Hello,
I recently tried to get the mRNA sequence of WIP1/PPM1D gene from NCBI, but it does not contain uracils. Therefore I thought the listed mRNA sequence was actually a cDNA. So I used BLAST to compare the mRNA sequence on NCBI with the DNA sequence and it was perfect match, proving that it is indeed a cDNA. Later, though, I found this: http://www.genecopoeia.com/product/search/view_features.php?cid=&prod_id=Q0156
It is again a cDNA of WIP1, but as you can see at " CDS length1818 (see ORF)" the ORF starts with ATG. I tried to do some research on google but managed to find only controversial opinions and they were not informative enough. That is why I wanted to ask how can ATG in a cDNA be transcribed as AUG or serve as start codon in ORF? From what I have read AUG is mainly used as initiation codon in eukaryotes and ATG can not be transcribed as AUG but UAC, which encodes tyrosine, and the initiator amino acid should be methionine.
The only way this can make a sense to me is that actually the mRNA sequence on NCBI is the actual mRNA with thymine in place of uracil, which I do not understand why would they do it like this, but then that arises a new problem - if it is the actual mRNA with thymine in place of uracil, it should not match the correspoding DNA sequence listed on NCBI, when I compare them, but as I already said, it matches, meaning it is not just complementary but the SAME(cDNA).
I tried Rfam as well, but the situation there is the same as with NCBI. So I am really confused and would very much appreaciate it if someone can explain me this situation. How can I find the actual mRNA sequence for a particular gene of interest?
Edit:
Nevermind, I have just found the answer. I will put the link here in case someone like me have the same or similar problem:
http://www.biology-pages.info/C/Codons.html
" These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of DNA (3' to 5') as the template "
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