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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…
HTT-DB
Dataset

HTT-DB Horizontal Transferred of Transposable elements Database

Allows easy access to all known cases of horizontal transfer of transposable…

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…

Dfam
Dataset

Dfam

An open access database of families of repetitive DNA elements, in which each…

An open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). Dfam families include…

ACLAME
Dataset

ACLAME A CLAssification of Mobile genetic Elements

Collects and classifies mobile genetic elements (MGEs) including phases and…

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…

HERVd
Dataset

HERVd Human Endogenous RetroVirus database

Provides complex information on and analysis of retroviral elements found in…

Provides complex information on and analysis of retroviral elements found in the human genome. HERVd can be used for searches of individual HERV families, identification of HERV parts, graphical…

TIGR Plant…
Dataset

TIGR Plant Repeat Databases

Assist in the compilation and identification of repeat sequences in plant…

Assist in the compilation and identification of repeat sequences in plant genomes.

L1Base
Dataset

L1Base

Contains putatively active LINE-1 insertions residing in human and rodent…

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…

Repbase
Dataset

Repbase

Provides representative eukaryotic repetitive sequences and other biologically…

Provides representative eukaryotic repetitive sequences and other biologically relevant information derived from printed journal articles, electronic journals, and public databases including a…

P-MITE
Dataset

P-MITE Plant MITE databases

A series of databases was constructed to host all MITE sequences from the 41…

A series of databases was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded…

DrosDel…
Dataset

DrosDel collection

Contains a collection of P-element insertion on an isogenic genetic background…

Contains a collection of P-element insertion on an isogenic genetic background that permits the construction of molecularly defined chromosomal aberrations in Drosophila. DrosDel collection is a…

euL1db
Dataset

euL1db

Provides a curated and comprehensive summary of L1-HS insertion polymorphisms…

Provides a curated and comprehensive summary of L1-HS insertion polymorphisms identified in healthy or pathological human samples and published in peer-reviewed journals. euL1db will help…

PlanTE-MIR DB
Dataset

PlanTE-MIR DB

Delivers positional intersections between annotated Transposable Elements (TEs)…

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…

GyDB
Dataset

GyDB Gypsy Database

A research project devoted to the evolutionary dynamics of viruses and…

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…

MAtDB
Dataset

MAtDB MIPS Arabidopsis thaliana Database

Aims to provide a comprehensive resource for Arabidopsis as a genome model that…

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,…

Maize Repeat Database
Dataset

Maize Repeat Database Maize Repeat Database

Contains maize repeat sequences. Maize Repeat Database exists as three separate…

Contains maize repeat sequences. Maize Repeat Database exists as three separate files: “characterized repeats” (623 sequences), uncharacterized repeats” (21,133 sequences), and…

RTCGD
Dataset
iMITEdb
Dataset

iMITEdb

Provides insight on insect Miniature Inverted Transposable Elements (MITEs) and…

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.…

gEVE
Dataset

gEVE Genome-based Endogenous Viral Element database

Provides nucleotide and amino acid sequences, genomic loci and functional…

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…

DPTEdb
Dataset

DPTEdb Dioecious Plant Transposable Element database

A comprehensive transposable element (TE) database for dioecious plants. DPTEdb…

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,…

MnTEdb
Dataset

MnTEdb

To better understand the roles of TEs in structural, functional and…

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.…

AluHunter
Dataset

AluHunter

Provides taxon-specific primate Alu elements. AluHunter offers information that…

Provides taxon-specific primate Alu elements. AluHunter offers information that can be reuse in phylogeny and population genetics. It characterizes all Alu elements in GenBank sequences and isolates…

TEclass
Web
Desktop

TEclass

Classifies unknown transposable element (TE) consensus sequences into four…

Classifies unknown transposable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, Long Terminal Repeats (LTRs), Long Interspersed…

dbRIP
Dataset

dbRIP Database of Retrotransposon Insertion Polymorphisms

An integrated and interactive database of human retrotransposon insertion…

An integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). Users can query the database by a variety of means and have access to the detailed information related…

MASiVEdb
Dataset

MASiVEdb Mapping and Analysis of SireVirus Elements database

A collective and systematic resource of Sireviruses in plants. MASiVEdb is…

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…

BrassicaTED
Dataset

BrassicaTED Brassica Tranposable Elements Database

A database of information regarding the characteristics and potential utility…

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,…

Maize TE database
Dataset

Maize TE database Maize transposable element database

Stores information about transposable elements (TEs). In addition to…

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…

C-GATE
Dataset

C-GATE Catalogue of Genes Affected by Transposable Elements

A catalogue of transposable element (TE) exaptation events, including…

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…

RepeatMasker
Desktop
Web

RepeatMasker

Screens DNA sequences for interspersed repeats and low complexity DNA…

Screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a…

BmTEdb
Dataset

BmTEdb Bombyx mori Transposable Elements Database

A collective database of transposable elements (TEs) in the silkworm (Bombyx…

A collective database of transposable elements (TEs) in the silkworm (Bombyx mori) genome. Users are entitled to browse, search and download the sequences in the database. Sequence analyses such as…

GrTEdb
Dataset

GrTEdb Gossypium raimondii transposable elements database

Gathers information about resources and information related with transposable…

Gathers information about resources and information related with transposable elements (TEs) in G. raimondii. GrTEdb intends to improve cotton genome evolution analyses among AA, DD and AADD genome…

Brassica ASTRA
Dataset

Brassica ASTRA

Incorporates expressed sequences with Swiss-Prot and GenBank comparative…

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…

RetrOryza
Dataset

RetrOryza

Provides some information and resources related to long terminal repeat…

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…

FREP
Dataset

FREP

Contains 31,396 RepeatMasker-identified non-redundant variant repeat sequences…

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…

ERE database
Dataset

ERE database

Presents a set of data obtained from surveying the entire C57BL/6J mouse genome…

Presents a set of data obtained from surveying the entire C57BL/6J mouse genome in silico, using a library of unique endogenous retroviral element (ERE)-mining probes cloned from C57BL/6J mouse…

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