Collecting Promoter Sequence of a Gene from NCBI Database

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6 жыл бұрын

In this video, we will teach you How to collect 5'(upstream) promoter sequence and also 3' downstream sequence of a gene. Here we have used the Ribosomal S15 gene as an example. We have extracted upstream sequence(-60) and downstream sequence upto +10. Learn the basics and explore on any gene of your choice.
Link for the video "Collecting promoter sequence of a Gene from Ensembl"
• Collecting promoter se...
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@rumanamehjabin8608 6 жыл бұрын

How to find those exact numbers of the nucleotides in the chromosome of a target gene??

@BioPandit 6 жыл бұрын

see the number of nucleotides in the NCBI gene page.

5 жыл бұрын

Hi, I have a question about how the sequence was extended. Do you always have to add 60 to the 3 'end? and should we always subtract 10 from the 5 'end? I mean, should the same be done for any protein?

@BioPandit 5 жыл бұрын

No, not always. Always check which strand the gene sequences are situated. If its forward strand, its from 5' and 3' for reverse strand. But I will always recommend to collect promoter sequences from Ensemble (kzfaq.info/get/bejne/a6qHoaag1KfRkmw.html) to avoid this confusion.

@Bennhanz 6 жыл бұрын

I'm sorry but I don't understand what you did at 2:36 can you explain?

@BioPandit 6 жыл бұрын

Dear Ibnu, we we have shown you how to download a nucleotide sequence that includes (i) some promoter region, (ii) the coding region of a gene and (iii) some downstream nucleotides. In 2:36, simply wrote the three regions in three separate sections. That's all. See that at 3:32 the three separated region are given their appropriate names: 5' promoter, exon and 3' flanking end. Got that buddy?

@Bennhanz 6 жыл бұрын

I mean, how do we determine which part of the sequence should be separated into those different regions?

@BioPandit 6 жыл бұрын

Yes in NCBI the exact numbers of the nucleotides in the chromosome are given. Those numbers are manually altered to take some promoter region of our choice. So we already know what is what.