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Reading Alignments (overlapping genes?)

alignment gene blast

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5 replies to this topic

#1 Manaka

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Posted 03 April 2018 - 10:43 AM

Hello there! 

 

Can somebody please help me read this graphic? (see attached file)

 

It seems like when expressing the ELOVL1 gene, the mir6734 is being expressed as well in experiments. 

 

Does this mean the ELOVL1 and mir6734 gene are overlapping? They have obviously sequence- similarities, but I don't quite understand if the mir-gene "sits" on the ELOVL1? 

 

Hopefully someone can help me out! 

 

Thank you a lot! 

 

 

 

 

 

Attached Thumbnails

  • ELOVL1 mir.png

Edited by Manaka, 03 April 2018 - 10:44 AM.


#2 bob1

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Posted 03 April 2018 - 02:10 PM

Looks like it - note that the designation miR usually indicates a microRNA, which are silencing RNAs.



#3 El Crazy Xabi

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Posted 03 April 2018 - 09:10 PM

If they are genes and not the mature transcripts, the miR can easily be sitting in an intron of ELOVL1.

Non-protein coding genes and repetitive elements are not rare in introns.



#4 Manaka

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Posted 04 April 2018 - 12:37 AM

Thank you very much for your answers! 

 

It seems like they are genes, IMO. Both sitting on Chr1. 

 

https://rgd.mcw.edu/...html?id=1349015

 

Yes you're right bob1. I found out they play a role in decreasing cell-proliferation mechanisms. 

 

Would you guys says one could argue that when expressing ELOVL1, miR6734 is being expressed as well just because it's "sitting in" the ELOVL1 gene?

 

https://www.ncbi.nlm...CF_000001405.38



#5 bob1

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Posted 04 April 2018 - 06:30 AM

I would argue not necessarily. miRNA and all the other silencing RNAs have independent activation and "expression" mechanisms and I think this is independent of the host gene too. There's bound to be a good review on the mechanisms around that would help you determine if this is likely. There will also be ways to test it experimentally - which is what should happen if you make any claims about expression.



#6 Manaka

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Posted 05 April 2018 - 03:13 AM

After some research it seems rather hard for me finding expression patterns of this miRNA. 

 

Additionally I can tell you that the expression of the ELOVL genes is being measured and for some reason, MIR6734 always is enlisted in the ELOVL gene expression too.

 

Therefor it might be another marker, since the expression might be linked together. 







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