Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.4K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.4K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

17.5K
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,...
17.5K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

11.3K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
11.3K
Genomics02:02

Genomics

38.9K
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...
38.9K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.2K
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...
11.2K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

3.7K
3.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Genome scale CRISPRi reveals both shared and strain-specific vulnerabilities in genetically diverse drug-resistant strains of Mycobacterium tuberculosis.

Nature communications·2026
Same author

Impaired retinoic acid receptor-γ signaling underlies a heritable form of urothelial keratinizing squamous metaplasia.

HGG advances·2026
Same author

Pervasive Transcription in the Human Genome Exceeds Background Noise.

Genome biology and evolution·2026
Same author

Towards a phylogenetically informed approach to solving protein-protein interactions.

Biochemical Society transactions·2025
Same author

Evaluating computational tools for protein-coding sequence detection: Are they up to the task?

RNA (New York, N.Y.)·2025
Same author

A bioinformatician, computer scientist, and geneticist lead bioinformatic tool development-which one is better?

Bioinformatics advances·2025
Same journal

Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.

Database : the journal of biological databases and curation·2026
Same journal

KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.

Database : the journal of biological databases and curation·2026
Same journal

PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.

Database : the journal of biological databases and curation·2026
Same journal

A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs.

Database : the journal of biological databases and curation·2026
Same journal

GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.

Database : the journal of biological databases and curation·2026
Same journal

Rosetta Statements: simplifying FAIR knowledge graph construction with a user-centred approach.

Database : the journal of biological databases and curation·2026
See all related articles

Related Experiment Video

Updated: Nov 28, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.4K

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls.

Harry Biggs1, Padmini Parthasarathy1, Alexandra Gavryushkina1,2

  • 1Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.

Database : the Journal of Biological Databases and Curation
|December 1, 2020
PubMed
Summary
This summary is machine-generated.

This study presents ncVarDB, a curated database of 721 non-coding human genome variants linked to phenotypic consequences. This resource aids in understanding non-coding variant function and developing predictive algorithms.

More Related Videos

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.4K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.1K

Related Experiment Videos

Last Updated: Nov 28, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.4K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.4K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.1K

Area of Science:

  • Genomics
  • Bioinformatics
  • Human Genetics

Background:

  • Non-coding genome variants are frequently linked to phenotypes in genome-wide association studies.
  • These regions play crucial roles in gene expression regulation, functional non-coding RNA encoding, and splicing.
  • Understanding the functional impact of non-coding variants is essential for genetic research.

Purpose of the Study:

  • To curate and present a comprehensive database of characterized non-coding human genome variants with documented phenotypic consequences.
  • To provide a reliable resource for training and evaluating algorithms that predict non-coding variant functionality.
  • To facilitate research into the functional roles of the non-coding genome.

Main Methods:

  • Curated a list of 721 non-coding variants based on published evidence of phenotypic consequences.
  • Independently verified supporting evidence for pathogenicity by two curators to minimize annotation errors.
  • Sampled 7228 covariate-matched benign controls from dbSNP151, controlling for linkage, annotation type, and variant type.

Main Results:

  • Established ncVarDB, a repository of 721 curated non-coding variants with supporting literature.
  • Included 7228 carefully selected benign control variants to ensure data quality and comparability.
  • The dataset is available at https://github.com/Gardner-BinfLab/ncVarDB.

Conclusions:

  • The ncVarDB provides a valuable, curated dataset for advancing the study of non-coding variant function.
  • This resource can significantly aid in the development and validation of computational tools for predicting variant pathogenicity.
  • Facilitates deeper insights into the contribution of non-coding variants to human phenotypes.