understand the gene result in ncbi

Question

[pingu77]

Hello!

I am trying to understand how to interpretate the gene information in ncbi website. I cannot understand what are the difference between those two results (I typed the gene name and those are the first 2 results I get):

https://www.ncbi.nlm.nih.gov/nuccore/AH008362.2

https://www.ncbi.nlm.nih.gov/nuccore/AF091214.1

Both webpages should be related to the same gene. However, it looks like that the second result is just the cdna and the first one the full sequence. Is it correct?

thank you in advance

[Andrzej Zielezinski]

If you're looking for information about genes on the NCBI website, the best place to go is the "Gene" database (https://www.ncbi.nlm.nih.gov/gene/7486).

Answer 1

[Mensur Dlakic]

Not sure what is unclear as everything is laid out in those records. The first record is ~180 kB of chromosome 8 genomic DNA, while the second is a processed mRNA transcript with 5' and 3' UTR regions. The summary is in the first two lines (LOCUS & DEFINITION).

[pingu77]

thank you for the help! so the first one if the complete DNA sequence.

But why is it specified in both that the cds is complete? Are there any other options? (this is my first time I searching for genes/sequence in ncbi).

Also, if I want to get the cds sequence, can I use the sequence in the second link (mRNA transcript), remove 5'/3' UTR region and take the complementary sequence? or is there a better way to do this?

Thank you again!

[Mensur Dlakic]

You can use the mRNA transcript as is, without converting to complementary sequence. That is the meaning of CDS in mRNA transcript - it literally represents processed mRNA which is translated into a protein.

The coding region of the gene is specified by this line:

CDS             232..4530

That means first 231 bases and everything after base 4530 are UTR regions to be removed.

[pingu77]

thank you! But should I have to convert it if I want to get the cDNA, right?

[Mensur Dlakic]

The first strand of cDNA to be synthesized is complementary to mRNA, but eventually both strands are made because we are talking about DNA. You don't need to do anything to convert mRNA to cDNA. It only signifies its difference from genomic DNA in that it doesn't contain introns, as it is made from processed mRNA transcripts.

https://www.genome.gov/genetics-glossary/Copy-DNA