Database For Regulatory Sequences

Question

[Anima Mundi]

Hello, could you please point me out a FASTA/GenBank-formatted sequences' database (if any) for enhancers, insulators or other regulatory sequences? I am especially interested in mouse and human. As a second choice, general purpose annotation tracks are also welcome.

Thanks in advance.

[seidel]

I'm not aware of such a database, but it might help if you were a little more specific about what you're actually after. "Enhancers" and "regulatory sequences" are pretty broad terms. Indeed there's disagreement even about the definition of enhancers, and Alex Stark recently showed that roughly %40 of assayed sequences can exhibit enhancer activity. So....that's a lot of sequence. What are you actually trying to do?

[Anima Mundi]

Hi seidel, thanks for your input. Are you referring to Arnold CD et al., Science, 2013, 339(6123):1074-7? This time I am specifically interested in cis-acting modules nearby genes putatively regulated by the same transcription factor, but I would actually like to know about broad databases, because it is not the first time that I feel like missing a comprehensive (for what is possible) database of regulatory sequences. Maybe a reason why is the one you pointed out: it is not easy to define unambiguously regulatory sequences. Gene entities for example are much probably more defined, but still we could define a regulatory sequence as something like any sequence whose removal and or knock-in is significantly altering the frequency of transcription of a given set of loci.

Answer 1

[jackuser1979]

RegTRansBase: http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main
ORegAnno: http://www.oreganno.org/oregano/
Pazar: http://www.pazar.info/