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Related Concept Videos

Organization of Genes02:07

Organization of Genes

Overview
Organization of Genes02:07

Organization of Genes

Overview
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jun 6, 2026

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast
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ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

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Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they

Miguel A Fuertes1, José M Pérez, Emile Zuckerkandl

  • 1Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain. mafuertes@cbm.uam.es

Journal of Molecular Evolution
|December 7, 2010
PubMed
Summary

Human gene sequences exhibit non-random compositional patterns, forming distinct clusters. These compositional clusters are conserved across species, revealing insights into gene sequence organization and evolution.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast
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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Understanding gene sequence composition is crucial for deciphering genomic function.
  • Existing methods often overlook sequence context and reading frame independence.
  • Human and mouse gene sequences offer a comparative model for evolutionary studies.

Purpose of the Study:

  • To analyze compositional properties of human gene sequences independent of reading frame.
  • To develop a novel coding system for DNA sequence analysis.
  • To investigate the conservation of compositional patterns across species.

Main Methods:

  • Developed a neighbor base dependent coding system compressing 64 DNA triplets into 14 'triplet composons'.
  • Analyzed overlapping DNA sequences using triplet composon usage frequencies.
  • Compared compositional clusters between human and mouse homologous genes.

Main Results:

  • Human gene sequences show significant deviation from random composition, even in non-coding regions.
  • Identified distinct compositional clusters within human coding sequences.
  • Intron sequences within a cluster share similar composon usage frequencies, despite differing base composition.
  • Discovered species-specific compositional clusters (two in humans absent in mice) and conserved clusters between human and mouse genes.

Conclusions:

  • Gene sequences possess inherent compositional biases that are not random.
  • Triplet composon analysis reveals a structured organization within gene sequences, forming stable clusters.
  • Compositional patterns are evolutionarily conserved, providing insights into gene regulation and function across species.