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Related Concept Videos

Leaky Scanning02:28

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
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Non-LTR Retrotransposons03:18

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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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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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LTR Retrotransposons03:08

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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.
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Updated: Mar 16, 2026

Lipid Droplet Isolation for Quantitative Mass Spectrometry Analysis
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HCVIVdb: The hepatitis-C IRES variation database.

Evan W Floden1,2,3, Anas Khawaja1, Václav Vopálenský1

  • 1Department of Genetics & Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.

BMC Microbiology
|August 17, 2016
PubMed
Summary
This summary is machine-generated.

Hepatitis C virus (HCV) genome variability impacts viral replication. The new HCV IRES Variation Database (HCVIVdb) centralizes over 1900 mutations in the HCV internal ribosomal entry site (IRES) for functional analysis.

Keywords:
DatabaseHCVHepatitis CIRESInternal ribosome entry siteTranslation efficiency

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A Protocol for Analyzing Hepatitis C Virus Replication
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Area of Science:

  • Virology
  • Molecular Biology
  • Bioinformatics

Background:

  • Hepatitis C virus (HCV) exhibits significant genomic sequence variability, leading to distinct genotypes and subtypes.
  • The conserved HCV 5' untranslated region contains an internal ribosomal entry site (IRES) crucial for cap-independent viral polyprotein synthesis.

Purpose of the Study:

  • To compile and analyze known nucleotide variants within the HCV IRES.
  • To investigate the impact of these IRES variations on viral protein production and replication efficiency.

Main Methods:

  • Development of the HCV IRES Variation Database (HCVIVdb) to collect naturally occurring and engineered IRES mutations.
  • Inclusion of genotypic background, publication links, and quantitative translation efficiency data (where available).
  • Data presentation in tabular and graphical formats for comparative analysis.

Main Results:

  • The HCVIVdb consolidates over 1900 documented mutations within the HCV IRES.
  • The database facilitates systematic analysis of IRES domains and their functional consequences.
  • Quantitative data on IRES efficiency across different experimental systems are collated.

Conclusions:

  • HCVIVdb serves as a central resource for researchers studying HCV IRES function and variation.
  • Enables detailed comparative and functional analysis of HCV IRES domains.
  • Provides a foundation for developing targeted antiviral therapies and guiding future research.