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CDS and mRNA - (Jan/17/2008 )

Hi All,

I am new to molecular biology and trying to figure out how one finds a cDNA sequence from database for cloning into expression vectors. I was looking for a human NADPH Cytochrome P450 reductase sequence and found this one on NCBI in core-nucleotide database,

http://www.ncbi.nlm.nih.gov/entrez/viewer....&id=9964002

The description for this sequence says "Homo sapiens NADPH-cytochrome P450 reductase mRNA, complete cds".

My questions are,

1. Do you find out cDNA sequence from mRNA sequence, if yes, how?
2. Is cds sequence and mRNA sequence same?
3. I tried locating the stop codon (in ORF) in above sequence but there are quite a few more nucleotides after stop codon, what are they?

I would appreciate if you guys could explain in detail.

Thanks

-exploresci-

Hi there!

1. Do you find out cDNA sequence from mRNA sequence, if yes, how?

The sequence given is the cDNA that could be generated from mRNA by reverse transcription. (there are "T" and no "U"). So what they give you is the cDNA.


2. Is cds sequence and mRNA sequence same?

When you access the page on PUBMED, the sequence they give is the complete mRNA, with the 5' and the 3' UTR. If you want only the coding sequence, you have to clic on the blue "CDS". It will redirect you to a PUBMED page with a shorter sequence, witch is only the complete coding sequence, from the start codon to the stop, without the UTRs.


3. I tried locating the stop codon (in ORF) in above sequence but there are quite a few more nucleotides after stop codon, what are they?

As I said, the original sequence contains the UTRs. So the nuclotides you see after the stop codon are not translated.

Hope this helps!

-Madrius-

Hi Madrius,

Thank you very much.

So even though the ncbi says it is mRNA sequence, it is not mRNA but cDNA sequence (Because there are Ts and no Us), is that right?

If one has to clone the gene in expression vector using a software and make a construct map, he/she will use the cds, add restriction sites at both the ends and use that sequence for cloning, is that right?

I am asking some very basic questions but please explain.

thanks again

-exploresci-

"So even though the ncbi says it is mRNA sequence, it is not mRNA but cDNA sequence (Because there are Ts and no Us), is that right?"

Yes, that's how I understood it.


"If one has to clone the gene in expression vector using a software and make a construct map, he/she will use the cds, add restriction sites at both the ends and use that sequence for cloning, is that right?"

That is correct.

-Madrius-

Thanks Madrius....

-exploresci-