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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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Human Genetics01:28

Human Genetics

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Updated: Oct 30, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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REVA as A Well-curated Database for Human Expression-modulating Variants.

Yu Wang1, Fang-Yuan Shi1, Yu Liang2

  • 1State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China.

Genomics, Proteomics & Bioinformatics
|July 5, 2021
PubMed
Summary
This summary is machine-generated.

Researchers created REVA, a database of over 11.8 million experimentally validated noncoding variants that affect gene expression. This resource aids in understanding noncoding genetic variations linked to diseases and traits.

Keywords:
BenchmarkDatabaseExpression-modulating variantMassively parallel reporter assayNoncoding variant

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Over 90% of human variants associated with diseases and traits reside in noncoding DNA regions.
  • Understanding the functional impact of these noncoding variants is crucial for disease mechanism elucidation.
  • Current computational tools have limitations in accurately identifying expression-modulating noncoding variants.

Purpose of the Study:

  • To compile a comprehensive, manually curated database of experimentally tested noncoding variants.
  • To provide functional annotations to elucidate the regulatory mechanisms of noncoding variants.
  • To benchmark existing computational tools for noncoding variant analysis.

Main Methods:

  • Systematic screening of multiple large-scale studies to identify relevant noncoding variants.
  • Manual curation of variants with experimentally validated expression-modulating potentials.
  • Development of functional annotations to interpret variant effects.
  • Benchmarking of state-of-the-art computational tools for variant analysis.

Main Results:

  • Compilation of REVA, a database containing over 11.8 million experimentally tested noncoding variants.
  • Inclusion of 2424 functional annotations to pinpoint regulatory mechanisms.
  • Demonstration of limited sensitivity in current computational tools for large-scale noncoding variant analysis.

Conclusions:

  • REVA offers a high-quality resource of experimentally validated expression-modulating noncoding variants.
  • The database and its annotations will significantly benefit researchers studying noncoding variants.
  • The findings highlight the need for improved computational methods for noncoding variant interpretation.