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Old 11-08-2020, 09:38 AM   #1
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Location: Western Europe

Join Date: Nov 2020
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Default Help with fasta analysis

Hello there,
I have what might a be a very basic and simple issue, but here it is :

Long story short, Master's degree student, tasked with the mission to analyse a "mysterious" fasta sequence, and find out : what it is, what its genomic structure is, what its biological role is, and make a slideshow out of it, clearly specifying the biological question this sequence poses, and my analytical train of thoughts in the analysing of said sequence.

Thing is, we've done it in class : we use BLAT and BLAST tool identify the sequence nature, genomic structure, find other similar ones, maybe compare some other relevant matches with it and illustrate why they are different (mutation, evolution) in structure or function, if they could be pseudogene, retrotranscribed gene, and so on and so forth.

So we know how to do that with coding DNA sequences, and everyone tasked with the same project happens to have a coding DNA sequence, or even a proteic sequence, to analyze.

I, for one, happen to have a non coding DNA sequence, that matches 100% to a ribosomal RNA sequence from rice. The GeneBank Accession number starts with AH, and I have no idea what that actually is. ("Segmented set header" according to the NCBI.)

I ran a Blastn from it and get a ton of matches, that have various prefixes (KM/BT/JN/AY/AH/EU/AP/DQ) in their accession numbers, I don't know what they are either.

What is expected, I suppose, is something regarding rRNA key role in gene expression regulation. But I don't how to get there, while starting with my fasta sequence.
I've ran it through ensembl blast > RFAM > NCBI Blast. All I can find is that it aligns with a tons or other loci containing rRNA sequences in numerous other rice species or other plants, and that there are some uncharacterized genes surrounding it (no annotation, no related protein identified or reviewed), as well other genes coding for ribosomal SSU components.

I'm not sure I've been clear about my issue, TL;DR would be : what can I do with an unknown DNA sequence coding for a rRNA sequence (partial 17S, full 5.8S, partial 25S, btw) to identify its purpose ? What's the angle/big deal/big thing about non coding DNA?

If someone could point me towards the right approach here, I'd be grateful.

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