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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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lncRNA - Long Non-coding RNAs02:39

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Related Experiment Video

Updated: Sep 9, 2025

Identification of Circular RNAs using RNA Sequencing
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Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

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Online Databases in Circular RNAs.

Sachiko Kuwamoto-Imanishi1, Hodaka Fujii2

  • 1Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori Prefecture, Japan.

Advances in Experimental Medicine and Biology
|August 31, 2025
PubMed
Summary
This summary is machine-generated.

Circular RNAs (circRNAs) are valuable biomarkers for diseases like cancer. Numerous databases now aid in identifying these non-coding RNAs (ncRNAs) and their functions.

Keywords:
BioinformaticsConservationDatabasesDisease associationFunction annotationInteractomeOntologySequence annotationcircRNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) recognized for their role in gene regulation and potential as disease biomarkers.
  • Their ability to act as sponges for ncRNAs and proteins, coupled with detectability in bodily fluids, highlights their clinical significance.
  • The development of specialized databases has facilitated the identification and study of circRNAs.

Purpose of the Study:

  • To provide a comprehensive overview of existing circRNA databases.
  • To introduce newly available circRNA databases and discuss their features.
  • To address challenges in circRNA database nomenclature and maintenance.

Main Methods:

  • Review and summarization of established circRNA databases (e.g., Circ2Traits, circBase).
  • Introduction of newly cataloged circRNA databases from Database Commons.
  • Discussion of database content, including annotation, interaction data, disease associations, and expression profiles.

Main Results:

  • Over 43 circRNA databases have been established since 2013, with many offering detailed annotations and interaction data.
  • Databases now incorporate RNA sequencing data and curated literature, simplifying circRNA exploration across diverse species, including plants.
  • Key databases like Circ2Traits, circBase, CircInteractome, CircNet, CircR2Disease, TSCD, and CSCD are highlighted.

Conclusions:

  • A growing number of circRNA databases are available, supporting research into their roles in various biological processes and diseases.
  • These resources facilitate the identification of circRNAs as potential biomarkers, particularly in oncology.
  • Ongoing efforts are needed to standardize nomenclature and ensure the continuous updating of these valuable bioinformatics tools.