predicting protein binding regions within LncRNA

Question

[mahi_a]

Dear members,

I am new to LncRNA resarch.

I aim to identify predicting protein binding regions within LncRNA promoters. I came to know that ENCODE can do this. Does anybody can kindly provide me a tutorial with an example.

Thank you in advance.

Best Regards

Shiva

[cpcantalapiedra]

As you are looking for binding regions maybe it could help RSAT or http://floresta.eead.csic.es/footprintdb/

Not sure if do you need something special being LncRNAs, though.

Answer 1

[Manvendra Singh]

UCSC has ChIP-seq data for encode TFs, you can enter the co-ordinates of your lncRNA promoter in UCSC browser, and enable All ChIP-seq display options and then see that in which cell line, which TFs binding to your promoter.

[mahi_a]

Thank you very much Manvendra :-)

[Manvendra Singh]

You are welcome, :) :)

We are here to help anyways :)