GyDB

Names

More detailed information about this field from each metasource. ×

GyDB

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

Gypsy Database (GyDB)

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

---

gydb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

Close

Other names: Gypsy Database (GyDB), gydb

Gypsy database of mobile genetic elements

Webpage:

Publications:

Publications

More detailed information about this field from each metasource. ×

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
PMID: 21036865

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

Close

• The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 PubMed citations: 145.

  145 articles citing: The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

  ×

  Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. PMID:35260071

  ---

  A Gypsy element contributes to the nuclear retention and transcriptional regulation of the resident lncRNA in locusts. PMID:35067197

  ---

  Repeatome-Based Phylogenetics in Pelargonium Section Ciconium (Sweet) Harvey. PMID:34893846

  ---

  Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus. PMID:34800971

  ---

  CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PMID:34762703

  ---

  ICTV Virus Taxonomy Profile: Belpaoviridae 2021. PMID:34761738

  ---

  Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution. PMID:34715903

  ---

  The genomic ecosystem of transposable elements in maize. PMID:34648488

  ---

  Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PMID:34491994

  ---

  Viruses Defined by the Position of the Virosphere within the Replicator Space. PMID:34468181

  ---

  The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. PMID:34304594

  ---

  Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. PMID:34295368

  ---

  Genome of the world's smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. PMID:34294872

  ---

  A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. PMID:34267227

  ---

  The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. PMID:34253727

  ---

  Computational Analysis of Transposable Elements and CircRNAs in Plants. PMID:34195962

  ---

  Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi. PMID:34157969

  ---

  TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. PMID:34154643

  ---

  The impact of endogenous Avian Leukosis Viruses (ALVE) on production traits in elite layer lines. PMID:33975038

  ---

  High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. PMID:33815435

  ---

  A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. PMID:33750287

  ---

  Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). PMID:33729490

  ---

  DNA Modification Patterns within the Transposable Elements of the Fig (Ficus carica L.) Genome. PMID:33673593

  ---

  A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. PMID:33561231

  ---

  InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning. PMID:33525408

  ---

  Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249

  ---

  Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development. PMID:33348863

  ---

  Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.). PMID:33297579

  ---

  Is the human T-cell lymphotropic virus type 2 in the process of endogenization into the human genome? PMID:33294211

  ---

  A Sister Lineage of Sampled Retroviruses Corroborates the Complex Evolution of Retroviruses. PMID:33249491

  ---

  Conservative route to genome compaction in a miniature annelid. PMID:33199869

  ---

  In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes. PMID:33193616

  ---

  Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA. PMID:33193489

  ---

  The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. PMID:33058468

  ---

  Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae. PMID:32988994

  ---

  Hermaphroditism in Marijuana (Cannabis sativa L.) Inflorescences - Impact on Floral Morphology, Seed Formation, Progeny Sex Ratios, and Genetic Variation. PMID:32670310

  ---

  Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. PMID:32561724

  ---

  Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis. PMID:32545790

  ---

  What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? PMID:32508870

  ---

  The draft genome sequence of an upland wild rice species, Oryza granulata. PMID:32350267

  ---

  Dialister massiliensis sp. nov., a new bacterium isolated from the human gut. PMID:32194963

  ---

  Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species. PMID:32183698

  ---

  Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. PMID:32111628

  ---

  Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. PMID:32071725

  ---

  A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.). PMID:31960179

  ---

  Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. PMID:31871489

  ---

  Draft genome of Tanacetum cinerariifolium, the natural source of mosquito coil. PMID:31796833

  ---

  Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus. PMID:31710678

  ---

  Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis. PMID:31549373

  ---

  Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes. PMID:31409850

  ---

  Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. PMID:31390781

  ---

  Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. PMID:31239280

  ---

  Structural Characterization of ABCB1, the Gene Underlying the d2 Dwarf Phenotype in Pearl Millet, Cenchrus Americanus (L.) Morrone. PMID:31208958

  ---

  Genome sequence and description of Alterileibacterium massiliense gen. nov., sp. nov., a new bacterium isolated from human ileum of a patient with Crohn's disease. PMID:31198562

  ---

  The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages. PMID:31107873

  ---

  Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. PMID:31064091

  ---

  Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. PMID:31011427

  ---

  Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes. PMID:30899254

  ---

  Investigating the Biological Relevance of In Vitro-Identified Putative Packaging Signals at the 5' Terminus of Satellite Tobacco Necrosis Virus 1 Genomic RNA. PMID:30814279

  ---

  Arbuscular mycorrhizal fungi induce the expression of specific retrotransposons in roots of sunflower (Helianthus annuus L.). PMID:30779767

  ---

  RepetDB: a unified resource for transposable element references. PMID:30719103

  ---

  Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848

  ---

  The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.). PMID:30675191

  ---

  Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics. PMID:30442098

  ---

  Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events. PMID:30319674

  ---

  Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers. PMID:30158460

  ---

  Biology and genome of a newly discovered sibling species of Caenorhabditis elegans. PMID:30097582

  ---

  Identification of transposable elements fused in the exonic region of the olive flounder genome. PMID:29934806

  ---

  Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics. PMID:29799487

  ---

  The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. PMID:29691383

  ---

  Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses. PMID:29618642

  ---

  A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396

  ---

  Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. PMID:29510672

  ---

  Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. PMID:29500236

  ---

  Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions. PMID:29497436

  ---

  Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases. PMID:29202119

  ---

  De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. PMID:29112324

  ---

  Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa. PMID:29104828

  ---

  Genome structure of Rosa multiflora, a wild ancestor of cultivated roses. PMID:29045613

  ---

  Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750

  ---

  Analysis of Human Endogenous Retrovirus Expression in Multiple Sclerosis Plaques. PMID:28868516

  ---

  Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.). PMID:28821238

  ---

  Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum. PMID:28776161

  ---

  The landscape and structural diversity of LTR retrotransposons in Musa genome. PMID:28601922

  ---

  Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi. PMID:28545447

  ---

  Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. PMID:28466793

  ---

  Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. PMID:28413161

  ---

  Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons. PMID:28314936

  ---

  Convergence of retrotransposons in oomycetes and plants. PMID:28293305

  ---

  Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families. PMID:28204924

  ---

  Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca. PMID:28082604

  ---

  Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes. PMID:28057732

  ---

  An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. PMID:28004836

  ---

  Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374. PMID:27979934

  ---

  A new look at the LTR retrotransposon content of the chicken genome. PMID:27577548

  ---

  Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. PMID:27506905

  ---

  Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae). PMID:27492982

  ---

  Virus-like attachment sites as structural landmarks of plants retrotransposons. PMID:27471551

  ---

  Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties. PMID:27458999

  ---

  gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. PMID:27242033

  ---

  DPTEdb, an integrative database of transposable elements in dioecious plants. PMID:27173524

  ---

  Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes. PMID:27037832

  ---

  Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.). PMID:27025914

  ---

  Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes. PMID:26781660

  ---

  The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. PMID:26634818

  ---

  Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. PMID:26613339

  ---

  Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. PMID:26608057

  ---

  In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae. PMID:26606051

  ---

  Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses. PMID:26386563

  ---

  Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. PMID:26245353

  ---

  A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). PMID:26243297

  ---

  Do larger genomes contain more diverse transposable elements? PMID:25896861

  ---

  Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification. PMID:25834645

  ---

  Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. PMID:25633377

  ---

  Draft genome sequence of adzuki bean, Vigna angularis. PMID:25626881

  ---

  Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses. PMID:25605791

  ---

  Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements. PMID:25573958

  ---

  Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes. PMID:25499090

  ---

  Genome sequence of mungbean and insights into evolution within Vigna species. PMID:25384727

  ---

  Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. PMID:25351875

  ---

  Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. PMID:25233906

  ---

  Activation of transcription and retrotransposition of a novel retroelement, Steamer, in neoplastic hemocytes of the mollusk Mya arenaria. PMID:25201971

  ---

  LTR retroelements are intrinsic components of transcriptional networks in frogs. PMID:25056159

  ---

  Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons. PMID:24849372

  ---

  Draft sequences of the radish (Raphanus sativus L.) genome. PMID:24848699

  ---

  TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. PMID:24832231

  ---

  Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry. PMID:24608367

  ---

  Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. PMID:24441736

  ---

  Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. PMID:24282021

  ---

  Reconstructing de novo silencing of an active plant retrotransposon. PMID:23852169

  ---

  On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. PMID:23550032

  ---

  Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. PMID:23542206

  ---

  Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts. PMID:23497320

  ---

  LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements. PMID:23469217

  ---

  Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration. PMID:23448600

  ---

  Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. PMID:23335122

  ---

  Drosophila errantiviruses. PMID:22754751

  ---

  Aphids: a model for polyphenism and epigenetics. PMID:22567389

  ---

  MASiVEdb: the Sirevirus Plant Retrotransposon Database. PMID:22545773

  ---

  Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. PMID:22507400

  ---

  Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PMID:22347367

  ---

  Next generation sequencing-based analysis of repetitive DNA in the model dioecious [corrected] plant Silene latifolia. PMID:22096552

  ---

  GyDB mobilomics: LTR retroelements and integrase-related transposons of the pea aphid Acyrthosiphon pisum genome. PMID:22016855

  ---

  Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. PMID:21850457

  ---

  BEL/Pao retrotransposons in metazoan genomes. PMID:21639932

Tags:

Tags

More detailed information about this field from each metasource. ×

nucleotide sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

coding and non-coding dna

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

phylogeny

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

---

mobile genetic elements

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

---

transcription factors and regulatory sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

---

sequence sites, features and motifs

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

---

virology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:25.010981

Close

nucleic acid sequence coding and non-coding dna phylogeny mobile genetic elements transcription factors and regulatory sites sequence sites, features and motifs virology