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Related Concept Videos

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

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)...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

Pieter-Jan Volders1, Kenny Helsens, Xiaowei Wang

  • 1Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.

Nucleic Acids Research
|October 9, 2012
PubMed
Summary
This summary is machine-generated.

LNCipedia is a new database featuring 21,488 human long non-coding RNA (lncRNA) transcripts and genes. This resource provides comprehensive data, including secondary structures and protein coding potential, to advance lncRNA research.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNA genes with largely uncharacterized functions.
  • Multiple high-throughput studies have generated fragmented lncRNA datasets, hindering comprehensive analysis.
  • A unified and curated resource is needed to facilitate lncRNA research.

Purpose of the Study:

  • To present LNCipedia, a novel, comprehensive database for human long non-coding RNA (lncRNA) transcripts and genes.
  • To integrate diverse lncRNA data, including transcript information, gene structure, secondary structures, protein coding potential, and microRNA binding sites.
  • To provide a publicly accessible platform for querying and downloading lncRNA data to support research.

Main Methods:

  • Compilation of 21,488 annotated human lncRNA transcripts from various sources.
  • Assessment of secondary structure, protein coding potential using CPC and HMMER, and microRNA binding sites for each lncRNA.
  • Integration of mass spectrometry data from PRIDE to identify potentially coding lncRNAs.
  • Development of a web interface for data submission and literature linking.

Main Results:

  • LNCipedia provides a centralized repository of 21,488 human lncRNA transcripts.
  • Analysis reveals that many lncRNAs possess significant secondary structures, suggesting functional roles.
  • Protein coding potential is assessed, and potentially coding lncRNAs are identified using novel strategies.
  • The database links to available literature and allows user submissions.

Conclusions:

  • LNCipedia serves as a valuable resource for initiating and conducting lncRNA studies.
  • The database facilitates exploration of lncRNA structure, function, and coding potential.
  • LNCipedia supports the advancement of long non-coding RNA research through integrated data and accessibility.