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Related Concept Videos

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Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Updated: Mar 11, 2026

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ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Alessandro Gorohovski1, Somnath Tagore1, Vikrant Palande1

  • 1Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.

Nucleic Acids Research
|December 1, 2016
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Summary

The ChiTaRS-3.1 database now offers enhanced access to chimeric RNA data, including predicted protein interactions and cross-references, aiding transcriptome research. This resource supports the study of complex chimeric transcripts and fusion proteins across eight organisms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Chimeric RNAs, arising from translocations or trans-splicing, increase transcriptome complexity.
  • Understanding these RNAs is crucial for advancing molecular and cancer research.

Purpose of the Study:

  • To enhance the ChiTaRS database with new features and expanded data.
  • To provide a centralized, user-friendly resource for chimeric RNA research.

Main Methods:

  • Data mining and curation of chimeric transcripts and cancer breakpoints.
  • Integration of cross-references to multiple biological databases (GeneCards, PubMed, etc.).
  • Development of a Chimeric Protein-Protein Interaction (ChiPPI) network prediction tool.

Main Results:

  • The ChiTaRS-3.1 database now contains 34,922 chimeric transcripts and 11,714 cancer breakpoints.
  • New features include extensive cross-references and predicted ChiPPI networks for human chimeras.
  • The database includes manual annotation of 200 sense-antiSense (SaS) chimeras across eight organisms.

Conclusions:

  • The enhanced ChiTaRS-3.1 database serves as a comprehensive central resource for studying chimeric transcripts and fusion proteins.
  • Improved functionality and data integration facilitate research in transcriptomics and related fields.