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Related Concept Videos

LTR Retrotransposons03:08

LTR Retrotransposons

20.1K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
17.9K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

19.9K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
19.9K
Retroviruses02:33

Retroviruses

15.3K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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Transposons01:24

Transposons

2.6K
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Related Experiment Video

Updated: Mar 8, 2026

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

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LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.

Cecile Monat1, Ndomassi Tando1, Christine Tranchant-Dubreuil1

  • 1UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.

Mobile Genetic Elements
|January 17, 2017
PubMed
Summary

LTRclassifier is a new tool for classifying plant Long Terminal Repeat (LTR) retrotransposons using Hidden Markov Models (HMM) and BLAST. It provides fast and robust superfamily classification and functional annotation for genomic data.

Keywords:
LTR retrotransposonsclassificationsuperfamily

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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Automatic classification of Long Terminal Repeat (LTR) retrotransposons is a significant challenge in large-scale genomics.
  • Existing tools often struggle with accurate and automated classification of these repetitive elements.

Purpose of the Study:

  • To develop a simple and effective method for automatic classification of plant LTR retrotransposons.
  • To assign LTR retrotransposons to their respective superfamilies and provide basic functional annotation.

Main Methods:

  • The study proposes LTRclassifier, a tool utilizing Hidden Markov Model (HMM) recognition followed by BLAST analyses.
  • The approach is designed for automated classification and annotation of LTR retrotransposons.

Main Results:

  • LTRclassifier demonstrated robustness and speed when tested on diverse transposable element (TE) databases.
  • The tool successfully classifies plant LTR retrotransposons into superfamilies and provides functional annotations.

Conclusions:

  • LTRclassifier offers a reliable and efficient solution for the automated classification and annotation of plant LTR retrotransposons.
  • The tool is available as a web service, facilitating its use in genomic research.