How are genes and transcripts organized?
A gene usually has multiple transcripts. What makes these transcripts assigned/organized/aggregated into one gene? Why are the two genes overlapping on the chromosomes not assigned to one gene?
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This is not a bioinformatics question, but anyway, what it makes a gene a gene is a serial of structural elements, such as a promoter region upstream the gene, start and stop codons among others.
This wiki gives you a good insight.
António