• Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
  • We also performed an example annotation and classification of LTR retrotransposon insertions in the Drosophila melanogaster 5.8 genome as a proof of concept. (uni-hamburg.de)
  • We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. (biomedcentral.com)
  • We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. (biomedcentral.com)
  • Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)
  • In coordination with FlyBase, we are transitioning almost all of the RefSeq Drosophila assemblies to annotation produced primarily by NCBI's eukaryotic genome annotation pipeline . (nih.gov)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
  • We'll continue to use the FlyBase annotation for Drosophila melanogaster (soon to be updated to Release 6.32), but we'll annotate the other species using available RNA-seq datasets and our latest software. (nih.gov)
  • To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development. (elifesciences.org)
  • the process that governs the early embryonic patterning of the Drosophila body plan is now the best understood example of a complex cascade of transcriptional regulation during development [ 14 , 15 ]. (biomedcentral.com)
  • It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
  • The bottom track contains a representation of a hierarchical LTR retrotransposon annotation graph, as reported by LTRdigest, collapsed into a single track. (uni-hamburg.de)
  • BCL2 proteins are described as 'crucial regulators of apoptosis' (PMID:15868100)and the intrinsic apoptosis pathway is initiated by the release of mitochondrial cytochrome c into the cytoplasm, which results in the activation of caspases (15102863) - help in generating a defintion for intrinsic apoptosis? (geneontology.org)
  • Sequence finishing and mapping of Drosophila melanogaster heterochromatin. (genscript.com)
  • These sequences represent the protein coding region of the EMC8-9 cDNA ORF which is encoded by the open reading frame (ORF) sequence. (genscript.com)
  • GenScript guarantees 100% sequence accuracy of all synthetic DNA constructs we deliver, but we do not guarantee protein expression in your experimental system. (genscript.com)
  • It accepts sequence data in a variety of formats and a basic LTR annotation in GFF3format as input. (uni-hamburg.de)
  • As output, LTRdigest creates GFF3 and CSV annotations as well as FASTA sequence files for all detected features. (uni-hamburg.de)
  • We now include 30 Drosophila species in the RefSeq dataset, with more planned. (nih.gov)
  • All RefSeq annotations are within the public domain. (nih.gov)
  • Although the amino acid sequences of mammalian and Drosophila calmodulins differ by only three conservative amino acid changes, the refined model reveals a number of significant differences between the two structures. (rcsb.org)
  • Here, we used a genomics/proteomics approach (including immunoblot experiments from pigs infected with T. suis ) to prioritize putative immunogenic excretory/secretory (E/S) proteins conserved across and specific to several gastrointestinal (GI) parasitic nematode species. (frontiersin.org)
  • This will allow us to provide consistent, high-quality annotations across the full spectrum of Drosophila species, and also rapidly provide annotations as new high-quality assemblies become available. (nih.gov)
  • Fine-grained annotation and classification of de novo predicted LTR retrotransposons. (uni-hamburg.de)
  • Drosophila melanogaster ER membrane protein complex 8-9 (EMC8-9), mRNA. (genscript.com)
  • Fertilization also leads to changes in mRNA translation and protein stability, which support a period of development driven off of maternal stockpiles. (elifesciences.org)
  • Drosophila melanogaster chaperonin containing TCP1 subunit 5, transcript variant A (CCT5), mRNA. (genscript.com)
  • Protein expression is influenced by many factors that may vary between experiments or laboratories. (genscript.com)
  • We have assembled an atlas of gene expression patterns during Drosophila embryogenesis. (biomedcentral.com)
  • A classic example is the heat shock protein system, particularly Hsp90 , whose expression is environmentally plastic and increases under thermal stress, but buffers phenotypic changes induced by mutations to maintain homeostasis 2 , a process termed canalization 3 . (nature.com)
  • An antibody-protein array of putative immunogenic proteins was developed from a combined bioinformatic, experimental, and literature-based prioritization of homologous parasite proteins. (frontiersin.org)
  • is a software tool for automated annotation of internal features of LTR retrotransposons. (uni-hamburg.de)
  • For further analysis, it is desirable to obtain an annotation of the internal structure of such candidates. (uni-hamburg.de)
  • It is able to identify protein coding regions associated with the retrotransposition process as well as internal regulatory features using local alignment and hidden Markov model-based algorithms. (uni-hamburg.de)
  • The crystal structure of calmodulin (Mr 16,700, 148 residues) from Drosophila melanogaster as expressed in a bacterial system has been determined and refined at 2.2-A resolution. (rcsb.org)
  • Complete annotations as well as the members and sequences of the 62 groups reported are available for download. (uni-hamburg.de)
  • One of these, the Yer156C protein, is highly conserved but of unknown function. (bvsalud.org)
  • Screening the array with sera and ileal fluid samples from immunized pigs suggested cross-reactivity among homologous proteins and a general activation of immunity. (frontiersin.org)
  • Proteins that activated immunity are potential antigens for immunization and the multi-omics phylum-spanning prioritization database that was created is a valuable resource for identifying target proteins in a wide array of different parasitic nematodes. (frontiersin.org)
  • A first characterization of the Yer156C neighborhood reveals an array of proteins linked to proteostasis and RNA binding. (bvsalud.org)
  • In Xenopus, zebrafish, and Drosophila the major activation of zygotic transcription occurs as the cell cycle lengthens and gastrulation begins, a developmental period referred to as the midblastula transition. (elifesciences.org)
  • does all activation of caspases require other proteins also involved in apoptosis - therefore shouldn't this term be a part of apoptosis? (geneontology.org)
  • Cytochrome c then forms a multi-protein complex known as the 'apoptosome' and initiates activation of the caspase cascade through caspase 9. (geneontology.org)
  • Chemical cross-linking (CX) of proteins in vivo or in cell free extracts followed by mass spectrometric (MS) identification of linked peptide pairs (CXMS) can reveal protein-protein interactions (PPIs) both at a proteome wide scale and the level of cross-linked amino acid residues. (bvsalud.org)
  • In addition, we used RepeatProteinMask (Version 3.2.2) implemented in RepeatMasker to detect the TE-relevant proteins. (biomedcentral.com)
  • You can download these annotation data from the NCBI genomes FTP site or you can try the new NCBI Datasets tool. (nih.gov)
  • Comment Open annotations (there are currently 0 annotations on this page). (elifesciences.org)
  • Protein-protein interaction (PPI) sites play a key role in the formation of protein complexes, which is the basis of a variety of biological processes. (bvsalud.org)
  • The grey blocks at the end of the element represent the LTRs, while the coloured elements in the middle represent protein domain hits. (uni-hamburg.de)