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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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 (lncRNA)...
lncRNA - Long Non-coding RNAs02:39

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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

Dapeng Wang1, Yubin Zhang, Zhonghua Fan

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China.

Evolutionary Bioinformatics Online
|January 24, 2012
PubMed
Summary
This summary is machine-generated.

LCGbase is a new database detailing animal gene clusters in vertebrates and arthropods. It aids research into gene co-regulation and evolutionary dynamics, offering tools for analysis and comparison across species.

Keywords:
co-regulated genesdatabaseevolutionvertebrate

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Animal genes are organized into dynamic chromosomal structures crucial for development and differentiation.
  • Gene clustering is a common genomic feature, exhibiting evolutionary stability and biological significance across lineages.
  • Understanding gene organization, minimal cluster size, and co-regulation drivers remains an ongoing challenge.

Purpose of the Study:

  • To introduce LCGbase, a user-friendly database for lineage-based co-regulated genes.
  • To provide insights into the evolutionary dynamics of gene clustering and ordering in vertebrates and arthropods.
  • To facilitate research on gene co-regulation and chromosomal structures.

Main Methods:

  • Developed a web-based database (Linux-Apache-MySQL-PHP) for gene cluster information.
  • Included comprehensive genome assemblies for vertebrates and representative arthropod species.
  • Mapped gene clusters from various species onto the human genome, defining clusters from gene pairs to larger structures.

Main Results:

  • LCGbase offers an inclusive collection of vertebrate and arthropod genome assemblies.
  • The database provides a human-centric view, mapping gene clusters across lineage ranks.
  • Users can search for adjacent genes, define flexible parameters, and access tools for sequence alignment, GO annotation, and evolutionary analysis.

Conclusions:

  • LCGbase enables the definition of lineage-specific and species-specific gene clusters.
  • The database supports future studies on gene co-regulation, epigenetic control, and chromosomal evolution.
  • LCGbase is a valuable resource for comparative genomics and evolutionary studies.