obtaining circular RNAs' sequences from circBase
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5 months ago
aminijavad4 ▴ 10

we can search circBase ID on the circBase website and get information about the circular RNA including DNA position and length of splice. However, it doesn't provide the circular RNAs sequence. My question is how to get a circular RNA sequence from its circBase ID?

circular-RNA • 610 views
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as you know

No I did not. I know this is a cultural mannerism but it's antiquated. Please abandon this phrase, it can come across as condescending.

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I didn't know

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5 months ago
Barry Digby ★ 1.3k

You won't find them on circBase.

circAtlas has the mature spliced sequence available. You can search for circRNAs and find the sequence. Alternatively, download all circRNA sequences in a FASTA file here.

The catch is that the circRNA IDs are in 'circAtlas format', not circBase. You can download the circRNA BED file provided by circBase and circAtlas and match the coordinates to generate circBase-circAtlas mapping keys for extracting the sequence from the FASTA file.

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Thank you for your reply, Barry. Upon further searching, I discovered that circular RNA sequences can be downloaded from the downloads section of circBase (http://circbase.org/cgi-bin/downloads.cgi) in FASTA format. However, I found out that all sequences must be downloaded in one file and cannot be downloaded one by one.

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Sorry my mistake! it’s been a minute since I’ve used these sites.

Yes that it is common place, what is the goal of your analysis using the sequences?

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No problem. Our aim is to predict their functions, and then test our theory in lab.

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