by making a assemble with the genomic fragment encompassing the entire gene from apoA-II and its regulatory areas. (inacj.com)

With the help of VarSeq software for the single nucleotide polymorphism (SNP) and indel analysis, they classified the variants according to ACMG standards and guidelines. (goldenhelix.com)
Multivariate Cox regression analysis showed that persistent AF (OR 1.677, 95% CI 1.176-2.381, p =0.004) and the number of variants (OR 1.552, 95% CI 1.099-2.222, p =0.015) were independent predictors for recurrence of AF. (e-arrhythmia.org)
Further analyses will be needed to fully ascertain the exact impact of those variants on breast cancer susceptibility, in particular for variants located in NBN promoter region. (biomedcentral.com)

Exome sequencing was performed in one affected family member. (molvis.org)

By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, genomic regions containing unusually high concentrations of predicted binding sites were identified for these factors. (sdbonline.org)
Specific genomic DNA segments that interact with the nuclear matrix are called scaffold or matrix attachment regions (SARs or MARs). (bdbiosciences.com)

Orthologous to human PHTF1 (putative homeodomain transcription factor 1). (nih.gov)
Putative homeodomain transcription factor 1 interacts with the feminization factor homolog fem1b in male germ cells. (nih.gov)

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)

Regulation of actin dynamics and analysis of genomic influences on actin function. (upstate.edu)

Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes. (atlasgeneticsoncology.org)

The leucine zipper of NRL interacts with the CRX homeodomain. (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)
Homeodomain interactions. (embl.de)
These include gene expression (by either facilitating or blocking interactions between enhancers and promoters), DNA recombination and repair (by influencing which linearly distant DNA sequences are accessible to each other and which are not), chromatin compaction during mitosis and meiosis, and epigenetic maintenance of gene expression. (jefferson.edu)

We are using state-of-the-art next generation sequencing combined with bioinformatic strategies, and developing stem cell-based approaches for gene therapy and drug discovery. (nih.gov)

Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)

The structures of the Drosophila Paired homodimer and the yeast a1/alpha2 heterodimer bound to DNA, along with a high-resolution study of a Drosophila eve-DNA complex, have deepened our understanding of how homeodomains locate their DNA targets. (embl.de)

To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. (bvsalud.org)

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 gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. (biomedcentral.com)

Past structural studies have focused on the binding of monomeric homeodomains to DNA, but two recent structures have revealed how homeodomains bind DNA as multimers. (embl.de)

Our analysis of NBN sequence variations indicated that potential NBN alterations are present, albeit at a low frequency, in our cohort of high-risk breast cancer cases. (biomedcentral.com)

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)
Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. (bvsalud.org)

Microsatellite genotyping was used for haplotype analysis. (molvis.org)

Next-generation sequencing (NGS) can overcome these limitations through its ability to perform parallel sequencing of billions of nucleotides at a low cost and high speed[ 1 - 4 ]. (biomedcentral.com)

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)
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)

The comparative expression analysis of Ms4 and Ms4_homologs across the soybean developmental and reproductive stages showed significantly higher expression of Ms4 in early flowering (flower bud differentiation) stage than its homolog. (biomedcentral.com)
Here we report the expression and functional analysis of cnd-1 , a C. elegans NeuroD homolog. (biologists.com)

They also used VarSeq in their trio analysis of copy number variations and structural variations. (goldenhelix.com)
Homozygous mok(m632) or nie(m743) mutants and their respective wild-type sibs, showed identical patterns of heterozygosity and sequence variations within each line. (zfin.org)

The transcription of Abd-B is tightly controlled by an array of cis-regulatory modules that direct its expression over extended genomic distances. (nih.gov)
These regulatory modules include promoters, insulators, silencers, enhancers, promoter targeting sequences and the recently identified promoter tethering element (PTE). (nih.gov)
However, the cis-regulatory sequence controlling this posterior expression pattern has not been precisely identified. (sdbonline.org)

Using CIS-ANALYST, the distribution of Bcd, Cad, Hb, Kr, and Kni binding sites were examined in a 1-Mb genomic region surrounding the well-characterized eve locus at a site_p value of 0.0003. (sdbonline.org)
Each of these domains contains a helical region resembling the homeodomain and the Hin recombinase. (embl.de)

We performed DNA methylation analysis for 57 PanNEN samples and found that distinct methylation profiles separated PanNENs into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. (biomedcentral.com)

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)

Chromatin Domains (9-state model, S2 cells)''' Demarcation of chromatin domains of nine major types based on analysis of 18 histone modification profiles. (flybase.org)

Anatomy14

Organisms18

Diseases1

Chemicals and Drugs61

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Phenomena and Processes115

Disciplines and Occupations3

Technology, Industry, Agriculture2

Information Science16

Health Care1

Genes24

Proteins11

Whole exome2

Sanger6

Genome5

Genomes2

Plant Homeodomain1

Phylogenetic3

CDNA2

Highly conserved1

Nucleotide sequences2

Repeats3

Transcriptional3

Genetic7

Chromosome1

Mutations3

Embryos4

Exon4

Variants3

Exome1

Regions2

Putative2

Zinc-finger1

Regulation1

Subsets1

Leucine zipper1

Interactions3

Bioinformatic1

Protein involved1

Targets1

Outcomes1

Gene expression2

Bind1

Alterations1

Nucleic2

Haplotype1

Next generation1

Specific2

Homolog2

Variations2

Regulatory3

Region2

Distinct1

NCBI1

Chromatin1