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Transposable element databases | Genome annotation

Transposable elements (TEs) are segments of DNA that self-replicate in a genome. DNA segments that originated from TE duplications may or may not remain transpositionally active but are herein referred to simply as TEs. TEs form vast families of interspersed repeats and constitute large parts of eukaryotic genomes, for example, over half of the human genome (Lander et al., 2001; de Koning et al., 2011; Wheeler et al., 2013) and over four fifths of the maize genome (Schnable et al., 2009). The repetitive nature of TEs confounds many types of studies, such as gene prediction, variant calling (i.e., the identification of sequence variants such as SNPs or indels), RNA-Seq analysis, and genome alignment. Source text: Hoen et al., 2015.

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ACLAME / A CLAssification of Mobile genetic Elements
Collects and classifies mobile genetic elements (MGEs) including phases and plasmids from various sources. ACLAME provides a platform for analyzing MGE diversity from a global scale down to specific groups of MGEs and tools for the detection of new MGEs integrated in bacterial genomes. The BLAST search interface allows for a simple querying of the ACLAME sequences, returning information such as for each hit sequence, the functional annotation, the MGE, host(s) and protein families it belongs to.
GyDB / Gypsy Database
A research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). GyDB is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives.
Contains putatively active LINE-1 insertions residing in human and rodent genomes: intact in the two open reading frames (ORFs), full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). L1Base includes the full-length (>6000 bp) non-intact L1s (FLnI-L1s). L1Base can be searched via the MySQL-driven query system by using criteria, such as conservation of the functional sites important for activity, chromosomal localization and families. The database can also be searched by executing Blastn-based queries with a user-specified L1 sequence.
A database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. TranspoGene contains information regarding specific type and family of the Transposed elements, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern.
MAtDB / MIPS Arabidopsis thaliana Database
Aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The MAtDB web interface allows access of the data through graphical or list browsing, searching by keywords, names or sequences, and through precompiled tables that summarize general, functional, structural or comparative features. All data from the Arabidopsis Genome Initiative (AGI) have been integrated into MAtDB.
Allows to bring some order to the system of short interspersed elements (SINEs) and to set a basis for further studies on these genomic elements. SINEBase introduces a set of formal definitions about SINEs. More than 170 families have been counted (concerning animals, flowering, plants, and green algae) on the base. These families are classified according to the modular structure of their nucleotide sequences. The website can be used in two ways: (1) exploring the database, (2) analyzing candidate SINE sequences.
MASiVEdb / Mapping and Analysis of SireVirus Elements database
A collective and systematic resource of Sireviruses in plants. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of coordinates, insertion age, and an analytical breakdown of the structure and gene complement of each element. All data are readily available through basic and advanced query interfaces, batch retrieval, and downloadable files. A purpose-built system is also offered for detecting and visualizing similarity between user sequences and Sireviruses, as well as for coding domain discovery and phylogenetic analysis. MASiVEdb is currently the most comprehensive directory of Sireviruses, and as such complements other efforts in cataloguing plant transposable elements and elucidating their role in host genome evolution.
DPTEdb / Dioecious Plant Transposable Element database
A comprehensive transposable element (TE) database for dioecious plants. DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data.
gEVE / Genome-based Endogenous Viral Element database
Provides nucleotide and amino acid sequences, genomic loci and functional annotations of endogenous viral elements (EVE) open reading frames ORFs for all 20 genomes. We comprehensively identified and annotated EVE open reading frame (ORF) sequences (i) encoding >80 amino acid (aa) sequences and (ii) harboring viral sequence motifs. The sequences and annotations of all EVEs can be downloaded from the database without registration. Our annotations of EVE ORFs offer a useful resource which enhances studies of EVEs, such as expression analysis using next-generation sequencing (NGS) data, facilitating studies of functional EVE sequences in various mammalian species.
ImmeDB / Intestinal microbiome mobile element database
Compiles putative mobile genetic elements (MGEs) derived from an application of the “Split Read Insertion Detection” method to characterize gut microbiome. The database is organized according to seven MGE classes (prophages, integrative conjugative elements (ICEs), integrative mobilizable elements (IMEs), transposons, group II introns, genomic islands and islets). Each entry provides downloadable genomic sequence and annotation.
BrassicaTED / Brassica Tranposable Elements Database
A database of information regarding the characteristics and potential utility of miniature form transposable elements (mTEs) including MITE, TRIM and SINEs in Brassica species. At present, BrassicaTED has datasets for 41 mTE families. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species.
Delivers positional intersections between annotated Transposable Elements (TEs) and pre-miRNAs in plant genomes. PlanTE-MIR DB provides 152 precursor miRNAs overlapping TEs in 10 plant species. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use.
Provides insight on insect Miniature Inverted Transposable Elements (MITEs) and improves assembly and annotation of insect genomes. iMITEdb has functions such as browse, search, BLAST and download. Each MITE family in the database includes species, superfamily name, family name, Terminal Inverted Repeats (TIRs), Target Site Duplications (TSDs), copies, length and consensus sequence. Users can also perform individual search based on a MITE name to obtain information about each MITE family.
Maize TE database / Maize transposable element database
Stores information about transposable elements (TEs). In addition to identifying all TEs in maize, this project will pay particular attention to the characterization of TEs such as Pack-MULEs and Helitrons that routinely capture and amplify gene fragments and thereby confound gene annotation. This project will generate a comprehensive and rigorously annotated TE database that will greatly assist all future maize genome annotations.
To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database was constructed. MnTEdb was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species.
Provides some information and resources related to long terminal repeat (LTR)-retrotransposons in rice genome. The aims of the RetrOryza database are to (i) assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) provide a means for identifying LTR-retrotransposons inserted near genes.
Brassica ASTRA
Incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Brassica ASTRA is a public database for genomic information on Brassica species. It has been developed for the analysis and interrogation of Brassica genomic information, the identification of candidate genes for agronomic traits and comparative analysis with the Arabidopsis genome.
Contains 31,396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein function or involvement in disease to identify Functional REPeats (FREPs). FREP is a unique resource for illuminating the role of transposons and repetitive sequences in shaping the coding part of the mouse transcriptome and for selecting the appropriate experimental model to study diseases with suspected repeat etiology contributions.
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