RNA binding motif

Question

[Aishwarya Kulkarni]

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.

Answer 1

[Devon Ryan]

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.

[Aishwarya Kulkarni]

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

[David Langenberger]

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

[Devon Ryan]

FTP is faster :)

[David Langenberger]

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

[Devon Ryan]

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).