Finding a target gene sequence in rat genome using a mice gene - How to find the delta opioid receptor gene in rat if the sequence is k (Oct/15/2007 )
Hi, I need help! I am an undergrad student and have never used any bioinformatics before this, and now I'm completely clueless.
The delta opioid receptor gene is already mapped out in the mice genome and I am suppose to use that to make a proposal of the d.o.r gene in the rat genome. I looked up the mice gene and used BLASTn to compare its sequences to the rat genome, but I could not understand the results at all! I would be incredibly grateful if someone could help me to decipher the blastn results and tell me where to go from there. How to I find out where the TATA boxes are, where the promoters are, etc? Thank you!
-this is the d.o.r. gene in mice
you should use the protein sequence to identify homolog of the gene in rat because protein sequences are more conserved than nucleic acid sequences.
From the mRNA sequence you gave I got the protein sequence for your gene http://www.ncbi.nlm.nih.gov/entrez/viewer....?val=AAA16009.1
I used the protein sequence to query the rat genome database here http://genome.ucsc.edu/cgi-bin/hgBlat?comm...;hgsid=98643862
it turns out the mouse gene has 97% homology with rat and the result are here:
Hope that helps.
Thank you . But I'm still confused on how to find the promoter sites and start codons and such on the rat sequence. Maybe I'm just being dense, but I still appreciate your help.