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Defective mRNA splicing can lead to multiple alternative transcripts including those with retained introns, cassette exons, alternate promoters/terminators, extended or truncated exons, and reduced exons.
The probes are 60-mers, mostly mapped within 1500 bases of the 3' end of the source transcript, and were designed to match common regions of multiple alternative transcripts for a particular gene.
In addition to unique probe sets, the Affymetrix GeneChip® consists of non-unique probe sets that recognize multiple alternative transcripts from the same gene (probe set type, "_a"), and probe sets with common probes among multiple transcripts from separate genes ("_s" suffix) (Affymetrix, 'Array Design and Performance of the GeneChip® Rat Expression Set 230').
Many genes have multiple alternative transcripts with a different TSS.
The extended NAT2 gene is much simpler than the multiple alternative transcripts of human NAT1.
For genes with multiple alternative transcripts we used the longest transcripts as the representative ones.
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Several species have multiple gene/transcript identifiers within the three main subtrees indicating the presence of either multiple alternative transcript isoforms or distinct close paralogous genes.
Multiple alternative mRNA transcripts were also identified experimentally from normal tissues and from prostate cell lines and a chondrosarcoma cell line, indicating that the ghrelin gene has a complex transcriptional pattern.
Note that the creation of annotations.gff' goes beyond simple interval intersection, as gene structures are normalized from multiple possible alternative transcripts to a single transcript that is chosen by the user depending on what is most relevant for the analysis.
Second, to account for the possibility that multiple tags represent alternative transcripts, we estimated transcript abundance based solely on the 3′-most position of the sense strand, or its matched position on the antisense strand (Additional file 1: Figure S6b).
Annotations are grouped if they represent multiple entries for the same variant (for example, alternative transcripts, multiple entries in ClinVar).
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many alternative transcripts
multiple alternative trees
multiple alternative theories
multiple alternative pathways
multiple alternative outcomes
multiple alternative performances
multiple alternative runs
multiple alternative designs
multiple alternative terms
multiple alternative annotations
multiple alternative sequences
multiple alternative splice-forms
multiple alternative workflows
multiple alternative explanations
multiple alternative exons
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