RNA binding motif
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7.5 years ago

I am doing an RNA binding motif scan on exons and I am using the bed files provided by ENSEMBL for scanning the exonic positions which are traced back to the genomic positions. My question is that , if I the binding consensus sequence for the RBP is GCTT then on the negative stranded position would we want to scan for the GCTT binding position or AAGC binding position.

RNA RBP • 2.6k views
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7.5 years ago

You'll look for the AAGC to catch binding on the other strand. BTW, you might just scan the transcriptome, since then everything will be on the same strand.

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Thanks, also since I am new to this area where can I find the whole transcriptome to download and using for scanning?

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In UCSC you can use the 'Table Browser' and in Ensembl the 'BioMart'

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FTP is faster :)

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It is, but for beginners the browser versions might be more convenient. :)

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From UCSC, it's the transcriptome.fa.gz file available on their FTP servers. For Ensembl it's under the cDNA directory (e.g., here is the directory for humans).

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