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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Cell Specific Gene Expression01:58

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Related Experiment Video

Updated: Feb 10, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.

Christina James-Zorn1, Virgilio Ponferrada2, Malcolm E Fisher2

  • 1Xenbase Curation Team, Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA. christina.james_zorn@cchmc.org.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2018
PubMed
Summary

Xenbase is a comprehensive resource for Xenopus research, integrating genomic data, bioinformatic tools, and reagent catalogs. It facilitates gene expression analysis, disease mapping, and access to curated biological information for Xenopus laevis and Xenopus tropicalis.

Keywords:
Anatomy ontologyBLASTGBrowseGene expression analysisGenome databasePolyploid genomeTextpressoXenopus

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Area of Science:

  • * Developmental Biology
  • * Genomics
  • * Bioinformatics

Background:

  • * Xenopus laevis and Xenopus tropicalis are crucial model organisms in biological research.
  • * Integrating diverse data for these species is essential for advancing research.
  • * Existing resources may lack comprehensive, unified data access.

Purpose of the Study:

  • * To describe the features and utility of Xenbase, a Xenopus model organism database.
  • * To guide researchers in utilizing Xenbase tools for data retrieval and analysis.
  • * To highlight Xenbase's role in consolidating genomic, genetic, and reagent information.

Main Methods:

  • * Web-based integration of genomic, transcriptomic, and phenotypic data.
  • * Development of bioinformatic tools for sequence analysis and comparative genomics (e.g., BLAST, GBrowse).
  • * Curation of gene expression patterns, functional annotations (Gene Ontology), and disease associations.
  • * Maintenance of the Xenopus Anatomy Ontology (XAO) for developmental studies.
  • * Compilation of reagent catalogs (antibodies, clones, morpholinos, transgenic lines).

Main Results:

  • * Xenbase provides access to current and archived genomes for X. laevis and X. tropicalis.
  • * Offers manually curated gene expression data, functional information, and disease links.
  • * Includes tools for sequence retrieval, gene expression pattern identification, and literature searches.
  • * Facilitates access to a wide range of research reagents and downloadable datasets, including gene-disease mapping files.

Conclusions:

  • * Xenbase serves as a vital, centralized resource for the Xenopus research community.
  • * Its integrated data and tools streamline research workflows and facilitate discoveries.
  • * Xenbase enhances comparative genomics and understanding of gene function and disease in Xenopus.