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transcript variant X - (Sep/19/2013 )


Do you know what is the meaning of transcript variant X?

Some genes have transcript variant X.


In what context?  Usually X implies an unknown in mathematics, but I suspect in this case they are referring to a known variant that they have called "X" in the paper you are reading.


I have seen it a lot during Primer Designing:

Lets check a pair of primers for ACTB:


Copy and Past these primers there:



Then click on "Get Primer". Now you see this link:


Which has these links below:



There is really little information about the nomenclature of "transcript variant Xn" on NCBI site. I guess they represent variants of all model mRNA (predicted mRNAs) refseqs. In the example of ACTB, there are 3 model RefSeqs (XM_005249819.1XM_005249820.1, and XM_005249818.1), corresponding to transcript variant X1, X2 and X3. So from this example, it is clear to me that "transcription x" is one of the model RefSeqs for a particular gene. 


The link given by Bob above tells the differences between model refseq (XM_xxxxxxxx) and experimentally derived refseq (NM_xxxxxxx).


pcrman: I thought that was the difference between the X variants and other sequences - they were predicted rather than experimental - could easily be wrong though, don't need to use the NCBI database to that extent very often, so still learning myself.