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From this image enter image description here

We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it possible for alternative splicing to behave like this? I only know that alternative splicing is just exon skipping and introns will just stay introns and not become exons. Can someone explain this to me and give any suggestions on which part of biology (or genetics) I need to learn. Thank you.

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    $\begingroup$ I'm not sure what you're asking. If a portion of sequence ends up in the mature RNA, it is by definition not an intron. $\endgroup$ – canadianer Apr 27 '15 at 2:02
  • $\begingroup$ Hmm, you are right. So, do you think from that picture, it's just exon skipping? What does that kind of gene called? Is it still called isoform? I have a hard time to do RNA-seq analysis for this gene because of overlap position near the end can be mapped to 9 gene. $\endgroup$ – Bharata Apr 27 '15 at 2:10
  • $\begingroup$ Just did some brief reading. It seems each form is under the control of its own promoter. This means that A8 will have to splice out the first exons of all other forms (this would be exon skipping). On the other hand, the A1 pre-mRNA doesn't contain any other first exons to begin with. These would be classified as gene isoforms. $\endgroup$ – canadianer Apr 27 '15 at 2:31
  • $\begingroup$ Thank you. Can you suggest where you read those explanation? My knowledge in biology is really limited so I need to read many material to improve my knowledge. $\endgroup$ – Bharata Apr 27 '15 at 2:36
  • $\begingroup$ ncbi.nlm.nih.gov/… $\endgroup$ – canadianer Apr 27 '15 at 2:40
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Most of the transcripts you show have different transcription start sites. In other words, this happens because of alternative transcription start sites. So this is not typical alternative slicing. Some genes have different transcriptional start sites, but the case you show has exceptionally many start sites.

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If a portion of sequence ends up in the mature RNA, it is by definition not an intron (save for abnormal splicing events and rare intron retention).

Specific to your question, it seems each form is under the control of its own promoter. This means that A8 will have to splice out the first exons of all other forms (this would be exon skipping). On the other hand, the A1 pre-mRNA doesn't contain any other first exons to begin with. These would be classified as gene isoforms

References:

Owens IS, Basu NK, Banerjee R. 2005. UDP-glucuronosyltransferases: gene structures of UGT1 and UGT2 families. Methods Enzymol 400:1-22.

NCBI Gene: UGT1

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