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. Transposable element databases gather predicted or experimentally determined information about TE and other types of repeats from various sources such as phylogenetic classification and data analysis.
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.
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.
A catalogue of transposable element (TE) exaptation events, including information on the TE copy but also on the affected gene. C-GATE is interactive and allows users to include missed or new TE exaptation data. C-GATE provides a graphic representation of the entire library, which may be used for future statistical analysis of TE impact on host gene expression.
Allows easy access to all known cases of horizontal transfer of transposable elements (HTT) reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using TEs and/or host species classification and export them in several formats.
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.
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.
Provides a database of transposable elements (TE) identified in the complete genome of fish. FishTEDB combines de novo structure-based and homology-based approaches to find TE. This repository is based on the Fishbase resource and offers TE of several species of fish (bony, cartilageneous, lamprey and lancelet). It allows users to analyse sequences with three tools included in the database: BLAST, HMMER and GetORF.