• 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 describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. (umsystem.edu)
  • cDNAs averaged 500-600 bp in length and were treated as expressed sequence tags (ESTs). (mpg.de)
  • Clustering analysis of 805 random cDNAs resulted in 179 and 155 different ESTs for the oxic and anoxic zones respectively. (mpg.de)
  • Taxonomic assignment was more powerful in discriminating between the aerobic and anaerobic bacterial communities than functional inference, as most ESTs in both oxygen zones were putative indicators of similar housekeeping functions, in particular ABC-type transporters. (mpg.de)
  • For genetic characterization of rapid cell elongation in cotton fibers, ∼ 14,000 unique genes were assembled from 46,603 expressed sequence tags (ESTs) from developmentally staged fiber cDNAs of a cultivated diploid species (Gossypium arboreum L.). Conservatively, the fiber transcriptome represents 35-40% of the genes in the cotton genome. (edu.sa)
  • National Centre for Biotechnology Information (NCBI): cDNA libraries and Expressed Sequence Tags (ESTs), EST analysis, Pairwise alignment techniques, Multiple sequence alignment. (cutm.ac.in)
  • The Atlantic Cod Genomics and Broodstock Development Project (www.codgene.ca) aims to generate an extensive set of molecular tools for cod, including a database containing approximately 160,000 expressed sequence tags (ESTs). (canada.ca)
  • To date approximately 25,000 ESTs have been generated from normalized cDNA libraries representing various tissues (e.g. gonad, liver, heart, gill, brain), and suppression subtractive hybridization (SSH) libraries are being created for the purpose of identifying cod genes responsive to immunogens or environmental stress. (canada.ca)
  • We identified 719 unique ESTs from a total of 1412 sequences so generated. (biomedcentral.com)
  • We identified 236 ESTs which are potentially important for molecular regulation of a functional symbiotic association in conifer host. (biomedcentral.com)
  • Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
  • The short cDNA sequence Fragments when making this method are called expressed sequence tags , or ESTs. (multi-mania.be)
  • The leaves were harvested at various times after cold stress for total RNA extraction, which was used to generate expressed sequence tags (ESTs). (geneticsmr.com)
  • After randomly choosing, cloning and sequencing, 227 ESTs with high quality were obtained and submitted to GenBank database. (geneticsmr.com)
  • Using BLASTX, 79.7% of the ESTs shared homology with known functional DNA sequences and 20.3% shared significant homology with unknown proteins. (geneticsmr.com)
  • As described in Materials and Methods, we constructed a cDNA library from fat body tissues of E. coli - challenged A. mylitta larvae and randomly sequenced a large number of inserts from the library. (biomedcentral.com)
  • Through cloning of functional p53-binding sites (p53-tagged sites) from the human genome, we isolated a novel gene inducible by wild-type p53. (aacrjournals.org)
  • First, Tim Graubert and colleagues describe the whole-genome sequencing of an MDS-derived secondary AML tumor and a matched normal (skin) sample. (massgenomics.org)
  • Genome and exome sequencing were performed for five unrelated cases of IRD with no identified variant. (nature.com)
  • 3 When no pathogenic variant is identified, exome sequencing or genome sequencing may help uncover the variants missed by panel-based screening. (nature.com)
  • As the common IRD variants have largely been identified, exome sequencing or genome sequencing identify rare variants that require functional validation. (nature.com)
  • Using exome sequencing and genome sequencing, we document four novel DYNC2H1 pathogenic variants, and one variant previously reported in five unrelated cases of nonsyndromic progressive IRD. (nature.com)
  • 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)
  • 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)
  • In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)
  • Venter believed therein shotgun sequencing was the fastest and must effective way to get useful human genome data. (multi-mania.be)
  • [26] The goal of the company was to sequence the entire human genome and release it into tje public domain for non-commercial use in much less time and for much less cost dan the public human genome project. (multi-mania.be)
  • The goal consequently put pressure on the public genome program and spurred verschillende groups to redouble hun policymaking to produce the full sequence. (multi-mania.be)
  • Here, we isolated the full-length cDNA (1161 bp) of a novel Chalcone Isomerase from safflower encoding 217 amino acid polypeptide using oligos from 5′ and 3′ ends. (springeropen.com)
  • We constructed a full-length cDNA library of peanut ( Arachis hypogaea ) seed via a large number of sequences of expressed sequence tag (EST) and gene functional annotation, a lysophosphatidic acid acyltransferase gene, designated AhLPAT, and its genomic DNA sequence were isolated from peanut. (chinacrops.org)
  • Two microbial cDNA libraries were constructed from composite samples using semi-randomly primed RT-PCR. (mpg.de)
  • The high-complexity cDNA libraries are being built from tissues collected in New Brunswick and Newfoundland, and individuals from the same populations have also been used to generate families for selective breeding. (canada.ca)
  • The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. (nih.gov)
  • In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. (nih.gov)
  • In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. (peerj.com)
  • The probes for the microarrays were obtained from endodormant and paradormant raspberry bud cDNA libraries. (dundee.ac.uk)
  • The expression profiles of 5300 clones from these libraries were subjected to principal component analysis to determine the most significant expression patterns. (dundee.ac.uk)
  • 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)
  • Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. (peerj.com)
  • Phylogenetic analysis. (cutm.ac.in)
  • The result of Sanger sequencing and phylogenetic analysis revealed that CtCHI is highly homologous to other plants, including typical polyadenylation signals AATAA and Poly A tail. (springeropen.com)
  • Phylogenetic analysis classified the TaSPL genes into five groups (G1-G5). (jipb.net)
  • Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. (jipb.net)
  • A cod gene microarray will also be developed for use in functional genomic studies. (canada.ca)
  • These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
  • cDNA microarray data (7). (lu.se)
  • An analysis of 555 randomly chosen clones in the library showed that 80 were derived from abundant mRNAs and were accounted for by 29 distinct sequences. (diabetesjournals.org)
  • Genes known to be highly expressed in β-cells were represented at a high frequency, namely insulin (15 of 80 clones), islet amyloid polypeptide (8 of 80 clones), proinsulin convertase 1 (6 of 80 clones), and neuropeptide Y (2 of 80 clones). (diabetesjournals.org)
  • According to the principle component analysis, UPASI clones were segregated into five distinct groups. (upasitearesearch.org)
  • Sequence analysis of these clones, in many cases, enabled their functional categorization and the development of hypotheses concerning the mechanisms of bud dormancy release. (dundee.ac.uk)
  • 2014). Where annotations were not present or were different, the online Softberry server (http://linux1.softberry.com/berry.phtml) was used to predict mRNA and protein sequences using the FGNESH+ prediction algorithm (Solovyev et al. (molquest.com)
  • An expressed sequence tag (EST) library was constructed from mRNA obtained from fat bodies of A. mylitta larvae that had been challenged by infection with Escherichia coli cells. (biomedcentral.com)
  • Northern blot analysis revealed that hOAT3 mRNA is expressed in the kidney, brain, and skeletal muscle. (aspetjournals.org)
  • Studies conducted on PRPF31 mRNA levels in lymphoblast cell lines isolated from family members with either deletion or splice site mutations indicate that penetrance requires the co-inheritance of a low expressing wild-type (WT) allele alongside the mutant allele [ 13 , 14 ], whereas the presence of a high expressing WT allele is protective. (molvis.org)
  • Genetic and molecular analyses have led to the identification, cloning and characterization of a few genes that contribute to parasitic fitness in the pathogens. (sisef.it)
  • Zhang B, Liu X, Zhao G, Mao X, Li A, Jing R (2014) Molecular characterization and expression analysis of Triticum aestivum squamosa‐promoter binding protein‐box genes involved in ear development. (jipb.net)
  • Initial characterization of SARS-CoV-2 spike indicates that it binds the same receptor as SARS-CoV angiotensin-converting enzyme, which is expressed in both upper and lower human respiratory tracts ( 8 ). (cdc.gov)
  • abstract = "Background: Expressed Sequence Tag (EST) sequences are generally single-strand, single-pass sequences, only 200-600 nucleotides long, contain errors resulting in frame shifts, and represent different parts of their parent cDNA. (umn.edu)
  • Conclusion The methods described have application for functional genomics studies, particularly among non-model organisms. (umsystem.edu)
  • These and many other functional genomics studies rely on full genomic sequence to establish well-annotated databases. (biomedcentral.com)
  • If the cDNAs contain translation initiation sites, they may be suitable for functional genomics studies. (umn.edu)
  • Its cDNA sequence contained an open reading frame encoding a 431-amino acid peptide that showed a significant homology with members of the P2X family. (aacrjournals.org)
  • Homology analysis showed the highest similarity to M2 muscarinic acetylcholine receptors and overall low homology to all other biogenic amine receptors. (aspetjournals.org)
  • Moreover, the in vitro enzymatic activity and HPLC analysis of transgenic Arabidopsis confirmed the de novo biosynthesis of Rutin. (springeropen.com)
  • Three independent Arabidopsis HAP subunit 2 (AtHAP2) cDNAs were cloned by functional complementation of a yeast hap2 mutant and two independent forms each of AtHAP3 and AtHAP5 cDNAs were detected in the expressed sequence tag database. (camregbase.org)
  • Additional homologs (two of AtHAP3 and one of AtHAP5) have been identified from available Arabidopsis genomic sequences. (camregbase.org)
  • Functional analyses of an E3 ligase gene AIP2 from wheat in Arabidopsis revealed its roles in seed germination and pre-harvest sprouting [J]. J Integr Plant Biol. (jipb.net)
  • Bioinformatic analysis showed that AhLPAT was composed of eleven exons and ten introns with typical GT-AG characteristic in comparison of its sequences of genomic DNA and cDNA by Splign in NCBI. (chinacrops.org)
  • Northern-blot analysis indicated ubiquitous expression for each AtHAP2 and AtHAP5 cDNA in a range of tissues whereas expression of each AtHAP3 cDNA was under developmental and/or environmental regulation. (camregbase.org)
  • Expressed sequence tags assigned to Alpha- and Betaproteobacteria were predominantly found in the oxic zone, while those affiliated with Deltaproteobacteria were more frequently detected in the anoxic zone. (mpg.de)
  • Northern blot analysis showed that it was expressed predominantly in skeletal muscle. (aacrjournals.org)
  • When combined with functional or immunological screening procedures, the approach will be useful for the isolation of β-cell-specific molecules for immunological and genetic investigations of β-cell function and pathology. (diabetesjournals.org)
  • In this article, we describe isolation of SARS-CoV-2 from a patient who had coronavirus disease (COVID-19) in the United States and described its genomic sequence and replication characteristics. (cdc.gov)
  • RNA Isolation and cDNA Microarrays. (lu.se)
  • SWISS PROT and Protein Data Bank (PDB): Protein features and motifs, annotation and curation, protein structure analysis. (cutm.ac.in)
  • Sequence Alignment: MSA using conserved domain and local sequence similarity information, COBALT, Protein sequence alignment, Nucleotide sequence alignment. (cutm.ac.in)
  • A chicken gene that produces a protein important for viral disease resistance was obtained and its DNA sequence was determined. (usda.gov)
  • The transient expression in tobacco mesophyll cells using Green Fluorescent Protein tagging determined the subcellular localization of CtCHI in cell membrane and nucleus. (springeropen.com)
  • The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)
  • The hOAT3 protein was shown to be localized in the basolateral membrane of renal proximal tubules and the hOAT3 gene was determined to be located on the human chromosome 11q12-q13.3 by fluorescent in situ hybridization analysis. (aspetjournals.org)
  • Missense mutations in PRPF31 have previously been shown to cause reduced protein solubility, suggesting insufficiency of functional protein as the disease mechanism. (molvis.org)
  • Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
  • 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)
  • In silico expression analysis revealed that rapidly elongating fiber cells exhibit significant metabolic activity, with the bulk of gene transcripts, represented by three major functional groups - cell wall structure and biogenesis, the cytoskeleton and energy/carbohydrate metabolism. (edu.sa)
  • To obtain the hands-on-training in in silico basics related to functional genomics. (cutm.ac.in)
  • Similarities between the physical structures of avian and mammalian MHC class I glycoproteins have been proposed by comparative alignment of their amino acid sequences. (usda.gov)
  • Of these, 17 were identical or homologous to known mammalian cDNAs or expressed sequence tags. (diabetesjournals.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)
  • This result together with some common structural features led to the suggestive hypothesis of a possible functional link between mammalian PrP and Sho proteins. (nih.gov)
  • To investigate the physical structure of the chicken class I glycoprotein we have cloned the cDNA representing the BFIV locus of the B21 haplotype. (usda.gov)
  • Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (umsystem.edu)
  • Although we detected no genetic alteration in the coding sequences, one of four rhabdomyosarcoma cell lines examined had completely lost expression of this gene. (aacrjournals.org)
  • The Hartig net is the site of metabolite exchange between fungal and root cells[ 1 ] The ontogenesis of a functional ECM symbiosis requires finely regulated cross talk in time and space between plant and fungal genetic programs involved in sensing the environment, and in cell-to-cell communication. (biomedcentral.com)
  • Mendelian genetic analysis of the pathogens is therefore easy and the heritability of any scorable phenotypic or genotypic trait can be assessed rapidly. (sisef.it)
  • Molecular and omic approaches, however, represent technological advances that should allow rapid developments in the genetic analysis of elms and bark beetle vectors of the disease. (sisef.it)
  • Genetic analysis of biomass and photosynthetic parameters in wheat grown in different light intensities [J]. J Integr Plant Biol. (jipb.net)
  • To analyze the regulatory mechanism involved in the high growth potential of C. virgata , we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. (frontiersin.org)
  • In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. (geneticsmr.com)
  • The present study has identified a number of potentially important molecular events responsible for the initiation and regulation of biochemical, physiological and morphological changes during development of a fully functional symbiosis that are relevant for gymnosperm hosts. (biomedcentral.com)
  • These sequences will be subjected to further researches on hardiness genes and their molecular mechanisms. (geneticsmr.com)
  • Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. (umsystem.edu)
  • Cloning and Expression Analysis of Lysophosphatidic Acid Acyltransferase (LPAT) Encoding Gene in Peanut[J]. Acta Agron Sin, 2012, 38(02): 245-255. (chinacrops.org)
  • A polymerase chain reaction-based subtractive hybridization procedure was applied to cDNAs prepared from mouse insulinoma (βTC3) and glucagonoma (αTC2) cell lines to construct a library of cDNAs that are highly expressed in pancreatic β-cells. (diabetesjournals.org)
  • are highly expressed in the human brain and show a strikingly similar regional distribution. (biorxiv.org)
  • In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. (nih.gov)
  • In summary, the soil metatranscriptome is accessible for global analysis and such studies have great potential in elucidating the taxonomic and functional status of soil bacterial communities, but study significance depends on the number and length of cDNAs being randomly analysed. (mpg.de)
  • An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (umsystem.edu)
  • A cDNA encoding a multispecific organic anion transporter 3 (hOAT3) was isolated from a human kidney cDNA library. (aspetjournals.org)
  • A cDNA library of Chinese wild Vitis amurensis , which is the most cold-resistant species in the genus Vitis , was constructed using young leaves of seedlings of the clone Heilongjiang potted and subjected to cold stress. (geneticsmr.com)
  • Some functional genes identified from the cDNA library have potential for plant defense. (geneticsmr.com)
  • This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (umsystem.edu)
  • The phylum-level affiliations of 93 16S rRNA sequences corresponded well with two taxonomically distinct EST patterns. (mpg.de)
  • These expression patterns suggest that each synuclein may partake in a distinct function, as suggested by some studies, although functional redundancy has been proposed as well. (biorxiv.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)
  • DNA Data Bank of Japan (DDBJ): Sequence Alignment Methods, Predictive Methods Using DNA Sequences. (cutm.ac.in)
  • Alignment of the BFIV21 sequence with previously published BFIV sequences revealed polymorphisms at position 34 (HLA34), a monomorphic residue in HLA and H-2. (usda.gov)
  • A: An alignment of amino acid sequences of rat preproapelin with human and bovine preproapelin. (phoenixpeptide.com)
  • B: An alignment of amino acid sequences of human apelin and angiotensin II. (phoenixpeptide.com)
  • Three methods are being used to generate markers within specific genes: 1) identification of gene-linked microsatellites, 2) development of exon-primed intron-flanking (EPIC) markers, and 3) analysis of single nucleotide polymorphisms (SNPs) within EST clusters. (canada.ca)
  • 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)
  • Functional analysis employing site directed mutagenesis identified BF amino acid residues forming serologic epitopes as well as residues important in antigen presentation to ALV induced cytotoxic T lymphocytes. (usda.gov)
  • Tools like the TIGR Gene index [ 35 ] and Unigene [ 36 ] provide significant information on many species, yet these databases do not meet the needs of functional genomics projects for many non-model species. (biomedcentral.com)
  • Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
  • The authors undertook systematic sequencing of U2AF1 exons in 150 MDS cases, and found that 8.7% had mutations at Ser34. (massgenomics.org)
  • In yeast a single complex of three proteins termed HAP2 HAP3 and HAP5 binds to this sequence and in mammals the three components of the equivalent complex (called variously NF-Y CBF or CP1) are also represented by single genes. (camregbase.org)
  • Subsequent analysis revealed a pharmacological profile practically indistinguishable from that for the histamine H 3 receptor. (aspetjournals.org)
  • The availability of the human H 3 receptor cDNA should greatly aid in the development of chemical and biological reagents, allowing a greater appreciation of the role of histamine in brain function. (aspetjournals.org)
  • Ornithine incorporation was restored in fibroblasts derived from patients with hyperornithinemia-hyperammonemia-homocitrullinuria syndrome by transforming the fibroblasts with transporter complementary DNA (cDNA). (medscape.com)
  • Kyoto Encyclopedia of Genes and Genomes (KEGG): Modules, Network, Genomes, Genes and KEGG analysis tools. (cutm.ac.in)
  • DAVID was used to perform the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis for the different expression genes (DEGs). (medscimonit.com)
  • The small genomes of the DED fungi also facilitate genomic analyses. (sisef.it)
  • We also identified several unknown proteins, some of which could have probable immune-related functions based on the results of the ProDom analysis. (biomedcentral.com)
  • On sequence level, we are investigating the evolution of short linear motifs in proteins (SLiMs) and look specifically at predatory, as well as mechano-sensing motifs (in collaboration with the team of Tam Mignot). (univ-amu.fr)
  • In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research. (peerj.com)
  • The tissue specific expression analysis by using quantitative RT-PCR assays indicated that AhLPAT was ubiquitously expressed in root, stem, leaf, flower, gynophore and seed of peanut with the highest level in gynephore and seed. (chinacrops.org)