Can RNA-seq detect splice variants?

Can RNA-seq detect splice variants?

RNA-seq allows not only the validation or invalidation of effects on splicing of variants of unknown significance16 but also allows the detection of de novo aberrant splicing events transcriptome-wide, including the activation of deep intronic cryptic splice sites16,17,19.

What is meant by splice variant?

Listen to pronunciation. (… VAYR-ee-unt) A genetic alteration in the DNA sequence that occurs at the boundary of an exon and an intron (splice site).

How do you identify a splice variant?

How to Detect Alternative Splicing Variants

  1. Semi-quantitative PCR. One approach involves a semi-quantitative RT-PCR to analyze alternatively spliced products.
  2. Real-time qPCR.
  3. Challenges to detecting AS events.

Why are splice variants important?

Splice variants play an important role within the cell in both increasing the proteome diversity and in cellular function. Splice variants are also associated with disease states and may play a role in their etiology.

How do you analyze alternative splicing?

Alternative splicing analysis consists of three main steps: detection, statistical comparison, and effect prediction. Here we leverage an existing tool for detection and implement new methods for the statistical analysis and effect prediction steps.

How is alternative splicing regulated?

Splicing is regulated by trans-acting proteins (repressors and activators) and corresponding cis-acting regulatory sites (silencers and enhancers) on the pre-mRNA.

What is the purpose of gene splicing?

Thus, gene splicing enables a single gene to increase its coding capacity, allowing the synthesis of protein isoforms that are structurally and functionally distinct. Gene splicing is observed in high proportion of genes. In human cells, about 40-60% of the genes are known to exhibit alternative splicing.

What does intron variant mean?

Intronic variants can impact alternative splicing by interfering with splice site recognition. For example, an intronic mutation near the 5′-splice site of exon 20 in the IKBKAP gene causes skipping of exon 20, resulting in malfunction of IKBKAP in 99.5% of familial dysautonomia (FD) cases [8, 22, 23].

What is the difference between splicing and alternative splicing?

The main difference between RNA splicing and alternative splicing is that the RNA splicing is the process of splicing the exons of the primary transcript of mRNA whereas the alternative splicing is the process of producing differential combinations of exons of the same gene.

Why is RNA splicing necessary?

In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.

What is RNA splicing and why is it important?

RNA splicing is a process that removes the intervening, non-coding sequences of genes (introns) from pre-mRNA and joins the protein-coding sequences (exons) together in order to enable translation of mRNA into a protein.

What is alternative polyadenylation?

Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that processes RNA products depending on its 3′-untranslated region (3′-UTR) specific sequence signal.

What are the different types of alternative splicing?

Five main types of alternative splicing events are depicted. (A) Constitutive splicing; (B) mutually exclusive exons; (C) cassette alternative exon; (D) alternative 3′ splice site; (E) alternative 5′ splice site; and (F) intron retention.

How does mRNA splicing work?

During the process of splicing, introns are removed from the pre-mRNA by the spliceosome and exons are spliced back together. If the introns are not removed, the RNA would be translated into a nonfunctional protein. Splicing occurs in the nucleus before the RNA migrates to the cytoplasm.

What is RNA splicing simple?

RNA splicing is a biological process where a newly synthesized pre-mRNA transcript is processed and transformed into mRNA. It involves the removing of non-coding regions of RNA (introns) and the joining of the coding regions (exons).

How do introns variants affect gene expression?

Intron variants could also be relevant as enhancers that could act on the gene they are found in or could possibly enhance the expression of many genes. For that you can look at predicted protein binding sites and see if there is any differential binding for a specific protein. This should all be done with caution.

What is intron and Extron?

Introns are noncoding sections of an RNA transcript, or the DNA encoding it, that are spliced out before the RNA molecule is translated into a protein. The sections of DNA (or RNA) that code for proteins are called exons.

Is RNA splicing and alternative splicing the same?

What does transcript variant mean?

Many genes have more than one transcript due to alternative splicing. We refer to the various transcripts (splice variants) for a particular gene as transcript variants.