What are splice reads?
splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events. splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
What is splice branch point?
During splicing, the branch point nucleotide initiates a nucleophilic attack on the 5′ donor splice site. The free end of the upstream intron then initiates a second nucleophilic attack on the 3′ acceptor splice site, releasing the intron as an RNA lariat and covalently combining the two exons (53).
What Is percent spliced in?
The exon-inclusion ratio, also known as percent spliced in (PSI), is a popular statistic for measuring alternative splicing events (2). It is defined as the ratio of the relative abundance of all isoforms containing a certain exon over the relative abundance of all isoforms of the gene containing the exon.
Where are splice sites located?
Introns are removed from primary transcripts by cleavage at conserved sequences called splice sites. These sites are found at the 5′ and 3′ ends of introns. Most commonly, the RNA sequence that is removed begins with the dinucleotide GU at its 5′ end, and ends with AG at its 3′ end.
What happens if 5 splice site is mutated?
A genetic alteration in the DNA sequence that occurs at the boundary of an exon and an intron (splice site). This change can disrupt RNA splicing resulting in the loss of exons or the inclusion of introns and an altered protein-coding sequence. Also called splice-site variant.
What are paired end reads?
The term ‘paired ends’ refers to the two ends of the same DNA molecule. So you can sequence one end, then turn it around and sequence the other end. The two sequences you get are ‘paired end reads’.
What is spliced alignment?
A spliced alignment is an alignment of a partial or full length spliced transcript sequence against an unspliced genomic sequence [1]. A spliced alignment allows to highlight the boundaries and the alignment of exons of the transcript sequence on the genomic sequence.
How does exon skipping work?
How does exon skipping work? Exon skipping uses small drugs called antisense oligonucleotides to help cells skip over a specific exon during splicing. This allows cells to join a different set of exons together to produce a protein that is shorter than usual but may have some function.
What is a PSI value splicing?
The percent spliced in index (PSI) indicates the efficiency. of splicing a specific exon into the transcript population of a gene. A PSI of. 1 indicates constitutive exons that are included in all transcripts and never. removed.
When does the junctions track Call a splicing event?
The junctions track calls a splicing event when at least a single read splits across two exons in the alignment track. The junctions track calls a splicing event when at least a single read splits across two exons in the alignment track.
How do I view the coverage of a splice junction?
Hovering the mouse over or clicking on a junction will display coverage information. The first screenshot shows multiple coverage detail panels for each three components of two splice junctions on opposite strands.
What is splice junction track in IgV?
When enabled, IGV dynamically computes the junctions track from alignment data. The junctions track displays arcs connecting alignment blocks from a single read. For RNA data these connections normally arise from splice junctions, thus the name Splice Junction Track.
What is a splicing event in IgV?
Splice Junctions Track. The junctions track calls a splicing event when at least a single read splits across two exons in the alignment track. IGV defines exons by your sample’s read alignments. IGV does not use the mate inner distance of paired reads for junctions.