• In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). (figshare.com)
  • Here, we describe the isolation and characterization of expressed sequence tags (ESTs) isolated from a chicken pineal gland cDNA library. (westminster.ac.uk)
  • 6% of the ESTs matched neither GenBank cDNA sequences nor the newly assembled chicken genomic DNA sequence, three ESTs aligned with sequences designated to be on the Z_random, while one matched a W chromosome sequence and could be useful in cataloguing functionally important genes on this sex chromosome. (westminster.ac.uk)
  • Additionally, single nucleotide polymorphisms (SNPs) were identified and validated in 10 ESTs that showed 98% or higher sequence similarity to known chicken genes. (westminster.ac.uk)
  • Results: We used a cDNA microarray containing 6,000 expressed sequence tags (ESTs) from the whitefly genome to study the parasitoid-whitefly interaction. (huji.ac.il)
  • The transcript profiles of uterine tissue were compared in treated versus control in both maternal and neonatal sites using cDNA microarray to determine the expression levels of approximately 13,000 genes and expressed sequence tags (ESTs). (diethylstilbestrol.co.uk)
  • Functional genomics has its foundation in the large-scale projects for collecting expressed sequence tags (ESTs) and for genome sequencing, begun in the 1980s. (biomedcentral.com)
  • This track shows alignments between mouse expressed sequence tags (ESTs) in GenBank and the genome. (ucsc.edu)
  • ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. (ucsc.edu)
  • For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. (ucsc.edu)
  • For most - but not all - ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. (ucsc.edu)
  • In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. (ucsc.edu)
  • Northern blot analysis revealed that hOAT3 mRNA is expressed in the kidney, brain, and skeletal muscle. (aspetjournals.org)
  • On one hand, codon redundancy (i.e. that 61 codons specify 20 amino acids [ 21 ]) potentially allows a wide variety of mRNA sequences carrying different codons to specify the same protein product. (biomedcentral.com)
  • To define the molecular basis of the IL-6-induced mitogenic response in myeloma cells, we applied STAR (subtractive transcriptional amplification of mRNA), a new differential expression analysis technology, to isolate mRNAs preferentially expressed in IL-6-treated versus untreated cultures of the factor-responsive myeloma cell line U266. (elsevierpure.com)
  • These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. (ucsc.edu)
  • In the present study, we report the characterization of the full coding sequence of rainbow trout PGMRC1 and mPR beta cDNAs, their tissue distribution, their ovarian expression profiles during oogenesis, their hormonal regulation in the full grown ovary and the in situ localization of PGMRC1 mRNA in the ovary. (biomedcentral.com)
  • While all three fields might use forms of mass spectrometry and chromatography to identify and study the functions of DNA, RNA, and proteins, proteomics relies on the assumption that current gene models are correct and that all relevant protein sequences can be found in a reference database such as the Proteomics Identifications Database. (wikipedia.org)
  • In addition, the emergence of novel protein sequences due to mutations often cannot be accounted for in traditional proteomic databases, but can be predicted and studied using a synthesis of genomic and transcriptomic data. (wikipedia.org)
  • The main idea behind the proteogenomic approach is to identify peptides by comparing MS/MS data to protein databases that contain predicted protein sequences. (wikipedia.org)
  • Below are some of the ways in which protein databases are generated: Six-frame translations can be utilized to generate a database that predicts protein sequences. (wikipedia.org)
  • We report evidence from cDNA isolation and expression analysis as well as analyses of genome, expressed sequence tag (EST), cDNA and expression databases for a new gene named SPRN (shadow of prion protein). (nih.gov)
  • A ) Pools of homology repair template plasmids containing different protein tags were co-injected with a plasmid encoding an sgRNA targeting the N-terminus of the target coding sequence into embryos expressing transgenic Cas9. (elifesciences.org)
  • PCR genotyping and DNA sequencing were used to find chromosomes containing tag insertions and to determine the identity of the inserted protein. (elifesciences.org)
  • The observed shifts in band size correspond to the size of fluorescently tagged Bcd or Zld protein. (elifesciences.org)
  • High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. (genscript.com)
  • These sequences represent the protein coding region of the PFDN6 cDNA ORF which is encoded by the open reading frame (ORF) sequence. (genscript.com)
  • Protein-coding genes are shown in blue with the different shades further indicating direction of transcription. (flybase.org)
  • The protein was then subjected to molecular characterization using bioinformatic methods, and the tissue expression pattern was further assayed by semi-quantitative reverse-transcription polymerase chain reaction. (geneticsmr.com)
  • These motifs contain 2 hydrophobic alpha-helical segments connected by an extensive hydrophilic sequence, resulting in 6 transmembrane portions of the protein. (medscape.com)
  • The transporter was identified by probing a mammalian-expressed sequence tag database with 2 fungal mitochondrial ornithine carrier protein sequences. (medscape.com)
  • Northern blot analysis documented that two transcription factor genes chosen for further study, c-myc promoter-binding protein (MBP-1) and X-box binding protein 1 (XBP-1), were up-regulated in U266 cells about 3-fold relative to the cell cycle-dependent β-actin gene 12 h after IL-6 treatment. (elsevierpure.com)
  • Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division. (karger.com)
  • Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)
  • 3] The latter technique has become more widely used over the last decade in large part due to the increasing affordability and speed of genomic sequencing techniques coupled with the increasing sensitivity of mass spectrometry-based proteomics. (wikipedia.org)
  • Here, we have described resources that may be useful in comparative and functional genomic analysis of genes expressed in an important organ, the pineal gland, in a model and agriculturally important organism. (westminster.ac.uk)
  • 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)
  • The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. (ucsc.edu)
  • This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. (ucsc.edu)
  • The system is capable of expressed sequence tag (EST) sequencing, the identification of small RNAs and transcription binding sites as well as whole genome sequencing and metagenomics. (outsourcing-pharma.com)
  • One of the things that is really important for high throughput DNA sequencing is for people to see that researchers can look at the whole genome of bacteria and viruses. (outsourcing-pharma.com)
  • As we recently reported, analysis of 77 FHWT by whole genome sequencing (WGS, 58 patients) or whole exomic sequencing (WES,19 patients) identified 825 high-quality somatic, non-synonymous variants, with an average of 11 candidate mutations/case (range 2-42) (ref. 6 ). (nature.com)
  • We will be looking at working towards the $100,000 genome sequence landmark in 2007. (outsourcing-pharma.com)
  • 2005) The genome sequence of the rice blast fungus Magnaporthe grisea. (prelekara.sk)
  • Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • Almost 2,000 expressed sequence tag (EST) cDNA clones were sequenced to analyze gene expression in control and Cd-treated leaf trichomes. (uni-bayreuth.de)
  • In this study, a suppression subtractive hybridization cDNA library approach was used for the identification of pathogen and plant genes that were differentially expressed during infection of the susceptible cultivar BRS Pérola of Phaseolus vulgaris L. A total of 979 unigenes (430 contigs and 549 singletons) were obtained and classified according to their functional categories. (frontiersin.org)
  • Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
  • These analyses have also helped identify genes that were differentially expressed in DED fungi grown under defined experimental conditions. (sisef.it)
  • These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. (figshare.com)
  • The following PFDN6 gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). (genscript.com)
  • The deduced amino acid sequence of hOAT3 showed 36 to 51% identity to those of other members of the OAT family. (aspetjournals.org)
  • The fish and mammalian sequences are also well conserved, particularly for zebrafish, to beyond the end of the hydrophobic sequence (identity 41-53%, 78 amino acids, zebrafish length). (nih.gov)
  • A fourteen-amino-acid biotinylation sequence was inserted immediately after the N-terminal, His-tagged end of the construct in order to enable the attachment of a biotin moiety in vivo. (bvsalud.org)
  • A database search showed that HAZ1 was most similar in its entire amino acid sequence to Zmhox1a (52% identity) and Zmhox1b (50%), PHD-finger family homeodomain proteins of maize. (elsevierpure.com)
  • The GnRH1 gene and amino acid sequences were subjected to bioinformatic analyses. (geneticsmr.com)
  • Proteomics deals with proteins in the same way that Genomics studies the genetic code of entire organisms, while Transcriptomics deals with the study of RNA sequencing and transcripts. (wikipedia.org)
  • Alternatively, it can also attract proteins that block gene transcription. (prohealth.com)
  • Reverse transcription-PCR (RT-PCR) analysis demonstrated that antipathogenic T-phylloplanin-like proteins, glutathione peroxidase and several classes of pathogenesis-related (PR) proteins were expressed specifically or dominantly in trichomes. (uni-bayreuth.de)
  • The number of transcription associated proteins (TAPs) encoded by the Pf genome is about one third the number of TAPs associated with the transcriptional process in free-living eukaryotes [ 10 ]. (biomedcentral.com)
  • Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)
  • Epigenetic modifications of the histone proteins, such as acetylation or methylation, affect how tightly the DNA is packed around the histones and thus how accessible the DNA sequence is. (lu.se)
  • Examining gene expression in the process of Dugesia regeneration more closely, the lab found Wnt is expressed in two phases, at days 1 and 3, with the Islet homolog required only for the second. (riken.jp)
  • Alterations in expression include metabolic genes (CYP11B1, MGMT), cell cycle control and DNA repair genes (GADD45, Cyclin G2, Cyclin D3, Cyclin A) and transcription factors (IF2, IF3). (cdc.gov)
  • Epigenetics, the study of changes in gene expression not caused by alterations in the DNA sequence, has revolutionized our understanding of genetics and its impact on health and longevity. (prohealth.com)
  • It does this by physically impeding the binding of transcription factors and other machinery necessary for gene expression. (prohealth.com)
  • This results in a more open or "relaxed" chromatin structure, enabling greater access for the transcription machinery, thereby promoting gene expression. (prohealth.com)
  • ORF sequences can be delivered in our standard vector, pcDNA3.1 + /C-(K)DYK or the vector of your choice as an expression/transfection-ready ORF clone. (genscript.com)
  • These were correlated with gene expression, which was measured by RNA-tag profiling. (flybase.org)
  • The expression levels of some known estrogen-responsive genes, i.e., complement component 3, epidermal growth factor receptor or c-fos oncogene and calbindin 3, as well as some other randomly selected genes, including general transcription factor IIa, transcription factor 4 and lymphocyte specific 1, were increased by OP and/or DES treatment in the uteri of both maternal and neonate groups. (diethylstilbestrol.co.uk)
  • Expression profiling is the direct offspring of these sequencing projects. (biomedcentral.com)
  • With genome or EST sequences in hand, microarrays or macroarrays can be constructed to analyze gene-expression profiles at the genome-wide level over a range of conditions. (biomedcentral.com)
  • TFBMs act as binding sites for transcription factors and coordinate the expression of the genes in whose promoter regions they appear. (biomedcentral.com)
  • Today we use epigenetics to mean changes to gene expression that are not caused by changes in the actual DNA sequence. (lu.se)
  • Gene expression is the process of several steps through which the information in a gene's DNA sequence is transferred to the structures and functions of a cell. (lu.se)
  • Transcription factors bind alongside the promoter and set off the gene expression. (lu.se)
  • From the resulting collection of STAR clones, sequence information was obtained for a total of 72 distinct transcripts. (elsevierpure.com)
  • 16 , 17 In particular, transgenic zebrafish lines that express nfsB in β cells, cardiomyocytes, or other cell types have been established, and their exposure to the metronidazole leads to the targeted loss of these cells. (cdc.gov)
  • To avoid potential problems associated with endogenous tagging of a multicopy locus, histone fusions were supplied as exogenous transgenes. (elifesciences.org)
  • Non-natural oligonucleotides are valuable probes of biological systems, as they can convey synthetic control of endogenous nucleic acids with high sequence specificity. (cdc.gov)
  • Proteogenomics emerged as an independent field in 2004, based on the integration of technological advancements in next-generation sequencing genomics, and mass spectrometry proteomics. (wikipedia.org)
  • Desiccation tolerance of peanut seeds was achieved during 45 to 65 DAP (days after pegging) embryogenesis, while a set of low molecular weight (9 to 15.5 kD) heat-stable polypeptides was preferentially expressed. (jipb.net)
  • They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. (figshare.com)
  • A new study by Tetsutaro Hayashi and others in the Genome Resource and Analysis Unit (Fumio Matsuzaki, Unit Leader) now reveals an additional factor, encoded by a planarian LIM- homeobox gene known as Djislet , is required for the posterior differentiation of Wnt-expressing cells. (riken.jp)
  • Systematic Analysis of ZnCys Transcription Factors. (prelekara.sk)
  • Systematic Analysis of ZnCys Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus. (prelekara.sk)
  • We show here that PML knockdown (KD) in MDA-MB-231, but not MCF7, breast cancer cells, prolonged stem-cell-like survival, and increased cell proliferation and migration, which is in line with gene-enrichment results from their RNA sequencing analysis. (bvsalud.org)
  • By using expressed-sequence-tag analysis of NPV (BmNPV)-infected BmN cells, Okano et al. (kentlandsinitiative.org)
  • The aim of this study was to sequence Acinetobacter baumannii phage AB3 and conduct bioinformatic analysis to lay a foundation for genome remodeling and phage therapy. (geneticsmr.com)
  • For example, our group has examined the genes regulated by the Zap1p transcription factor in S. cerevisiae using DNA microarrays and promoter motif analysis [ 1 ] (Figure 1 ). (biomedcentral.com)
  • Co-dominant simple sequence repeat (SSRs) are popular DNA markers, widely applied in oil palm genetic studies, especially in genetic mapping, marker-trait association, diversity analysis and detecting illegitimacy. (mpob.gov.my)
  • Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers [J]. J Integr Plant Biol. (jipb.net)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Gusev et al [ 22 ] report the results of a systems biology based analysis of aberrantly expressed miRNAs in five human cancers. (biomedcentral.com)
  • When expressed in Xenopus laevis oocytes, hOAT3 mediated the transport of estrone sulfate ( K m = 3.1 μM), p -aminohippurate ( K m = 87.2 μM), methotrexate ( K m = 10.9 μM), and cimetidine ( K m = 57.4 μM) in a sodium-independent manner. (aspetjournals.org)
  • Xenopus laevis oocytes expressing hOAT1 supported probenecid-sensitive uptake of [ 3 H] p -aminohippurate ( K m = 4 μM), which was trans -stimulated in oocytes preloaded with glutarate. (aspetjournals.org)
  • The recent cloning and sequencing of a gene coding for a membranous progesterone receptor [ 5 ] in African clawed frog ( Xenopus laevis ) brought evidence for the existence of both intracellular and membrane progestin receptors [ 6 ]. (biomedcentral.com)
  • Expressed Sequence Tags" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (ouhsc.edu)
  • We characterize the activation kinetics of these reagents in vitro and demonstrate their efficacy in zebrafish embryos that express NfsB either ubiquitously or in defined cell populations. (cdc.gov)
  • In vertebrates, the Islet family of LIM-homeobox transcription factors is known to be involved in the proliferation, maintenance and migration of stem and progenitor cells in a range of tissues. (riken.jp)
  • Epi-", a Greek term meaning "above" or "on top of," in the term epigenetics , refers to modifications that do not change the DNA sequence itself but can turn genes on or off, affecting how transcription factors read genes. (prohealth.com)
  • These modifications (methyl and acetyl tags) can be influenced by a variety of factors, including lifestyle and environmental factors. (prohealth.com)
  • Homeobox genes that encode transcription factors play important roles in development and differentiation of both plant and animal systems. (elsevierpure.com)
  • Chromatin remodeling complexes and histone acetylases and deacetylases, which modulate the accessibility of DNA to transcription factors, are also present. (biomedcentral.com)
  • This chemical process can be affected by different environmental factors, such as diet, exercise, stress etcetera, that make the gene behave in different ways, and that let the gene be expressed to a greater or lesser degree. (lu.se)
  • Certain transcription factors do not bind when the DNA is methylated while others only bind when the DNA is methylated. (lu.se)
  • and they are associated with altered histone acetylation and transcription factor (nerve growth factor-induced clone A [NGFIA]) binding to the glucocorticoid receptor promoter. (deepdyve.com)
  • Biotin labeled cRNA transcript was synthesized using cDNA, fragmented and hybridized to HuGeneFL GeneChip probe arrays representing more than 6800 human genes and expressed sequence tags. (cdc.gov)
  • RNA''' Like the Gene:transcript view track, this track shows the complete intron/exon structure (exons indicated by wider bars, introns by black lines) of each annotated transcript with direction of transcription indicated by a small arrow at the downstream edge. (flybase.org)
  • We developed a high-throughput gene knockout system, and using this system, we obtained null mutants of 104 fungal-specific Zn2Cys6 transcription factor (TF) genes by screening 8741 primary transformants in M. oryzae. (prelekara.sk)
  • Methylation generally serves to suppress gene transcription, meaning that genes with methyl tags are less likely to be expressed. (prohealth.com)
  • They are about 6-8 nucleotides (nt) in length and occur upstream of the gene transcription start site (TSS). (biomedcentral.com)
  • These fragments are then ligated by two short adaptors, which provide primers for both amplification and sequencing of the fragment as well as a biotin tag that immobilises it onto a streptavidin-coated bead. (outsourcing-pharma.com)
  • If you sequence more than one nucleotide at once you get a stronger signal and we see a very linear response between the signal strength and the number of nucleotides added. (outsourcing-pharma.com)
  • 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)
  • Some of the newer cap-selected libraries cover transcription start reasonably well. (ucsc.edu)
  • Conservation of order and transcription orientation of two proximal genes between fishes and mammals strongly indicates gene orthology. (nih.gov)
  • Gene span''' Shows the extent of all annotated gene models with direction of transcription indicated by a small arrow at the downstream edge. (flybase.org)
  • It bears no relationship to the direction of transcription of the RNA with which it might be associated. (ucsc.edu)
  • In situ hybridization showed that HAZ1 was expressed at a higher level in the outer layers of a developing embryo than in the inner parts of the embryo at 3 DAP. (elsevierpure.com)
  • A subset of cell wall modification and stress related genes was further assessed by quantitative reverse transcription PCR at late stages of mycorrhizal development coinciding with Hartig net formation. (biomedcentral.com)
  • Zap1p activates the transcription of its target genes in zinc-limited but not in zinc-replete yeast cells. (biomedcentral.com)
  • All of these isoforms are commonly expressed in the kidney, and their potential roles in renal handling of organic anions have been indicated. (aspetjournals.org)
  • epithelial cells of the small intestine and kidney also express these enzymes to a lesser extent, but their contribution to urea production is not significant. (medscape.com)
  • Expressed at lower levels in lymphoid organs, kidney, colon and liver. (abcam.com)
  • Each mutation was verified by Sanger sequencing of PCR products spanning the variants ( Fig. 1 ). (nature.com)
  • 2 − 6 These nuclease-resistant polymers persist in live organisms for days and are typically designed to recognize 25-base sequences that span intron-exon junctions or translational start sites. (cdc.gov)
  • For example, we have applied light-activatable cMOs to interrogate transcription factor function during zebrafish notochord, pancreas, and vascular patterning. (cdc.gov)
  • While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. (biomedcentral.com)
  • The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf . (biomedcentral.com)
  • The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf . (biomedcentral.com)
  • Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
  • The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. (biomedcentral.com)
  • Dr. Hood is the recipient of numerous national and international awards, including the Lasker Award for Studies of Immune Diversity (1987), the Kyoto Prize in advanced technology (2002), the Heinz Award for pioneering work in Systems Biology (2006), the National Academy of Engineering Fritz J. and Delores H. Russ Prize for developing automated DNA sequencing (2011), and the National Academy of Science Award for Chemistry in Service to Society (2017). (isbscience.org)