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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
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...
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Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
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Transcription Factors02:16

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Transcription Elongation Factors02:35

Transcription Elongation Factors

14.1K
Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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Related Experiment Video

Updated: Feb 10, 2026

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

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Interactive web-based identification and visualization of transcript shared sequences.

Alaleh Azhir1, Louis-Henri Merino2, David W Nauen3

  • 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

Genomics
|May 16, 2018
PubMed
Summary
This summary is machine-generated.

We developed TraC (Transcript Consensus), a free web tool to find and visualize shared sequences in mRNA transcripts. This tool helps researchers explore similarities and differences between splice variants with interactive plots.

Keywords:
Alternative splicingRNASplice variantVisualization

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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Understanding transcript sequence similarity is crucial for analyzing gene expression and function.
  • Identifying shared sequences among mRNA splice variants aids in functional annotation and comparative genomics.

Purpose of the Study:

  • To introduce TraC (Transcript Consensus), a novel web-based tool for detecting and visualizing shared sequences within multiple mRNA transcripts.
  • To provide researchers with an intuitive platform for exploring transcript similarities and differences, particularly for splice variants.

Main Methods:

  • Development of a web-based application, TraC, for sequence analysis.
  • Implementation of algorithms to detect and visualize shared sequences and exon-exon boundaries among transcripts.
  • Creation of interactive, data-rich plots for user exploration.

Main Results:

  • TraC successfully identifies and visualizes shared sequences among multiple mRNA transcripts.
  • The tool generates intuitive plots highlighting exon-exon boundaries and sequence similarities/differences.
  • Results are presented in an interactive format for detailed analysis.

Conclusions:

  • TraC offers a valuable, free resource for researchers studying mRNA transcript variation.
  • The tool facilitates the exploration of transcriptomes, aiding in the understanding of gene regulation and function.
  • Availability of the web tool and source code promotes accessibility and further development in transcript analysis.