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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!

Anna

http://www.ncbi.nlm.nih.gov/entrez/viewer....e&id=S65335
-this is the d.o.r. gene in mice

-anna1028-

Hi,

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:
http://genome.ucsc.edu/cgi-bin/hgTracks?hg...79448-151013961.

Hope that helps.

-pcrman-

Thank you smile.gif . 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.

-anna1028-