Seeking House keep gene under 200nt - (Jun/13/2006 )
Hello! Everyone.
I would like to use Real Time-PCR for miRNA detection. I have several miRNAs that I am interested in. Now I try to seek house keep gene which's transcript length is under 200 nt. This gene wiil be used as a control.
Do you have any idea?
Any suggestion is well appreciated.
I would like to use Real Time-PCR for miRNA detection. I have several miRNAs that I am interested in. Now I try to seek house keep gene which's transcript length is under 200 nt. This gene wiil be used as a control.
Do you have any idea?
Any suggestion is well appreciated.
U6 or 5.8S or 5S rRNA
Dear Rye,
Thank you very much for the help!
Now I have two additional questions:
1). what is U6? is it a snRNA?
2). When chose between U6, 5.8S and 5S rRNA, does species make any difference, for example rat and mouse?
Thanks again! 
Thank you very much for the help!
Now I have two additional questions:
1). what is U6? is it a snRNA?
2). When chose between U6, 5.8S and 5S rRNA, does species make any difference, for example rat and mouse?
Thanks again!
Yes U6 is a snRNA, see following link for its conservation across species
http://mips.gsf.de/proj/yeast/reviews/intron/snRNA_U6.html
I not clear with rat and mouse, but I found Ambion provide different primer set for U6 and 5S rRNA used for rat and mouse, without sequence of their primers, I am not sure they are the same or not.
http://www.ambion.com/catalog/supp/Ambion_primer_sets.xls
you'd better check sequence from NCBI if you hope design your primers
How long is the U6 sequence in mouse? How long for human?
The U6 sequence I find on NCBI for mouse is 108nt.
The one for humans is 45nt and it is actually called "U6b"
The human U6b sequence matches the last 45nt of the 108nt of mouse.
Thank you for your great help!
I really appreciate it. 