• novel
  • Ludidi N, Gehring C. Identification of a novel protein with guanylyl cyclase activity in Arabidopsis thaliana. (uwc.ac.za)
  • We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. (biomedcentral.com)
  • Sphingosine kinase 1 phosphorylates sphingosine to sphingosine-1-phosphate (S1P) SK1 is normally a cytosolic protein but is recruited to membranes rich in phosphatidate (PA), a product of Phospholipase D (PLD) Sphingosine-1-phosphate (S1P) is a novel lipid messenger with both intracellular and extracellular functions. (wikipedia.org)
  • This gene is a novel gene isolated based on its expression in the human adrenal gland. (wikipedia.org)
  • Peptide Sequences
  • The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. (wikipedia.org)
  • encode
  • Actually, a small fraction of the genes encode RNA molecules that are never translated into a protein. (psu.edu)
  • A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. (wikipedia.org)
  • The human and the murine GPR84 ORFs both encode proteins of 396 amino acid residues length with 85% identity and are therefore considered as orthologs. (wikipedia.org)
  • These alleles encode slightly different versions of a protein, which cause different phenotypical traits. (wikipedia.org)
  • human
  • Three human PHDs (prolyl hydroxylase domain proteins, PHD1-PHD3) initiate oxygen-dependent degradation of HIF-α-subunits in normoxia. (biochemj.org)
  • A significant fraction of the fly and human genomes are heterochromatic, yet our current understanding of the sequence and organization of heterochromatin is very limited. (biomedcentral.com)
  • The Human Protein Atlas (HPA) [ 20 , 21 ] is based on immunohistochemistry (IHC) data. (biomedcentral.com)
  • Human CNTNAP4 genome location and CNTNAP4 gene details page in the UCSC Genome Browser. (wikipedia.org)
  • mRNA
  • Foster GD, Robinson SW, Blundell RP, Roberts MR, Hodge R, Draper J, Scott RJ (1992) A Brassica napus mRNA encoding a protein homologous to phospholipid transfer proteins is expressed specifically in the tapetum and developing microspores. (springer.com)
  • Roberts MR, Robson F, Foster GD, Draper J, Scott RJ (1991) A Brassica napus mRNA expressed specifically in developing microspores. (springer.com)
  • In eukaryotes, the mRNA is transported out of the nucleus (to the cell's cytoplasm ), where it is converted to a protein sequence in a process called translation . (psu.edu)
  • In eukaryotic genes with multiple exons, ORFs span intron/exon regions, which may be spliced together after transcription of the ORF to yield the final mRNA for protein translation. (wikipedia.org)
  • physiological
  • These results provide new insight for further study of FKBP genes and their functions in abiotic stress response and multiple metabolic and physiological processes in apple. (biomedcentral.com)
  • The protein has a physiological function in regulation of water transport mainly in apocrine glands in the axilla, vulva, eyelid and ear canal, serous cells of the submandibular salivary gland, serous cells of the submucosal glands of the bronchi, and accessory lacrimal glands as well as cutaneous eccrine glands. (wikipedia.org)
  • Maize
  • We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and discuss potential application of the pipeline to other genomes. (usda.gov)
  • Promoters
  • the high conservatism of initiation sites may be connected with their location inside promoters of the relevant genes. (wikipedia.org)
  • nucleotide
  • The sequence of HsIPMK has been deposited with the GenBank ® , DDBJ, EMBL and GSDB Nucleotide Sequence Databases under the accession no. (biochemj.org)
  • Only 21 clones showed significant homology to the nucleotide sequences in databases. (springer.com)
  • Each letter in a DNA sequence is called a base , basepair , or nucleotide . (psu.edu)
  • For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons. (wikipedia.org)
  • Arabidopsis
  • Thus, we isolated a 1.2 kb fragment of the 5′ flanking region of JcUEP and evaluated its activity as a constitutive promoter in Arabidopsis and Jatropha using the β -glucuronidase ( GUS ) reporter gene. (springer.com)
  • Burke TJ, Callis J, Vierstra RD (1988) Characterization of a polyubiquitin gene from Arabidopsis thaliana . (springer.com)
  • Paul W, Hodge R, Smartt S, Draper J, Scott R (1992) The isolation and characterization of the tapetum-specific Arabidopsis thaliana A9 gene. (springer.com)
  • hybridization
  • We isolated and characterized the riok-2 gene from S. japonicum , and detected the transcriptional profiles of Sj-riok-2 by using real-time PCR and in situ hybridization. (biomedcentral.com)
  • analysis
  • By sequence analysis, we predicted a promoter approx. (biochemj.org)
  • This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. (biomedcentral.com)
  • Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes. (biomedcentral.com)
  • Chen M-S, Wang G-J, Wang R-L, Wang J, Song S-Q, Xu Z-F (2011) Analysis of expressed sequence tags from biodiesel plant Jatropha curcas embryos at different developmental stages. (springer.com)
  • Transcriptional Analysis of Drought-Induced Genes in the Roots of a Tolerant Genotype of the Common Bean (Phaseolus vulgaris L. (mdpi.com)
  • Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. (ox.ac.uk)
  • ORF Finder: Tmhe ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. (wikipedia.org)
  • Coding region Reading frame Sequerome - A sequence profiling tool that links each BLAST record to the NCBI ORF enabling complete ORF analysis of a BLAST report. (wikipedia.org)
  • ontology
  • Among 1301 clusters, 343 were categorized according to Gene Ontology (GO) hierarchy and were compared to the GO mapping of A. thaliana tentative consensus sequences. (purdue.edu)
  • analyses
  • The results from sequence alignments, 3-D structures, phylogenetics, and analyses of conserved domains indicated that apple FKBPs are highly and structurally conserved. (biomedcentral.com)
  • Regulation
  • In addition, we observed a fluctuation in gene regulation over time for both the genotypes, which seem to adopt and adapt different strategies in order to develop tolerance against this stress. (mdpi.com)
  • subunit
  • Protein phosphatase 1 regulatory subunit 14B is an enzyme that in humans is encoded by the PPP1R14B gene. (wikipedia.org)
  • Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. (wikipedia.org)
  • transcription
  • We found sequences for transcription factors, carbohydrates metabolism, proline-rich proteins, aquaporins, chaperones and ubiquitins, all of them organized according to their biological processes. (mdpi.com)
  • Under rather unusual conditions, an RNA molecule can be converted back to the reverse complement DNA ( cDNA ) sequence by a process called reverse transcription , which performed by a protein called reverse transcriptase . (psu.edu)
  • If transcription were to cease before the stop codon, an incomplete protein would be made during translation. (wikipedia.org)
  • ORFs
  • Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA-coding regions in a DNA sequence. (wikipedia.org)
  • On the other hand, it has been proven that some short ORFs (sORFs) that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. (wikipedia.org)
  • murine
  • A consensus HIF-1-binding site that is conserved in the murine phd2 gene was detected in the CpG island. (biochemj.org)
  • functional
  • We conclude that the phd2 gene is transcribed exclusively from the downstream promoter that contains a functional hypoxia-responsive, cis -regulatory element. (biochemj.org)
  • The RNA can be directly functional or be the intermediate template for a protein that performs a function. (wikipedia.org)
  • Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. (wikipedia.org)
  • Sixteen years later, in 1905, Wilhelm Johannsen introduced the term 'gene' and William Bateson that of 'genetics' while Eduard Strasburger, amongst others, still used the term 'pangene' for the fundamental physical and functional unit of heredity. (wikipedia.org)
  • methods
  • Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. (pubmedcentralcanada.ca)
  • However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. (pubmedcentralcanada.ca)
  • Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements. (pubmedcentralcanada.ca)
  • Using bioinformatics-based methods, RT-PCR, and qRT-PCR technologies, we identified 38 FKBP genes and cloned 16 of them in the apple genome. (biomedcentral.com)
  • We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. (biomedcentral.com)
  • Highsmith, W. E. (2006) Electrophoretic Methods for Mutation Detection and DNA Sequencing, chapter 9 in "Molecular Diagnostics for the Clinical Laboratorian", Humana Press Lander, E.S. and Green, P. (1987) Construction of multilocus genetic-linkage maps in humans. (wikipedia.org)
  • alignments
  • ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. (pubmedcentralcanada.ca)
  • Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. (pubmedcentralcanada.ca)
  • Multiple sequence alignments are an essential prerequisite in alignment based phylogenetic reconstructions, because they establish fundamental homology assessments of primary sequence characters. (pubmedcentralcanada.ca)
  • For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. (wikipedia.org)
  • mRNAs
  • A popular laboratory technique is to reverse transcribe mRNAs and perform a simple sequencing process, resulting in sequence data for pieces of about 500 bp (bp = basepair) and having a 1-3% error rate. (psu.edu)
  • Domains
  • The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. (wikipedia.org)
  • This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. (wikipedia.org)
  • promoter
  • In reporter vectors containing both promoter sequences, luciferase activity was equal to vectors containing only the downstream promoter. (biochemj.org)