Hey,
I really do not get your question. What exactly are you looking at? If you look at the reference sequence, it is stated as three letter code, as well as the usual mRNA e.g. www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Search&doptcmdl=GenBank&term=NM_000533.5 which is a reference mRNA. Uracil and thymine both have the same three letter code and only differ in the one letter code with U and T differentiating between DNA and RNA. The question I have now is, why should anybody denote the reference sequences as one letter code in which no one can identify any mutations/SNPs. Therefore it is clear to use the three letter code where you do not have a difference between those two.
Hope this helps. Maybe you can provide more information if not.
Regards,
André
André Marquardt
Thank you to answer my question. Maybe I should describe my question more.
Putting T instead of U in the RNA sequence at NCBI has led to the notion that the sequence that NCBI represents as RNA is cDNA. If it is cDNA, to use this RNA for bioinformatics work, its complementary strand must first be created and then used. This question has been asked by another person before me. But it didn't answered right. https://www.researchgate.net/post/How_to_obtain_a_proper_mRNA_sequence_of_a_gene_from_NCBI
I know NCBI Put T instead of U in the RNA sequence and sequences are not cDNA.But I think it should have a reason. I want to know that reason. Way NCBI does not use U in RNA sequences ?
Hey,
thank you for clarifying your question. The answer still is the same, there is, in a reference sequence, no difference for the three letter code between U and T. The answer of the question you quoted is stating this as well:
" 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 "
Still, you are right considering the antisense strand. The reason will mainly be convention from the beginnings of the database.
Hope this helps.
Regards,
André
To study with PCR the genome of RNA viruses we reverse transcribe RNA to DNA. So we "transcribe" its RNA in DNA sequences and so instead of uracil you find thymine.
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